Taming the beast: a revised classification of Cortinariaceae based on genomic data

Family Cortinariaceae currently includes only one genus, Cortinarius, which is the largest Agaricales genus, with thousands of species worldwide. The species are important ectomycorrhizal fungi and form associations with many vascular plant genera from tropicals to arctic regions. Genus Cortinarius contains a lot of morphological variation, and its complexity has led many taxonomists to specialize in particular on infrageneric groups. The previous attempts to divide Cortinarius have been shown to be unnatural and the phylogenetic studies done to date have not been able to resolve the higher-level classification of the group above section level. Genomic approaches have revolutionized our view on fungal relationships and provide a way to tackle difficult groups. We used both targeted capture sequencing and shallow whole genome sequencing to produce data and to perform phylogenomic analyses of 75 single-copy genes from 19 species. In addition, a wider 5-locus analysis of 245 species, from the Northern and Southern Hemispheres, was also done. Based on our results, a classification of the family Cortinariaceae into ten genera—Cortinarius, Phlegmacium, Thaxterogaster, Calonarius, Aureonarius, Cystinarius, Volvanarius, Hygronarius, Mystinarius, and Austrocortinarius—is proposed. Seven genera, 10 subgenera, and four sections are described as new to science and five subgenera are introduced as new combinations in a new rank. In addition, 41 section names and 514 species names are combined in new genera and four lecto- and epitypes designated. The position of Stephanopus in suborder Agaricineae remains to be studied. Targeted capture sequencing is used for the first time in fungal taxonomy in Basidiomycetes. It provides a cost-efficient way to produce -omics data in species-rich groups. The -omics data was produced from fungarium specimens up to 21 years old, demonstrating the value of museum specimens in the study of the fungal tree of life. This study is the first family revision in Agaricales based on genomics data and hopefully many others will soon follow.


Introduction
Genomic-level data have revolutionized our views on fungal relationships and helped us create better phylogenies for previously unresolved lineages (e.g., Chang et al. 2021;Li et al. 2021). These data have been used to tackle macroevolutionary events, e.g., mushroom morphological evolution (Varga et al. 2019 or the evolution of symbiotic traits (Miyauchi et al. 2020). High-throughput sequencing (HTS) techniques have also allowed genomic data to be generated from fungarium specimens (Dentinger et al. 2016).
Fungal genomes are small, ranging from 7.67 to 720.2 Mbp/1C (Kullman et al. 2005), with an average size of ~ 63 Mbp/1C in Ascomycota (Hill et al. 2021) and ~ 50 Mbp/1C in Basidiomycota (Mohanta and Bae 2015;Li et al. 2018), compared to those of plants and animals, e.g., ranging 64 Mbp/1C to 140 Gbp/1C in angiosperms (Pellicer et al. 2018) and 1.6 to 6.3 Gbp/1C in mammals (Kapusta et al. 2017). Therefore, in phylogenomics studies of fungi, in depth or shallow whole genome sequencing (WGS) have been an affordable option to generate HTS data, with the vast majority of the fungal genomic studies to date having relied on this approach. However, for species-rich groups where hundreds to thousands of samples might be included, targeted capture sequencing provides a more cost-effective alternative (Hale et al. 2020). Enrichment methods have been widely used to study the systematics of plants and animals (e.g., Johnson et al. 2019;Faircloth 2017) and they have recently been applied in fungal systematics to study lichen-forming Ascomycota families Lobariaceae (Widhelm et al. 2019) and Parmeliaceae (Grewe et al. 2020), as well as the Peltigeralean backbone (Widhelm et al. 2021).
As currently delimited, Cortinarius is by far the largest genus of Agaricales, and its representatives are found from the tropics to arctic habitats in the Northern and Southern Hemispheres. To date, over 5000 taxa, including subspecies and varieties, have been recorded in Index Fungorum (2021). ITS sequence data exist for close to 3000 species (UNITE 2021, using an SH threshold of 1.5%), including both described and undescribed taxa. However, sequence data from many regions of the world are still lacking and, thus, many more species are in urgent need of sequencing and/or description.
The first study based on molecular data (Høiland & Holst-Jensen 2000) indicated that many of the traditional infrageneric groupings of Cortinarius were unnatural (e.g., Moser 1983;Brandrud et al. 1989;Bidaud et al. 1994). During the following 20 years many studies were conducted to gain a better understanding of their natural relationships. Most of these datasets were based only on sequences from the ITS and LSU regions (Høiland & Holst-Jensen 2000;Peintner et al. 2004;Garnica et al. 2005;Harrower et al. 2011;Liimatainen et al. 2014Liimatainen et al. , 2020aStensrud et al. 2014), and only two extensive studies of the genus also included data from RPB1 and/or RPB2 regions (Garnica et al. 2016;Soop et al. 2019). So far, the only study to include more than a handful 1 3 of DNA markers (ITS, nLSU, GPD, MCM7, RPB1, RPB2, and TEF1) was conducted by Stefani et al. (2014) for the delimitation of Australian dermocyboid Cortinarius species. Despite these efforts, no genus-wide, revised subgeneric classification of Cortinarius has been presented because it has not been possible to resolve the backbone of the phylogeny. Existing sequence data have, however, allowed the revision of various sections within Cortinarius, with studies by Soop et al. (2019), Liimatainen et al. (2020a), Ammirati et al. (2021), and Niskanen and Liimatainen (2021) presenting the most updated morpho-genetic, section-level classification of Cortinarius, including a total of 172 sections.
The aim of this study was to conduct the first phylogenomic study of family Cortinariaceae to resolve higherlevel relationships and allow for a revised genus-level classification of the group.

Molecular sampling
Sampling was designed to cover as many of the major lineages of Cortinariaceae as possible, based on the latest phylogenetic trees published for the family (Garnica et al. 2016;Soop et al. 2019). Vouchers of 19 dried fungarium specimens sampled for genomics work are deposited in the collections of the Royal Botanic Gardens, Kew, United Kingdom (K) and/or (H) University of Helsinki, Finland.

DNA extraction and genomic library preparation
DNA was extracted from 2 to 4 mg of dried grounded lamella with the DNeasy Plant Mini kit (Qiagen, Germantown, USA). Extracted DNA was quantified using a Quan-tus™ fluorometer and the Quantifluor dsDNA system kit (Promega Corporation, Madison, WI, USA). To get an estimation of the average fragment size, samples were assessed on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), using the appropriate DNA chips and reagents, or a 4200 TapeStation System (Agilent Technologies), using the corresponding Genomic DNA ScreenTapes and reagents. The DNA was then fragmented using an M220 Focused-ultrasonicator™ (Covaris, Woburn, MA, USA) with varied shearing times (30-45 s) depending on the DNA fragment size profile. The average fragment size in the specimens that were used for WGS ranged from 680 to 745 bp, and from 660 to 880 bp for the specimens used for the targeted capture sequencing.
Dual-indexed libraries for WGS were prepared using a TruSeq® Nano DNA LT (Illumina Inc.) sample kit following the manufacturer's protocols. Dual-indexed libraries for the targeted capture sequencing were prepared using the NEBNext® Ultra™ II Library Prep kit and the NEB-Next® Multiplex Oligos for Illumina® (Dual Index Primer Set 1), according to the manufacturer's protocols (New England BioLabs, Ipswich, MA, USA), although at half the recommended volumes. The resulting genomic libraries were quantified and qualified as above (i.e. Quantus and Bioanalyzer/TapeStation).

WGS, genome assembly, and extraction of single-copy orthologs
For WGS, five to six libraries were pooled following Dentinger et al. (2016). The sequencing was performed on an Illumina MiSeq with v3 (2 × 300 bp paired-end reads) chemistry (Illumina, San Diego, CA, USA) at Jodrell Laboratory, Royal Botanic Gardens, Kew.
Next, the 208 single-copy genes identified by Dentinger et al. (2016) were extracted from the nine assembled genomes using exonerate v2.2.0 (Slater and Birney 2005) with Cortinarius glaucopus (Miyauchi et al. 2020) amino acid (AA) sequences (for the 208 single-copy genes) as queries in searches against our nine assemblies. The top-scoring hit was retained in each case. Additionally, we included the AA sequences of the five single-copy loci currently used in phylogenetic studies of family Cortinariaceae, which were not part of the 208-gene queries in the exonorate search: RPB1 (RNA polymerase II largest subunit B220; also RPO21; C. odorifer GenBank no. DQ083857), RPB2 (RNA polymerase II second largest subunit B150; also RPO22; Coprinopsis cinerea, GenBank no. XM_001829088), MCM7 (component of the Mcm2-7 hexameric helicase complex; also CDC47; C. basirubescens Genbank no. JN985546), GPD (glyceraldehyde-3-phosphate dehydrogenase (GAPDH), isozyme 3; also TDH3; C. austrosanguineus JX675721), and TEF1 (Translational elongation factor EF-1 alpha; also eEF1A; C. sodagnitus GenBank no. DQ061275) to also retrieve sequences of those regions from the genome assemblies. These regions were compared against the assemblies to verify that they were truly single-copy ones in our species.

Enrichment panel probe design
Our goal was to design a 20,000-probe custom myBaits® enrichment panel for target capture of phylogeneticallyinformative, single-copy nuclear orthologs. Four out of 1 3 nine Cortinarius species (C. victoriaensis, C. neofurvolaesus, C. scaurus, and C. typicus), for which most single-copy orthologs recovered by exonorate and representing different lineages across Cortinariaceae, were selected for probe design. The size of the dataset exceeded the limits of the 20,000 probe enrichment panel and we therefore discarded 20 target genes with the most missing data from all four species. The final dataset included 188 targets, from those identified by Dentinger et al. (2016), with the addition of the currently used loci (RPB1, RPB2, MCM7, GPD, and TEF1), resulting in a total of 193 targets. For the probe design, nucleotide sequences containing both intron and exon regions were used. Based on the visual inspection of the alignments of each target, the intron regions were generally short (< 50 bp) and largely conserved within the family making it possible to include them in the enrichment panel. The design and production of the probes was done by Arbor Biosciences (Ann Arbor, Michigan, USA) based on the sequence data provided. The probes were 120 nucleotides long and designed with ~ 2 × tiling density.

Hybridisation and targeted capture sequencing
Dual-indexed genomic libraries were pooled and hybridised with our custom myBaits® enrichment panel, following v3.0 manufacturer's protocols, with the exception of pooling four or nine libraries per hybridisation reaction and each reaction having a total of ¼ of the recommended volume. Hybridisations were performed at 65 °C for 20 h in Vapo Protect Mastercycler 6325 thermocycler (Eppendorf, Arlington, UK). Captured targets were amplified with a KAPA HiFi 2 × Hot-Start ReadyMix PCR kit (Roche, Basel, Switzerland) for 10 cycles, and the PCR products were cleaned using Agencourt AMPure XP magnetic beads. Final products were quantified and qualified as above. Thirteen enriched libraries were further pooled for sequencing on an Illumina MiSeq platform (Illumina, San Diego, CA, USA) using v2 Nano chemistry (2 × 250 bp paired-end reads) at the Jodrell Laboratory, Royal Botanic Gardens, Kew.
Third, the intronate.py script was used to generate supercontigs (scaffolded merged SPAdes contigs containing both complete exon and intron sequences) and retrieve_ sequences.py was used to retrieve the final supercontig sequences (of the target loci from each of our specimens) to build the data matricess required for subsequent phylogenetic analyses. Finally, summary statistics (e.g., percent of reads mapped to target) were generated using SAMtools (Li et al. 2009) and the hybpiper_stats.py script.

Data mining and data matrix generation
Two different data matrices were assembled for downstream phylogenetic analyses. The first consisted of the single-copy orthologs from both the shallow WGS and the targeted capture sequencing data, for a total of 19 species. Of the original 193 single-copy orthologs targeted, 75 of them (including RPB1, RPB2, MCM7, GPD, and TEF1), present at least in > 50% of the species sampled and with > 500 bp of average length recovered, were selected for further analysis. For Cortinarius crassus, the data matrices originating from WGS versus targeted capture sequencing were kept separate to allow direct comparison of these two approaches.
For the second data matrix, we mined NCBI GenBank for RPB1 sequences from Cortinariaceae species, which we combined with 17 newly generated RPB1 sequenced from the WGS and targeted capture sequencing data. When available, we also mined RPB2 (from 18 genomes), MCM7 (9), GPD (12), and TEF1 (10) for these same samples. The final data matrix included 245 species.

Multiple sequence alignment and phylogenetic analyses
For both data matrices, all loci were individually aligned using MAFFT v7 with iterative refinement (i.e., E-INS-i algorithm; Katoh and Standley 2013) and, then, manually adjusted in SeaView (Galtier et al. 1996) following the guidelines summarized in Morrison (2006). The individual alignments were then concatenated in Mesquite v3.2 (Maddison and Maddison 2017). Phylogenetic trees were generated from the two concatenated data matrices, with model parameter estimation partitioned by loci, using RAxML v8.2.12 with 1000 traditional bootstrap (BS) replicates under the GTR + Γ model (Stamatakis 2014), as advised by Young & Gillung (2020). For the first data matrix, Crepidotus sp. (Dentinger et al. 2016) and Hebeloma cylindrosporum (Kohler et al. 2015) were used as outgroups. For the second data matrix, the backbone topology inferred from the first data matrix was used as a topological constraint.

Data availability
The nine new Cortinariaceae genomes sequenced for the present study are deposited in the European Nucleotide Archive (Study ID PRJEB49625) and the raw reads resulting from the targeted capture sequencing in the NCBI GenBank Sequence Read Archive, SRA (BioProject PRJNA791499). The DNA sequences used to design the enrichment panel probes are available on Dryad (https:// doi. org/ 10. 5061/ dryad. 0p2ng f238).

WGS and targeted capture sequencing performance
Summary statistics for the WGS, targeted capture sequencing, and locus mining used in the phylogenomic analysis are presented in Tables 1 and 2. There was substantial variation in the quality of the assemblies from WGS data and, thus, in the recovery rate of the targeted single-copy orthologs. Anywhere from 33 to 100% of the 75 target markers chosen for the final phylogenomics analysis were recovered and the recovery rate was > 70% for only four out of nine specimens. The recovery rate for the targeted capture sequencing was far better: it was > 85% (of the 75 loci) for nine out of eleven specimens and substantially less (35% and 45%) in only two specimens. Reads mapped to the initial 193 targets ranged from 10,101 to 93,312. On average, over 23,000 reads were needed to reach > 85% coverage for the 75 loci, and over 33,000 reads were needed to reach > 95% coverage. Pooling nine specimens in one baiting reaction generally produced good results: in 8 out of 9 specimens > 88% of the 75 target loci were recoved, only in one specimen the recovery rate was low, < 35%.

Phylogenomic inference and systematic rearrangements
The phylogeny inferred from 75 single-copy nuclear orthologs for 20 accessions is shown in Fig. 1. The results of the wider 5-locus analysis, containing 245 species, are presented in Fig. 2. Nodal support BS values below 85% are considered weak, between 85 and 95% moderate, between 95 and 99% BS strong, and lastly, 100% denotes full support. Based on the results, the division of the family Cortinariaceae into ten putative genera is proposed and these names are used hereon.
In the phylogenomics tree ( Fig. 1), Thaxterogaster (BS 68%) is sister to a clade encompassing all other genera (BS 79%), both weakly supported. This latter clade is further divided into a strongly supported Cortinarius (BS 95%) and a weakly supported clade containing the remaining genera (BS 82%). The strongly supported (BS 95%) crown of this latter clade is composed of fully supported Aureonarius (BS 100%), Phlegmacium (BS 100%), as well as Calonarius, here represented by just one species. Austrocortinarius, also represented by one accession, and fully supported Cystinarius (BS 100%) are in a grade leading to the aforementioned crown clade. From the sampled genera represented by more than one species, only one, Thaxterogaster, received a suboptimal BS value (< 95%).

Taxonomy
New and emended generic descriptions are presented below, as well as descriptions of new subgenera and short notes on the previously existing subgenera. The diversity, distribution Table 1 Cortinariaceae specimens used for WGS and summary statistics for the genome assembly and recovery rate of the single-copy nuclear orthologs curated by Dentinger et al. (2016) The four species used to design the baits for the Cortinariaceae Description: Basidiomata small-to large-sized, agaricoid or sequestrate, development type stipitocarpic or pileocarpic. Pileus at first conical to hemispherical, then low conical to low convex to plane, with or without an umbo; surface smooth, innately fibrillose, tomentose or ± scaly; ± brown, ± yellow/ochraceous, white, ± grey, more or less purple or blackish brown to black, more rarely orange, red, or green/olivaceous; dry, viscid or glutinous, hygrophanous, with hygrophanous spots or streaks or nonhygrophanous. Lamellae crowded to distant; adnate, adnexed or emarginate; when young greyish white, pale grey, pale to dark brown, or with a purplish tint or purple, more rarely yellow, green/olivaceous, orange or red. Stipe cylindrical, clavate, bulbous or rooting; usually silky-fibrillose, white, pale to dark brown, with purplish tints or purple or ± yellow/ochraceous, more rarely green/olivaceous, orange, red or blackish; dry to glutinous. Universal veil white, yellow/ ochraceous, purple, grey/brown, pink/red, or green/olivaceous, in some species changing colour with age or on exposure; sparse to abundant, in pileocarpic species found from the margin of the bulb, in species of the genus Volvanarius often forming a volva at the base of the stipe. In stipitocarpic species forming incomplete and/or complete girdles on the stipe, or a sock-like sheet on the lower part of the stipe, more rarely forming a ring at the upper part of the stipe; dry or viscid. Odour in many species indistinct, when present in most species then best observed in Fig. 1 Topology resulting from the RAxML analysis of 75 singlecopy nuclear orthologs. The tree is rooted with Crepidotus sp. and Hebeloma cylindrosporum as the outgroup. Bootstrap (BS) val-ues > 50% are indicated above branches. The four species used to design the baits for the targeted capture sequencing are in purple lamellae and then raphanoid, fruity, earthy, cellar-like, cedar tree-like, perfume-like, yeast-like, farinaceous, grassy, rubbery, pelargonium-like, curry-like, anise or unpleasant. The honey-like odour, typical to part of the species of Cortinarius subgen. Myxacium, Thaxterogaster subgen. Multiformes and T. subgen. Scauri, is best observed in the context of the stipe. In part of the species of C. subgenus Iodolentes the base of the stipe has an odour of iodorm that is best observed when the basidiomata are slightly dried and in Aureonarius subgen. Callistei the odour of the surface of the pileus in some species is like a recently extinguished candle (ozone) or apple-like. KOH/NaOH reaction useful in identification of the species of Calonarius and Phlegmacium. Basidiospores 4.5-20 × 3-10 μm, in vast majority of the species ± amygdaloid, ± ellipsoid, ± citriform or ± subglobose, less commonly obovoidly ellipsoid, fusoid, lacrymoid, or boletoid, finely to strongly verrucose, somewhat to strongly dextrinoid in Melzer's reagent, some species non-dextrinoid. Cystidia present in genus Cystinarius, Cortinarius subgen. Cortinarius, C. sect. Camphorati, C. sect. Subtorti, and some species of C. subgen. Iodolentes, C. sect. Bicolores and genus Volvanarius. Pileipellis in vast majority of the taxa ± duplex with a more or less developed hypoderm, simplex in Calonarius, Austrocortinarius, Phlegmacium subgen. Cyanicium, Cortinarius subgen. Cortinarius and C. sect. Subtorti and in part of the species of Phlegmacium subgen. Phlegmacium, Cortinarius sect. Delibuti. In genus Cystinarius somewhat duplex-like, the hypoderm is poorly developed but the hyphae beneath the epicutis are hypoderm-like (elements that are short and wide).
Ecology and Distribution: With a world-wide distribution; species occur both in Northern and Southern Hemisphere from tropical to arctic-alpine habitats. The species of Cortinariaceae are ectomycorrhizal and form associations with the trees and shrubs from Fagales, Salicaceae, Cistaceae, Dipterocarpaceae, Myrtaceae, Fabaceae (e.g., Dicymbe), Rhamnaceae, Rosaceae, and Pinaceae, as well as with some herbaceous angiosperms in the Cyperaceae, Orchidaceae, and Polygonaceae.
Notes: Typical for the species of the family Cortinariaceae are ornamented basidiospores that are cinnamon brown in deposit. Most species also have a cobweb-like inner veil covering the young lamellae and the remnants of it can often still been found at the upper part of the stipe in older basidiomata. Characteristic is also the silky-fibrillose stipe, at least easily observed at the top of the stipe. Majority of the species lack cheilo-and/or pleurocystidia which are only found in genus Cystinarius and some lineages of genera Cortinarius and Volvanarius. The structure of the pileipellis in the majority of genera and subgenera is duplex with a more or less developed hypoderm.
Description: Basidiomata small-to large-sized, agaricoid or sequestrate, development type stipitocarpic, very rarely pileocarpic. Pileus 0.3-13 cm, at first conical to hemispherical, then low conical, to low convex to plane, with or without an umbo; surface smooth, innately fibrillose, tomentose or ± scaly; in the vast majority of the species pale to dark red-, ochraceous-or grey-brown, in other species ± yellow/ orange, ± white, ± red, greenish/olivaceous, purple, umber to blackish; dry, viscid or glutinous, hygrophanous, with hygrophanous spots or streaks or non-hygrophanous. Lamellae in most species medium spaced, in others crowded or distant; adnate, adnexed or emarginate; when young greyish white, pale grey, pale to dark brown, or with a purplish tint or purple, more rarely yellow, green/olivaceous, orange or red. Stipe 1.5-13 cm long, 0.1-2.5 cm wide at the apex, up to 5 cm at the base; in the vast majority of the species cylindrical to clavate, less often rooting or bulbous; silkyfibrillose, white, pale to dark brown, with purplish tints or purple, more rarely yellow, green/olivaceous, orange or red; dry to viscid. Universal veil in the majority of the species white, in others yellow/ochraceous, purple, green/olivaceous, pink or red, in some species at first white and then turning pink; sparse to abundant, forming incomplete and/ or complete girdles on the stipe, or a sock-like sheet on the lower part of the stipe, more rarely forming a ring at the upper part of the stipe; dry or viscid. Context in the vast majority of the species brownish white, pale to dark red-, ochraceous-or grey-brown, sometimes with a purplish tint, in other species ± yellow/orange, ± red, greenish/olivaceous, purple, umber or blackish. Odour in many species indistinct or raphanoid, usually best observed in lamellae, in certain groups pelargonium-like, cedar tree-like, fruity, perfumelike, iodoform-like, earthy or unpleasant: in some taxa best observed in the context of the stipe and honey-like, sweet or raphanoid; in most species of C. sect. Obtusi and Acetosi the odour is iodoform-like and best observed at the base of the stipe when somewhat dried. KOH reaction in most species negative in pileus, context and/or stipital veil, in some groups red, yellow to orange-yellow, brown or black. Basidiospores 4.5-20 × 3-10 μm, in vast majority of the species ± amygdaloid, ± ellipsoid or ± subglobose, less commonly obovoidly ellipsoid, fusoid, lacrymoid, citriform or boletoid, finely to strongly verrucose. Cystidia absent in vast majority of the species, cheilo-and/or pleurocystidia present in some groups. Pileipellis ± duplex, hypoderm usually more or less developed, lacking from C. subgen. Cortinarius. Ecology and Distribution: In the Northern and Southern Hemisphere with a wide range of hosts.
Notes: The species of this globally distributed, exceptionally species-rich genus of Cortinariaceae are characterized by mainly stipitocarpic development and a pileipellis duplex with a more or less developed hypoderm. The basidiomata range from very small to large, from dry to glutinous, and are of varied colours although brown colours are the most common. Secondary metabolites containing nitrogen are currently only known from this genus of the family and are present in the subgenera Cortinarius, Infracti, Orellani, and section Subtorti (Stensrud et al. 2014  violet, stipitocarpic, agaricoid (cortinarioid) with a dry pileus and a dry stipe. The pileus is tomentose to scaly and non-hygrophanous, and the KOH reaction on any surface of the basidiomata is red. Pleurocystidia and cheilocystidia are present and the pileipellis lacks a well-developed hypoderm. For a recent morpho-genetic revision see Harrower et al. (2015a, b).
to glutinous, innately fibrillose pileus, clavate to sometimes almost cylindrical stipe and subglobose to broadly ellipsoid spores. The development type is stipitocarpic.
Etymology: The name refers to the iodoform-like odour that many of the species of this subgenus have.
Description: Basidiomata small-to medium-sized, agaricoid (telamonioid) or sequestrate, development type stipitocarpic. Pileus 1-7 cm, at first conical to hemispherical, then low conical to low convex to plane, with an acute or broader umbo, pileus margin in many smaller species more or less pellucid-striate, surface often somewhat rimy; yellow brown, red brown to dark brown; dry; hygrophanous. Lamellae medium spaced to distant, adnate, adnexed or emarginate, yellow brown to strong brown, often with a white edge. Stipe 2.5-11 cm long, 0.15-1.4 cm wide at the apex, cylindrical or rooting; at first white fibrillose, later very pale brown to yellow brown. Universal veil white, sparse, or forming complete and/or incomplete girdles on stipe. Context in pileus ± brown, usually somewhat paler in stipe. Odour in lamellae indistinct or in some species raphanoid or cellar-like, at the base of stipe indistinct, raphanoid or iodoform-like, the latter best observed when slightly dried. Basidiospores 6.5-10.5 × 4.5-6.5 μm, ovoid, amygdaloid to ellipsoid, in C. fragrantior ovoid-subglobose, finely to strongly verrucose. Cheilocystidia present in part of the species, clavate to balloon-shaped. Pileipellis duplex, hypoderm developed.
Ecology and Distribution: In Northern and Southern Hemisphere with a wide range of hosts plants.
Notes: Cortinarius subgenus Iodolentes includes small-to medium-sized telamonioid species with dry, ± brown pileus and dry, initially white stipe. The context of the stipe is often somewhat paler than in the pileus and does not become darker towards the base of the stipe. Many species have an iodoform-like odour at the base of the stipe and clavate to balloon-shaped cheilocystidia.
The species of this subgenus were traditionally included in the C. subgen. Telamonia due to their dry pileus and dry stipe, but the first molecular studies showed that they should be recognized as a separate taxon (Høiland and Holst-Jensen 2000;Peintner et al 2004;Garnica et al. 2005), which is also supported by our phylogenetic analysis. Iodolentes belongs to a well-supported branch (BS 94%) in genus Cortinarius that also includes subgenera Dermocybe, Leprocybe, Illumini and Orellani. Since the species of Iodolentes morphologically differ from the species of other related subgenera we here describe the subgenus as new.  [1836][1837][1838]. Neotype: S F-44846, in Ammirati et al., Persoonia 46: 221 (2021).
Currently included sections: Leprocybe, Fuscotomentosi, Melanoti, Persplendidi, Squamiveneti, Veneti, and Veronicae. Notes: The species of this subgenus occur in both the Northern and Southern Hemispheres. The basidiomata are small-to medium-sized (occasionally large-sized), agaricoid (leprocyboid/dermocyboid) or sequestrate, and with a dry pileus and dry stipe and with yellow, red, or greenish-olive colours. At least some parts of the basidiomata are fluorescent. For a recent morpho-genetic revision of Northern Hemispheric Leprocybe see Ammirati et al. (2021) and Bidaud et al. (2021 Notes: This is a bihemispherical subgenus with about 50 species. The basidiomata are medium-sized to small, agaricoid (cuphocyboid, myxacioid) or sequestrate with a viscid to glutionous pileus and glutinous to dry stipe with white, brown and/or purplish colours. Cylindrical stipes and relatively large (up to 20 μm long), mainly amygdaloid to citriform basidiospores are also typical. For a recent morpho-genetic revision of the subgenus see Soop et al. (2021).
The type species of the subgenus, C. collinitus, is described from Britain. Recently, a lectotype for the species was designated by Gómez and Cadiñanos-Aguirre (2018). They also challenged the current interpretation of the name and concluded the species to be more C. trivialis-like. We agree with this conclusion and materials from Britain will need to be sequenced for selection of a suitable epitype. However, since both the current species called as C. collinitus as well as C. trivialis-like fungi belong to this subgenus, we conclude that the subgeneric name Myxacium can be confidently used for this clade although the fixing of the name C. collinitus still requires a selection of an epitype. Notes: This small bihemispherical subgenus is characterized by the lethal nephrotoxin bipyridine orellanine that has caused severe poisonings and deaths in humans (Schumacher & Høiland 1983;Danel et al. 2001) and is not found in any other lineage in Cortinariaceae. The basidiomata of the species of C. subgen. Orellani are medium-sized, stipitorcarpic, agaricoid (cortinarioid) with yellow, orange-brown and saturated reddish-brown colours, and with a dry pileus and stipe. A tomentose to finely scaly pileus and cylindrical to somewhat clavate stipe is also typical. The pileipellis is duplex with a well-developed hypoderm. Currently included sections: Cuphocybe, Paramyxacium, Rozites, Subcastanelli and clade/Achroi.
Notes: The centre of the diversity of this subgenus is in the Southern Hemisphere with only a few species occurring in the Northern Hemisphere. This subgenus contains agaricoid (rozitoid, cuphocyboid) and sequestrate species and the development type of agaricoid species is stipitocarpic. Typical for the agaricoid species of this subgenus is the membraneous veil that in most species forms a distinct ring or collar on the stipe, or in a few species, thick girdles or scales on the stipe. The pileus is viscid/glutinous to dry, and many species also have squamules or scales on the pileus, or the pileus is innately fibrillose, radially wrinkled and/or rimy. The basidiomata are usually medium-to large-sized. The basidiospores are medium to large-sized (8-16 × 5.5-9.5 μm), usually ovoid, amygdaloid or citriform, more rarely ellipsoid to very short and broadly ellipsoid.  Currently included sections: 80 sections, see Liimatainen et al. (2020a).
Notes: This predominantly Northern Hemispheric lineage is the most species-rich subgenus in Cortinariaceae including hundreds of species. The basidiomata are smallto medium-sized (to large), stipitorcarpic, agaricoid (telamonioid) with a dry pileus and stipe. The basidiomata are predominantly with brown, grey, white, and/or purplish colours. The pileipellis is duplex, with a more or less developed hypoderm. For a recent morpho-genetic revision of the subgenus see Liimatainen et al. (2020a). Etymology: Derived from the latin word aureus meaning golden, since species of this genus have yellow colours in their basidiomata, and the generic name Cortinarius.
Description: Basidiomata small-to medium-sized (rather large-sized), agaricoid, development type stipitocarpic. Pileus 1-11 cm, at first hemispherical or conical, then low convex or low conical to almost plane, some species with an umbo; smooth, finely scaly, innately fibrillose or almost tomentose yellow; orange, orange-red, orange-brown, brownish red, yellow-brown, red-brown, umber or blackish brown; dry or viscid, hygrophanous or not. Lamellae rather crowded, medium spaced to distant, adnate, adnexed to emarginate, white, ± yellow, bright orange, yellow-brown or ± red. Stipe 2-11 cm long, 0.2-1.8 cm wide at the apex, up to 2.5 cm wide at the base, clavate, cylindrical or tapering downwards, yellowish white, yellow, yellow-brown to orange-brown, in some species becoming more brownish when pressed with the thumb or with age, dry to somewhat viscid. Universal veil yellow, ochraceous, yellow-brown, orange-red, orange-brown, brown-red or purple-brown, sparse or more abundant and then forming complete and incomplete girdles on the stipe. Context in pileus white, pale yellow, yellow-brown, orange, orange-brown, redbrown to umber, in stipe yellow, yellow-brown, orange or red-orange. Odour of pileus surface or context indistinct or like a recently extinguished candle (ozone) or apple-like, odour in lamellae indistinct, raphanoid, cellar-like or raw potato-like. KOH reaction ± red in stipital veil, pileus and/or context, or negative. UV fluorescence somewhat yellow or absent. Basidiospores 5-10.5 × 4.5-7 μm, subglobose, ovoid, broadly ellipsoid, ellipsoid or amygdaloid, finely, moderately to coarsely verrucose. Chrysobasidia present in two species, A. rubrocastaneus and A. rubrimarginatus. Cystidia absent. Pileipellis duplex, hypoderm at least somewhat developed.
Ecology and Distribution: In the Northern and Southern Hemispheres, with a centre of the diversity in the Southern Hemisphere. In coniferous (Pinaceae) and deciduous forests (Nothofagaceae, Fagaceae, Betulaceae).
Notes: The species of the bihemispheric genus Aureonarius are characterised by vivid yellow, orange, or red colours, at least in some parts of the basidiomata. The basidiomata are small-to rather large-sized, agaricoid (cortinarioid/leprocyboid), and the development type is stipitocarpic. No sequestrate species are yet known to belong to this genus. Some species have a weak yellow UV fluorescence, and some species exhibit a ± red KOH-reaction in stipital veil, pileus, or context. This taxon is well supported in our phylogenomic analyses, and we here describe it as a new genus.

Aureonarius subgenus Aureonarius
IndexFungorum IF552145 Etymology: Derived from the latin word aureus meaning golden, since species of this genus have yellow colours in their basidiomata, and the generic name Cortinarius.
Description: Basidiomata small-to medium-sized, agaricoid (cortinarioid/leprocyboid), development type stipitocarpic. Pileus 1-8 cm, at first hemispherical or conical, then low convex or low conical to almost plane, often with an umbo, yellow, orange, orange-red, orange-brown, brownish red, yellow-brown, red-brown, umber, or blackish brown, dry or viscid, hygrophanous or not. Lamellae rather crowded, medium spaced to somewhat distant, adnate, adnexed to emarginate, ± yellow, bright orange, pale yellow-brown or ± red. Stipe 2-11 cm long, 0.2-1.8 cm wide at the apex, cylindrical to fusoid, often tapering downwards, yellowish white, yellow, yellow-brown to orange-brown, dry to somewhat viscid. Universal veil yellow, ochraceous, yellow-brown, orange-brown, or brown-red, sparse or more abundant and then forming complete and incomplete girdles on the stipe. Context in pileus yellow-brown, orange, orange-brown, red-brown to umber, in stipe yellow, yellow-brown, orange or red-orange. Odour in lamellae or pileus surface indistinct. KOH reaction red to dark red in stipital veil, pileus and/or context, or negative. UV fluorescence weak or absent . Basidiospores 5-10.5 × 4.5-7 μm, subglobose, broadly ellipsoid, ellipsoid or amygdaloid, finely, moderately to coarsely verrucose. Chrysobasidia present in two species, A. rubrocastaneus and A. rubrimarginatus. Cystidia absent. Pileipellis duplex, hypoderm developed, some species with a thin gelatinous layer at the top of the epicutis.
Ecology and Distribution: The centre of the diversity of this lineage is in New Zealand where the species occur in Myrtaceae and Nothofagaceae forests. The three species known from the Northern Hemisphere, associated with Fagaceae and Pinaceae, are clustered in one monophyletic lineage within one of the New Zealand lineages.
Notes: The species of this small, bihemispheric subgenus have small-to medium-sized, stipitocarpic, agaricoid (cortinarioid/leprocyboid) basidiomata with yellow, orangered and reddish-brown colours. The pileus is dry to viscid, and the stipe is cylindrical to fusoid and dry. The lamellae are ± yellow, bright orange, pale yellow-brown or ± red and the basidiospores are subglobose, broadly ellipsoid, ellipsoid or amygdaloid. A distinct odour in the lamellae or at the pileus surface is lacking. The species of the sister subgenus Callistei differ from the species of subgenus Aureonarius by having white, pale yellow or greyish ochraceous lamellae at least when young and somewhat yellow UV fluorescence. In addition, some species of the subgenus Callistei have a clavate stipe and a distinct smell at the pileus surface, context or lamellae, and none of the species have amygdaloid or ellipsoid spores. Description: Basidiomata small-to medium-sized, agaricoid (cortinarioid/leprocyboid), development type stipitocarpic. Pileus 2-11 cm, at first hemispherical to somewhat conical, then low convex to almost plane, some species with an umbo, smooth, finely scaly, innately fibrillose or almost tomentose, yellow, yellow-orange, yellow-brown, orangebrown, brownish red to mahogany-red, dry, hygrophanous or not. Lamellae medium spaced to distant, adnate to emarginate, at first almost white, pale yellow or yellowish brown, later brownish yellow to brown. Stipe 3.5-11 cm long, 0.5-1.5 cm wide at the apex, up to 2.5 cm wide at the base, clavate, cylindrical to somewhat tapering; yellowish white, pale yellow, yellow-brown, becoming more brownish when pressed with the thumb and with age. Universal veil yellow, yellow-brown, orange-red or purple-brown, forming complete and/or incomplete zones on the stipe, or sparse. Context in pileus white to pale yellow, in stipe pale yellow, yellow-brown to orange-brown, in many species becoming darker with age. Odour of pileus surface or context like a recently extinguished candle (ozone), apple-like or indistinct, odour in lamellae indistinct, raphanoid, cellar-like or raw potato-like. KOH reaction in pileus and/or stipital veil brownish red to red. UV fluorescence somewhat yellow. Basidiospores 5.5-9 × 5-7 μm, subglobose, ovoid to broadly ellipsoid, finely to moderately verrucose. Cystidia absent. Pileipellis duplex, hypoderm at least somewhat developed.

Ecology and Distribution: In the Northern and Southern Hemispheres in coniferous and deciduous forests.
Notes: The species of this small, bihemispheric subgenus have small-to medium-sized, stipitocarpic, agaricoid (cortinarioid/leprocyboid) basidiomata with yellow, orange and brownish-red colours. The pileus is dry, and the stipe is clavate or cylindrical and dry. The lamellae are at first almost white, pale yellow or yellowish brown and the basidiospores are subglobose, ovoid to broadly ellipsoid. Many species have a distinct odour either at the pileus surface or in the lamellae. The species of the sister subgenus Aureonarius have ± yellow, bright orange, pale yellow-brown or ± red lamellae and an indistinct odour in the lamellae or at the pileus surface. In addition, there is no UV fluorescence in the basidiomata of the species of subgenus Aureonarius. Etymology: Named after A. callisteus, a species belonging to this section.
Description: Basidiomata medium-sized (to largesized), agaricoid (cortinarioid/leprocyboid), development type stipitocarpic. Pileus 3-11 cm, at first hemispherical, then low convex to almost plane, smooth to finely scaly to almost tomentose, yellow, yellow-orange, yellow-brown to orange-brown, dry, somewhat to not hygrophanous. Lamellae medium spaced to distant, adnate to emarginate, at first almost white, pale yellow or yellowish brown, later brownish yellow to brown. Stipe 3.5-11 cm long, 0.6-1.5 cm wide at the apex, up to 2.5 cm wide at the base, clavate or cylindrical; pale yellow, yellow brown, becoming more brownish when pressed with the thumb and with age. Universal veil yellow to yellow-brown, forming complete and/ or incomplete zones on the stipe, sometimes sparse. Context in pileus white to pale yellow, in stipe yellow-brown to orange-brown, becoming darker with age. Odour of pileus surface like a recently extinguished candle (ozone), applelike or indistinct, odour in lamellae raphanoid, cellar-like or raw potato-like. KOH reaction in pileus and/or stipital veil brownish red to red. UV fluorescence somewhat yellow. Basidiospores 6.5-9 × 5.5-7 μm, subglobose to ovoid, moderately verrucose. Cystidia absent. Pileipellis duplex, hypoderm somewhat developed.
Ecology and Distribution: In the Northern Hemisphere in coniferous and deciduous forests.
Notes: A Northern Hemispheric lineage in A. subgenus Callistei. The representatives of the sister lineage, A. sect. Collybiani from the Southern Hemispheric Nothofagaceae 1 3 forests, often have a somewhat more reddish-coloured pileus and darker universal veil. The group received full support in the phylogenetic analysis of Soop et al. (2018Soop et al. ( , 2019. Etymology: Named after the type species of the section. Currently included species: C. collybianus, C. eucollybianus, C. rubrodactylus.
Ecology and Distribution: In the Southern Hemisphere in Nothofagaceae forests.
Notes: A Southern Hemispheric lineage in A. subgenus Callistei. The representatives of the sister lineage, A. sect. Callistei from the Northern Hemisphere, often have a somewhat paler, less reddish pileus and a yellow to yellow-brown universal veil. The group received full support in the phylogenetic analysis of Soop et al. (2018Soop et al. ( , 2019 Etymology: A genus of family Cortinariaceae that is currently only known from the Southern Hemisphere.
Currently included subgenera: The genus includes only a few species and no infrageneric classification is proposed at present.
Ecology and Distribution: In the Southern Hemisphere in Australia and New Zealand. In Myrtaceae forests.
Notes: Austrocortinarius is a small, Southern Hemispheric genus currently only known from Australia and New Zealand. The representatives of the genus are easy to recognize by the combination of pileipellis simplex, large, ± white basidiomata and a peronate universal veil often forming a distinct ring at the upper part of the rooting stipe. In addition, the basidiomata are agaricoid (phlegmacioid), stipitocarpic and the spores are rather large and amygdaloid. The sequence data deposited in the public repositories, as well as morphology, indicates that C. australiensis would also belong to this genus but the type specimen of the species has not been studied to confirm the placement. The species of genus Austrocortinarius are most reminiscent of those in P. subgenus Phlegmacium, sect. Arguti and clades Obsoleti and Caligati but those lineages of Phlegmacium are only known from the Northern Hemisphere. Rooting, phlegmacioid species are also found from genus Thaxterogaster, but none of those species has the same, unique combination of characters than the representatives of the genus Austrocortinarius. Based on the morphological and molecular data we here consider this distinct lineage as its own genus. Currently included subgenera: Calonarius, Calochroi and Fulvi (Fig. 4).
Description: Basidiomata medium-to large-sized, usually agaricoid (phlegmacioid) but a few species sequestrate, development type pileocarpic. Pileus 3-15 cm, at first hemispherical, then convex to plano-convex, surface in part of the species with small appressed scales or patches of veil and/or innately fibrillose, often colourful with white, yellow, orange, green, olivaceous, brown, blackish and/or purple colours, glutinous. Lamellae crowded, adnate to adnexed to emarginate, white, pale grey, yellow, greenish, olivaceous, pale brown or purple. Stipe 3-12 cm long, 0.7-3 cm wide at the apex, with more or less, usually distinctly, marginated bulb at the base (up to 4.5 cm wide), bulb in some species flattened; white, pale grey, yellow, olivaceous green or purple. Universal veil white, ochraceous yellow, olivaceous/greenish yellow, orange, brown, brown-olive or purple, found at the bulb margin. Context white, greyish white, yellow or greenish yellow, in some species with a purplish, greenish or olivaceous tint. Odour in lamellae indistinct, earth-like, malty or yeast-like, curry-like, sweet, in one species of anise. KOH reaction pink, red, yellowish or orangebrown, olivaceous green, black or in some species negative. Basidiospores 8.5-16 × 5.5-9.5 μm, amygdaloid to citriform, distinctly and coarsely verrucose. Cystidia absent. Pileipellis simplex with a well-developed gelatinous layer, hypoderm not developed.
Notes: This species-rich genus is currently only known from the Northern Hemisphere. The species are predominantly calcicolous or calciphilous, many are rare and have narrow ecological preferences and are thus included in national red lists in several countries and/or used as indicator species. One species, C. meinhardii, is also included in the global red list of fungi. Typical for the members of this genus are medium-to large-sized, pileocarpic, agaricoid (phlegmacioid) or sometimes sequestrate, often brightly coloured basidiomata with a more or less, usually distinctly marginated bulb at the base of the stipe. Amygdaloid to citriform coarsely verrucose basidiospores and simplex pileipellis are also typical. Some species have a positive KOH-reaction (± red, yellowish or orange-brown, olivaceous green, black). The species are most reminiscent of those in the genera Phlegmacium and Thaxterogaster, but the combination of simplex pileipellis, marginated bulb and amygdaloid to citriform, coarsely verrucose basidiospores distinguish the members of Calonarius from the other phlegmacioid species. This group has been recognized as a separate, well-supported lineage since early molecular studies (Peintner et al. 2004;Garnica et al. 2005) and is also supported by morphological characteristics, and here were propose a name for it in generic level. For the most recent morpho-genetic study of the group see Frøslev et al. (2007) and Garnica et al. (2009).

Calonarius subgenus Calonarius
IndexFungorum IF552151 Etymology: Derived from the section name Calochroi and the generic name Cortinarius.
Description: Basidiomata medium-to large-sized, usually agaricoid (phlegmacioid) but at least one species sequestrate, development type pileocarpic. Pileus 4-14 cm, at first hemispherical, then convex to plano-convex, surface in some species with patches or scales of veil or spots, with grey, greenish, olivaceous, yellow, orange-brown, copper brown, red brown, umber brown and purplish colours, rarely creamcoloured, glutinous. Lamellae crowded, adnate to adnexed to emarginate, greyish white, pale ochraceous grey, pale yellow, greenish grey, greyish green, yellowish green or olivaceous, rarely with a purplish tint. Stipe 4-12 cm long, 0.8-2.5 cm wide at the apex, with a marginated or more rarely rounded bulb at the base (up to 4.5 cm wide), bulb in a few species flattened; white, in some species purplish, greyish green or yellowish green or with a purple, yellow or olivaceous tint. Universal veil white, yellow, greyish or yellowish green, brown, brown-olive, purple or purplish red, in some species somewhat glutinous, found at the bulb margin. Context white to grey, rarely greenish yellow, in some species with a purplish, greenish or olivaceous tint at the stipe. Odour in lamellae indistinct, earth-like, malty or yeast-like, curry-like, sweet, in two species of anise. KOH reaction negative or in some species yellow-brown, orange-brown, olivaceous green, brown-red or purplish, rarely blood-red. Basidiospores 10-16 × 6-9.5 μm, amygdaloid to citriform, distinctly and coarsely verrucose. Cystidia absent. Pileipellis simplex with a well-developed gelatinous layer, hypoderm not developed.
Ecology and Distribution: In the Northern Hemisphere. Forming ectomycorrhizal associations mainly with the species of Fagaceae, Pinaceae, Betulaceae, and Malvaceae. Most species are rare and have narrow ecological preferences, and the majority are calcicolous or calciphilous.
Notes: The species of this subgenus mainly have lamellae without purple tones and the context is white to grey, rarely greenish-yellow, and in some species with a purplish, greenish or olivaceous tint at the stipe. The KOH-reaction, if present, is not red for most species. The basidiomata are medium-to large-sized, pileocarpic, agaricoid (phlegmacioid) and the pileipellis is simplex. Etymology: Named after the type species of the section. Currently included species: C. anaunianus, C. caroviolaceus, C. elotus, C. elotoides, C. glaucoelotus, C. hildegardiae, C. humolens, C. lavandulochlorus, C. mariekristinae, C. osloensis, C. praetermissus, C. pseudoglaucopus, C. rapaceoides, C. saporatus, and C. xanthodryophilus.
Description: Basidiomata medium-to large-sized, agaricoid (phlegmacioid), development type pileocarpic. Pileus 4-14 cm, at first hemispherical, then convex to plano-convex, in some species with small drop-like spots or appressed scales, or more rarely innately fibrillose; with ochraceous/yellow, grey, greenish/olivaceous, and/ or ochraceous brown colours, rarely orange/reddish brown, glutinous. Lamellae crowded (to medium spaced), adnate to adnexed to emarginate, at first pale ochraceous grey, more or less yellow, olivaceous or with a yellow, olivaceous or greenish tint, later more ochraceous brown. Stipe 3-8 cm long, 0.8-2.5 cm wide at the apex, with a marginated or rounded bulb at the base (up to 4.5 cm wide), bulb in some species flattened; white, pale yellow, or with a yellow, olivaceous or purple tint. Universal veil white, yellow, greyish or yellowish green, purple or brown, in some species somewhat glutinous, found at the bulb margin, in some species volva-like when young. Context white, grey, in some species with an olivaceous, yellow or purplish tint. Odour in most species in flesh/lamellae earth-like or raphanoid, in some species malty. KOH reaction negative. Basidiospores 9-14 × 5-8 μm, amygdaloid to citriform, distinctly and coarsely verrucose. Cystidia absent. Pileipellis simplex with a well-developed gelatinous layer, hypoderm not developed.
Ecology and Distribution: In the Northern Hemisphere. In deciduous and coniferous forests on calcareous or baserich ground. Forming ectomycorrhizal associations mainly with the species of Fagaceae, Pinaceae, Betulaceae and Tilia.
Notes: The species of this section are found from the Norther Hemisphere and grow on calcareous or base-rich ground ground with deciduous or coniferous trees. Basidiomata have ochraceous/yellow, grey, greenish/olivaceous and ochraceous brown colours and most species have an earth-like or raphanoid odour in flesh/lamellae. In addition, the species lack KOH reaction and they do not have purplish colours in lamellae. The basidiomata are medium-to largesized, pileocarpic, agaricoid (phlegmacioid) and the pileipellis is simplex.
The clade name/Humolentes was first introduced for this group by Brandrud et al. (2019) and includes clades/Pseudoglaucopodes and Caroviolacei recognized by Garnica et al. (2009). For the most recent phylogenetic study of the group see Brandrud et al. (2019) and Fellin et al. (2021). Description: Basidiomata medium-to large-sized, usually agaricoid (phlegmacioid) but at least one species sequestrate development type pileocarpic. Pileus 3-10 cm, at first hemispherical, then convex to plano-convex, surface in most species with small appressed scales or patches of veil, ochraceous white, yellow, ochraceous to brown, in some species with bluish, purplish, greenish or olivaceous tints, in some species completely purple, glutinous. Lamellae crowded, adnate to adnexed to emarginate, greyish white with a purplish tint to pale greyish purple to distinctly purple, in a few species yellow to brown. Stipe 3-12 cm long, 0.7-2.5 cm wide at the apex, with a distinctly marginated bulb at the base (up to 4 cm wide), bulb in some species flattened, greyish white, in many species with a purplish tint at the top of the stipe, in some species completely purple at least when young. Universal veil whitish to ochraceous yellow, in some species purple or olivaceous, found at the bulb margin. Context whitish to greyish white, in part of the species pale purple to purple at least at the top of the stipe. Odour in many species in lamellae somewhat earth-like in older basidiomata. KOH reaction in many species pink, reddish brown or blood red in some parts of the basidiomata, indistinct in part of the species. Basidiospores 8.5-13 × 5.5-8.5 μm, amygdaloid to citriform, distinctly and coarsely verrucose. Cystidia absent. Pileipellis simplex with a well-developed gelatinous layer, hypoderm not developed.

Calonarius
Ecology and Distribution: In the Northern Hemisphere. Forming ectomycorrhizal associations mainly with the species of Fagaceae, Pinaceae, Betulaceae, Cistaceae and Malvaceae. Most species are rare and have narrow ecological preferences, and the majority are calcicolous or calciphilous.
Notes: This is the most species-rich lineage within the genus Calonarius. Most species are characterized by a combination of lamellae with a purplish tint or completely purplish and lack of anthraquinonoid pigments (Frøslev et al. 2007). The basidiomata are medium-to large-sized, pileocarpic, agaricoid (phlegmacioid) and the pileipellis is simplex. The clade Calochroi was also recovered as a wellsupported lineage in previous studies by Frøslev et al. (2007) and Garnica et al. (2009) Etymology: Named after C. nymphicolor, a species belonging to the section.
Ecology and Distribution: In the Northern Hemisphere. In deciduous forests on calcareous ground. Forming ectomycorrhizal associations mainly with the species of Fagaceae.
Notes: The species of the section are found from the Northerh Hemispheric deciduous forests on calcareous ground. Typical are purplish colours in pileus and stipe and often also in lamellae as well as initially white or yellow universal veil. The KOH reaction is pink on pileus and bulbipellis and the spores are amygdaloid to ellipsoid, coarsely verrucose. The basidiomata are medium-to large-sized, pileocarpic, agaricoid (phlegmacioid) and the pileipellis is simplex. The clade received full support in our phylogenetic analysis. Description: Basidiomata medium-to large-sized, agaricoid (phlegmacioid), development type pileocarpic. Pileus 3-15 cm, at first hemispherical, then convex to plano-convex, surface in many species with small appressed scales and/or innately fibrillose, ± yellow, olivaceous green, greyish green, yellow brown, orange-brown, rose brown to red brown, in some species with purplish tints, in one species completely purplish, center saffron orange, brown, chestnut brown, purplish brown to blackish; glutinous. Lamellae crowded, adnate to adnexed to emarginate, greyish white, grey, yellow, greenish yellow, olivaceous yellow, ochraceous brown to olivaceous green, in some species with a purplish tint. Stipe 4-12 cm long, 1-3 cm wide at the apex, with more or less, usually distinctly marginated bulb at the base (up to 4.5 cm wide), bulb in some species flattened; white, pale yellow, yellow, greenish yellow to olivaceous green, in some species with a purplish tint or completely purplish. Universal veil ± yellow, orange or purple, found at the bulb margin. Context yellow, greenish yellow, pale yellow or white, in some species with a purplish tint. Odour in lamellae indistinct or malt-like. KOH reaction pink, vinaceous, blood-red, olivaceous green, olivaceous brown, red brown or black. Basidiospores 9-15 × 5.5-9 μm, amygdaloid to citriform, distinctly and coarsely verrucose. Cystidia absent. Pileipellis simplex with a well-developed gelatinous layer, hypoderm not developed.
Ecology and Distribution: In the Northern Hemisphere. Forming ectomycorrhizal associations mainly with the species of Fagaceae, Pinaceae, Betulaceae, and Malvaceae. Most species are rare and have narrow ecological preferences, and the majority are calcicolous or calciphilous.
Notes: Most species of this subgenus are characterized by yellow colours in the lamellae and/or stipe. If the lamellae are purple, then the pileus is not yellow. Part of the species have anthraquinonoid pigments (Frøslev et al. 2007). The basidiomata are medium-to large-sized, pileocarpic, agaricoid (phlegmacioid) and the pileipellis is simplex. The group also received good support (BS 96%) in the analysis by Garnica et al. (2009) Etymology: Derived from the word cystidia, a property of this genus, and the generic name Cortinarius.
Description: Basidiomata medium-to large-sized, agaricoid (phlegmacioid/cortinarioid), development type stipitocarpic. Pileus 1.5-11 cm, at first hemispherical, then convex to plano-convex, surface fibrillose to tomentose, orange yellow, yellow brown, ochraceous brown, greyish brown, red brown to blackish brown, in some species with spots, dry or somewhat viscid. Lamellae crowded to medium spaced, adnate to adnexed to emarginate, white to greyish yellow. Stipe 3-11 cm long, 0.7-2.5 cm wide at the apex, cylindrical, clavate to fusiform, white, pale grey to greyish yellow, in some species staining yellow or pinkish, dry to somewhat viscid. Universal veil white, pale grey, ochraceous yellow to brown, in some species darkening, often sparse, forming thin bands on the stipe. Context in stipe white to yellowish brown, in some species darker in the pileus, in subgenus Rubicunduli staining more or less yellow when exposed. Odour in lamellae indistinct. KOH reaction negative. Basidiospores 6-9 × 3.5-5 μm, ellipsoid to amygdaloid to subfusoid, almost smooth to very finely and indistinctly verrucose. Lamellae with cylindrical, clavate or capitate cheilo-and pleurocystidia. Pileipellis somewhat duplex-like, the hypoderm is poorly developed but the hyphae beneath the epicutis are hypoderm-like (elements that are short and wide).
Ecology and Distribution: In the Northern and Southern Hemisphere with coniferous and deciduous trees.
Notes: This small bihemispheric genus is easy to recognize by the unique combination of small basidiospores (6-9 × 3.5-5 μm) and presence of cheilo-and pleurocystidia. The basidiomata are medium-to large-sized, stipitocarpic and agaricoid (phlegmacioid/cortinarioid). The pileipellis is somewhat duplex. The species form a well-supported lineage (BS 99%) distinct from the other genera of Cortinariaceae, a relationship already recovered by the phylogenetic analysis of Stensrud et al. (2014) and Soop et al. (2019), and we here describe the genus as new.

Cystinarius subgen. Cystinarius
IndexFungorum IF552339 Currently included sections: Cystinarius. Description: Basidiomata medium-to large-sized, agaricoid (cortinarioid), development type stipitocarpic. Pileus 1.5-8 cm, at first hemispherical, then convex to plano-convex, surface fibrillose, orange yellow, yellow brown, greyish brown, red brown to blackish brown, in some species with spots, dry or viscid. Lamellae crowded to medium spaced, adnate to adnexed to emarginate, white to greyish yellow. Stipe 3-8 cm long, 0.7-2 cm wide at the apex, cylindrical to clavate, white, pale grey to greyish yellow, staining yellow or pinkish, dry to somewhat viscid. Universal veil white, pale grey to ochraceous yellow, in some species darkening, often sparse, forming thin bands on the stipe. Context in the whole basidiomata white to yellowish brown, in some species darker in the pileus, staining more or less yellow when exposed. Odour in lamellae indistinct. KOH reaction negative. Basidiospores 6-9 × 3.5-5 μm, ellipsoid to amygdaloid to subfusoid, very finely and indistinctly verrucose. Lamellae with cylindrical, clavate or capitate cheilo-and pleurocystidia. Pileipellis somewhat duplex-like, the hypoderm is poorly developed but the hyphae beneath the epicutis are hypoderm-like (elements that are short and wide).
Ecology and Distribution: In the Northern and Southern Hemisphere with coniferous and deciduous trees.
Notes: This small bihemispheric subgenus includes medium-to large-sized, stipitocarpic, agaricoid (cortinarioid) species whose context stains more or less yellow when exposed. Small basidiospores and the presence of cheiloand pleurocystidia is also typical. The pileus is dry to viscid and the stipe is dry and the pileipellis is somewhat duplex with a poorly developed hypoderm. The species of the sister group, C. subgen. Crassi, lack bright yellow colours in their basidiomata.  -2.5 cm wide at the apex, fusiform, cylindrical to clavate, white, in one species becoming brownish red from the apex, dry. Universal veil white, ochraceous to red brown, sparse. Context in stipe white, in pileus very pale brown to brown. Odour in lamellae indistinct. KOH reaction negative. Basidiospores 6.5-9 × 3.5-4.5 μm, ellipsoid to amygdaloid, almost smooth to very finely and indistinctly verrucose. Lamellae with cylindrical or clavate cheilo-and pleurocystidia. Pileipellis somewhat duplex-like, the hypoderm is poorly developed but the hyphae beneath the epicutis are hypoderm-like (elements that are short and wide).
Ecology and Distribution: In the Northern and Southern Hemisphere with coniferous and deciduous trees.
Notes: The members of this small bihemispheric subgenus have medium-to large-sized, stipitocarpic, agaricoid (phlegmacioid) basidiomata with dry to somewhat viscid, ± brown pileus and a white, dry stipe. Small, narrow basidiospores and the presence of cheilo-and pleurocystidia is also typical. The pileipellis is somewhat duplex with a poorly developed hypoderm. The species of the sister subgenus Cystinarius differ by having bright colours at least in some parts of their basidiomata and a context that stains more or less yellow when exposed. Currently included subgenera: Hygronarius and Visincisi (Fig. 4).
Ecology and Distribution: In the Northern and Southern Hemisphere with deciduous and coniferous trees.
Notes: This small bihemispheric genus includes small-to medium-sized, stipitocarpic, agaricoid (telamonioid) species with yellow-brown to red-brown colours. The stipe is dry and the pileus is dry or viscid and hygrophanous. The basidiospores are subglobose or ellipsoid and the pileipellis is duplex with a more or less developed hypoderm. The species are morphologically reminiscent of those in Cortinarius subgenus Iodolentes and Telamonia but are genetically distinct from them (Garnica et al. 2005;Stensrud et al. 2014) and for a well-supported clade (BS 92%) in our phylogenetic analysis. Thus, we here recognize them as their own genus.
Ecology and Distribution: In the Northern and Southern Hemisphere with deciduous and coniferous trees.
Notes: Typical for this small bihemispheric subgenus are small-to medium-sized, stipitocarpic, agaricoid (telamonioid) basidiomata with red-brown colours, absent or sparse universal veil and subglobose to broadly ellipsoid basidiospores. They can most easily be distinguished from the species of H. subgen. Viscincisi by the size of the basidiospores: the basidiospores of Viscincisi species are larger, 7-10 × 4.5-6 μm.  Etymology: Named after the type species of this genus. Currently included sections: Austroduracini, Viscincisi. Description: Basidiomata small-to medium-sized, agaricoid (telamonioid), development type stipitocarpic. Pileus 1-6 cm, at first somewhat hemispherical or conical, then convex to plano-convex, with or without an umbo, yellow-brown to red-brown, dry to viscid, hygrophanous. Lamellae medium spaced to almost crowded, adnate to emarginate, pale brown to rusty brown. Stipe 2.5-9 cm long, 0.3-0.8 cm wide at the apex, cylindrical to somewhat clavate; greyish white, pale brown, brownish yellow to brown, in some species covered by silky-white fibrils when young. Universal veil white to yellow-brown, sparse to distinct. Context ± brown. Odour in lamellae indistinct or slightly raphanoid. Basidiospores 7-10 × 4.5-6 μm, ellipsoid, moderately to coarsely verrucose. Cystidia absent. Pileipellis duplex, hypoderm developed.
Ecology and Distribution: In the Southern Hemisphere in forests of Nothofagaceae.
Notes: The members of this small subgenus only occur in the Southern Hemisperic Nothofagaceae forests. The basidiomata are small-to medium-sized, stipitocarpic, agaricoid (telamonioid) with yellow-brown to red-brown colours, sparse to distinct universal veil and ellipsoid basidiospores. They can most easily be distinguished from the species of H. subgen. Hygronarius by the basidiospores: the basidiospores of Hygronarius species are smaller, 6-7 × 4.5-6 μm and subglobose to broadly ellipsoid. Etymology: Derived from the latin word "mysticus" and the generic name Cortinarius.

Ecology and Distribution: In Northern and Southern
Hemisphere in coniferous and Nothofagaceae forests.
Notes: The species of this small, bihemispheric genus have medium-sized, stipitocarpic, agaricoid (myxacioid/ phlegmacioid) basidiomata with a yellow to reddish brown, somewhat viscid to almost dry pileus and a white to yellow, dry stipe. The basidiospores are medium-sized and the pileipellis is duplex. The species of this genus resemble morphologically most of those in Thaxterogaster subgenus Multiformes, T. sect. Pinophili or T. sect. Vibratiles. However, they are not closely related to Thaxterogaster or other genera of Cortinariaceae and we here propose a new genus, Mystinarius, for them. Currently included subgenera: Phlegmacium, Bulbopodium, Carbonella and Cyanicium (Fig. 5).
Description: Basidiomata medium-to large-sized, rarely small, agaricoid (phlegmacioid, rarely telamonioid), some species sequestrate, development type stipitocarpic or pileocarpic. Pileus (1-)3-12(-20) cm, at first hemispherical to convex, low convex to almost plane when old, rarely with a broad umbo; surface in some species innately fibrillose or radially wrinkled, rarely scaly or with patches of veil; from white, pale ochraceous and yellow to dark brown and umber with yellow, orange, red, greyish, greenish or purplish tints, in some species completely purple; dry, viscid or glutinous. Lamellae in the vast majority of species crowded, in some species medium spaced, emarginate, at first pale greyish white to purple, later pale brown to purplish brown, darker in the species of subgenus Carbonella. Stipe 3-13(-20) cm long, (0.4-)0.8-2(-3) cm wide at the apex, up to 5 cm at base, clavate to bulbous with a rounded or a marginate bulb, or cylindrical to rooting, in the vast majority of the species more or less white, sometimes with purplish tints, in some species grey, dry. Universal veil white, grey, yellow, greenish yellow, more or less brown or purple, sparse to abundant, forming incomplete and complete girdles on the stipe. Context in many species in pileus and stipe white, sometimes with purplish colours, in some species grey, yellow-greenish, olive-grey, pale greyish purple to vinaceous brown, in the species of subgenus Cyanicium becoming vinaceous red on exposure. Odour in lamellae indistinct or in some species raphanoid, earthy, grassy, rubbery, sweetish, fruity or farinaceous. KOH reaction in pileus context negative, yellow, orange, reddish lilac, olivaceous or pale brown. Basidiospores 7-12.5(-17) × 4-8.5(-10) μm, amygdaloid, ellipsoid or citriform, in some species subglobose, finely to strongly verrucose. Pileipellis duplex, simplex in P. subgen. Cyanicium and some lineages of P. subgen. Phlegmacium, epicutis in many species ± gelatinous.
Ecology and Distribution: In the Northern Hemisphere with the species of Fagales, Pinaceae and Tilia. In the Southern Hemisphere at least in Nothofagaceae forests. The centre of the diversity is in the Northern Hemisphere: two of the four subgenera, Bulbopodium and Cyanicium, are only know from the Northern Hemisphere and the vast majority of the species of the P. subgenus Bulbopodium are also boreal.
Notes: This genus includes many of the species traditionally placed in the Cortinarius subgenus Phlegmacium. Typical for the species are a dry stipe and viscid to glutinous pileus, or if dry, then the KOH reaction in the context of the pileus is usually yellow. Most species have a pileipellis duplex with a more or less developed hypoderm but the species of the subgenus Cyanicium and some lineages of P. subgen. Phlegmacium have a simplex pileipellis. The species of the genus Calonarius that were previously included in this group can be distinguished from the species of the genus Phlegmacium by the combination of pileocarpic basidiomata, a marginated bulb and simplex pileipellis. For the phlegmacioid species in the genus Thaxterogaster, a distinguishing combination of characters that would work for all groups is harder to give, but as a rule the phlegmacioid species encountered in the Southern Hemisphere mainly belong to the genus Thaxterogaster and the lineages in the Northern Hemisphere that can be confused with the species of the genus Phlegmacium are subgenera Multiformes, Riederorum, Scauri and Varieagati and sections Pinophili and Vespertini. Some phlegmacioid lineages also exist in the genus Cortinarius, namely Infracti and Subtorti, but they have stipitocarpic basidiomata and round spores. The species of the small Southern Hemispheric genus Volvanarius have a phlegmacioid appearance as well, but they are small in size and the majority of the species have a volva. Some species of the genus Cystinarius may also be confused with the species of the genus Phlegmacium, but Cystinarius species have distinct cheilo-and pleurocystidia and a dry pileus. Lastly, the basidiomata of the genus Austrocortinarius resemble those in P. subgenus Phlegmacium, sect. Arguta and clades/Obsoleti and Caligati but those lineages of Phlegmacium are only known from the Northern Hemisphere whereas the genus Austrocortinarius occurs in the South Pacific.
Notes: The centre of the diversity of this species-rich lineage is in the Northern Hemisphere but some members of the group are also encountered in the Southern Hemisphere. Basidiomata are medium-to large-sized, predominantly stipitocarpic, agaricoid (phlegmacioid). The stipe is dry, and the pileus is viscid to glutinous, or if dry then the KOH reaction in the context of the pileus is usually yellow. The pileipellis is either duplex or simplex. The members of the other species-rich subgenus, Bulbopodium, have mainly pileocarpic basidiomata. Currently included sections: Carbonella. Notes: The species of this subgenus occur in the Nothofagaceae forests of New Zealand. The species are characterized by small-sized, agaricoid (telamonioid), stipitocarpic basidiomata with dark grey-brown to bluish-grey, or purple-brown to umber colours and dry, hygrophanous pileus and dry stipe. The universal veil is pale grey-brown, purple to pale brownish-red and sparse. The alkaline reaction is orange to reddish-lilac in the context and red on lamellae (Soop 2017;Soop et al. 2019). Morphologically the species of this subgenus are most reminiscent of those in Cortinarius subgenus Telamonia (dry pileus and stipe, development type of the basiodiomata stipitocarpic) but phylogenetically the subgenus is most closely related to the genus Phlegmacium (pileus viscid to glutinous, or if dry then KOH-reaction usually yellow, stipe dry, development type of the basiodiomata stipito-or pileocarpic). Since they represent a well-supported lineage within the genus Phlegmacium and are morphologically distinct from their closest relatives we here recognize them in a subgeneric level.  Liimatainen et al., Persoonia 33:118 (2014).
Notes: This small Northern Hemispheric subgenus includes species with a unique combination of characters: basidiomata are (medium-to) large-sized, agaricoid (phlegmacioid) and stipitocarpic with greyish-blue, greyish-brown to darker purplish-brown colors. The pileus is at first viscid but soon dry. A context that becomes vinaceous-red on exposure and lamellar trama hyphae with abundant small to large to worm-like blood red guttules in Melzer's reagent is typical. The KOH reaction is negative in the context and the pileipellis structure is simplex. Currently included subgenera: Thaxterogaster, Cretaces, Multiformes, Riederorum, Scauri, and Variegati (Fig. 5).
Description: Basidiomata small-to large-sized, agaricoid (phlegmacioid, myxacioid) or sequestrate, development type stipitocarpic to pileocarpic. Pileus 1-12 cm, at first hemispherical, then convex to plano-convex; surface smooth, innately fibrillose or somewhat scaly; ± white, ± yellow, pale to dark brown with greyish, ochraceous or reddish tints, umber to blackish, ± purple or with a purplish tint, some species with olivaceous colours; dry, viscid or glutinous, with hygrophanous spots or streaks or non-hygrophanous. Lamellae crowded to medium spaced, adnate, adnexed or emarginate; when young white, pale grey, pale brown, green, ± purple or with a purplish tint. Stipe 4-13 cm long, 0.3-2.5 cm wide at the apex, up to 5 cm at the base; cylindrical, clavate, rooting or bulbous, bulb rounded to ± marginate; white, pale brown, ± purple, some species with greenish colours, in species of sect. Purpurascentes usually turning deeper purple when bruised, dry. Universal veil white, purplish white, purple, in some species turning pink; sparse to more abundant, in pileocarpic species at the bulb margin and pileus margin, in stipitocarpic species forming a 1 3 thin sock-like sheet or incomplete and complete girdles on the stipe, usually dry but in some species viscid. Context in pileus white, pale brown, purple or dark blue/blackish green, in stipe white, ± yellow, pale brown, ± purple or with purplish or green/olivaceous colours. Odour in lamellae indistinct, in the context of the stipe indistinct, honey-like or sweet, garlic-like in T. crypticus. KOH reaction negative or red in pileus, context and/or stipital veil. Basidiospores 6-18 × 3.5-9 μm, subglobose, amygdaloid, fusoid to ellipsoid, finely to strongly verrucose (subglobose, smooth and very large in T. crypticus 25-35 μm in diam.). Cystidia absent. Pileipellis duplex, hypoderm present.
Ecology and Distribution: In the Northern Hemisphere with species of Fagaceae, Betulaceae, Tilia and Pinaceae. In the Southern Hemisphere in Nothofagaceae forests.
Notes: The species of this bihemispherical genus have traditionally been classified in phlegmacioid and myxacioid taxa in genus Cortinarius or in sequestrate genera/ taxa. The size of the basidiomata ranges from small to large and vary in coloration from white, ochraceous, greenish, brown to purple. Typical for all agaricoid species, however, is a pileipellis duplex and a negative or, more rarely, red (in pileus, context and/or stipital veil) KOH reaction. Several lineages of this genus have a honey-like or sweet smell in the context, not typical in other genera of the family Cortinariaceae and otherwise known only in Cortinarius subgenus Myxacium. The development type of basidiomata ranges from stipitocarpic to pileocarpic.
Ecology and Distribution: In New Zealand and South America, in Nothofagaceae forests.
Notes: This small Southern Hemispheric subgenus includes medium-to large-sized, stipitocarpic, agaricoid (phlegmacioid) and sequestrate species. The pileus is viscid and the stipe is cylindrical to rooting. The species resemble those in South American T. subgenus Cretaces but the species of subgenus Cretaces have smaller basidiospores (6-10 × 3-5.5 μm) and a sparse universal veil. Currently included sections: Cretaces. Notes: The representatives of this small subgenus are only encountered in the Southern Hemisphere. The basidiomata are medium-to large-sized, stipitocarpic, agaricoid (phlegmacoid) with a viscid pileus and a dry stipe. The colour of the pileus ranges from white to yellow-brown, lamellae are white to pale grey and crowded, the stipe is usually rooting and the universal veil is sparse. The odour in the lamellae is indistinct or marzipan-like. Basidiospores are fusoid-amygdaloid, 6-10 × 3-5.5 μm and weakly verrucose. The species are most reminiscent of those in T. subgen. Thaxterogaster but the agaricoid species in subgenus Thaxterogaster have larger basidiospores and more abundant universal veil. Etymology: Named after C. multiformis, a species belonging to this subgenus.

Thaxterogaster subgen. Cretaces (Soop & Dima) Nis
Currently included sections: Multiformes. Description: Basidiomata medium-to large-sized, agaricoid (phlegmacioid), development type pileocarpic. Pileus 4-12 cm, at first hemispherical, then convex to plano-convex, in some species innately fibrillose, white, cream-coloured, pale yellow, ochraceous yellow, orange-yellow, greybrown or red brown, rarely bluish brown, viscid to glutinous, with hygrophanous spots or streaks. Lamellae crowded to almost crowded, emarginate, at first greyish white, later very pale greyish brown, in some species with a bluish tint. Stipe 4-13 cm long, 0.7-2 cm wide at the apex, up to 3.5 cm at the base, clavate to bulbous, bulb rounded to slightly marginate, rarely almost cylindrical, at first white, later pale brown, in some species with a bluish tint at the apex, dry. Universal veil white, sparse, at the bulb margin, rarely somewhat viscid. Context in pileus white or pale brown to brown near the pileus surface, in stipe white, in some species with a bluish tint at the apex of the stipe. Odour in the flesh of the bulb and/or stipe honey-like. KOH reaction negative. Basidiospores 7.5-11 × 4.5-6.5 μm, ovoid-amygdaloid, amygdaloid, fusoid to ellipsoid, finely to rather strongly verrucose. Cystidia absent. Pileipellis duplex, epicutis with a glutinous layer on the top, hypoderm present.
Ecology and Distribution: In the Northern Hemisphere with coniferous (Pinaceae) and deciduous trees (Fagaceae, Betulaceae).
Notes: The species of this Northern Hemispheric subgenus are medium-to large-sized and phlegmacioid with a viscid to glutinous pileus and a dry stipe. They are characterised by having a pileocarpic development type of the basidiomata, pileipellis duplex, greyish-white lamellae when young and a honey-like smell in the context. In addition, the colour of the pileus ranges from cream-coloured to yellowochraceous to red-brown and the stipe is white. Some species have bluish tints in their basidiomata. The phylogenetic analysis of Soop et al. (2019) indicated that morphologically similar species of T. sect. Cremeolini could also belong to this subgenus as well as species of sect.Malvacei Moser, but the group did not receive strong support. Etymology: Named after C. riederi, a species belonging to this subgenus.
Currently included sections: Riederorum. Description: Basidiomata medium-to large-sized, agaricoid (phlegmacioid), development type pileocarpic. Pileus 2.5-12 cm, at first hemispherical, then convex to planoconvex, innately fibrillose; cream-coloured, greyish white, pale grey, yellow ochraceous, ochraceous brown, fulvous brown or grey-brown, sometimes with an olivaceous tint; viscid to glutinous, in some species with hygrophanous spots or streaks. Lamellae crowded, emarginate, at first violetblue, later greyish brown. Stipe 5-12 cm long, 0.7-2.5 cm wide at the apex, up to 5 cm at the base; clavate to bulbous, bulb rounded to ± marginate; at first white with a bluish tint to completely bluish violet, later greyish white to pale ochraceous brown, becoming ± brown if damaged, bruised or with age, dry. Universal veil bluish white, very sparse, remnants, if visible, near the bulb margin and on the pileus margin. Context in pileus and bulb bluish white to white, in stipe bluish white to bluish violet, violet colour fading with age. Odour in lamellae indistinct. KOH reaction negative. Basidiospores 10-14.5 × 6-9 μm, ellipsoid to amygdaloid, moderately to strongly verrucose. Cystidia absent. Pileipellis duplex, epicutis with a glutinous layer on the top, hypoderm present, well to somewhat developed.
Ecology and Distribution: In the Northern Hemisphere with coniferous (Pinaceae) and deciduous trees (Fagaceae, Betulaceae, Tilia).
Notes: The species of this small Northern Hemispheric subgenus are characterized by having medium-to largesized, agaricoid (phlegmacioid), pileocarpic basidiomata with a viscid to glutinous, innately fibrillose pileus, dry stipe and bluish-violet colours in the lamellae and stipe. Typical are also large (> 10 μm long) ellipsoid to amygdaloid basidiospores, a negative KOH-reaction and pileipellis duplex. For a recent morpho-genetic revision of the group see Brandrud et al. (2018). Etymology: Named after C. scaurus, a species belonging to this subgenus.
Currently included sections: Scauri and Purpurascentes. Description: Basidiomata medium-to large-sized, agaricoid (phlegmacioid), in T. sect. Purpurascentes some species sequestrate, development type pileocarpic (Scauri) or somewhat stipitocarpic to stipitocarpic (Purpurascentes). Pileus 1-10 cm, at first hemispherical, then convex to plano-convex; surface innately fibrillose or not; greyish white, pale (greyish) ochraceous, pale ochraceous brown, olivaceous brown, red brown, dark brown, blackish brown, purplish grey or pale purple; viscid to glutinous, many species with hygrophanous spots or veins. Lamellae crowded to medium spaced, emarginate, greyish brown, green to olivaceous, soon brown, in part of the species with a purplish tint, completely purple or bluish grey. Stipe 3-12 cm long, 0.3-2 cm wide at the apex, up to 3.5 cm at the base; cylindrical, clavate or more or less bulbous, bulb usually ± marginate; at first pale greyish purple/blue, pale purple to purplish green, later yellowish grey, yellow-brown or purple, in species of sect. Purpurascentes usually turning deeper purple when bruised, dry. Universal veil green, purple, ochraceous yellow or white, sparse to more abundant, in pileocarpic species at the bulb and pileus margin, in stipitocarpic species forming a sock/like sheet or incomplete and/or complete girdles on the stipe. Context in pileus white, brownish white, pale brown, purple or dark blue/blackish green, in stipe pale purple, greenish purple, pale olivaceous to yellow-green. Odour in the context of the stipe honey-like or sweet in many species. KOH reaction negative, in a few species blood red on pileus and/or stipital veil (Soop 2017). Basidiospores 7-12 × 4.5-7 μm, broadly ellipsoid, ellipsoid to amygdaloid, moderately to coarsely verrucose. Cystidia absent. Pileipellis duplex, epicutis with a glutinous layer on the top, hypoderm present.
Ecology and Distribution: In the Northern Hemisphere with coniferous (Pinaceae) and deciduous trees (Fagaceae, Betulaceae, Tilia), and in the Southern Hemisphere in Nothofagaceae forests.
Notes: Typical for the species of this bihemispheric subgenus are medium-to large-sized, agaricoid (phlegmacioid) basidiomata with purplish and/or greenish tints/colours and a pileipellis duplex. The pileus is viscid to glutinous, and the stipe is dry, and many species have a honey-like or sweet smell in the context. The iodine (lugol) reaction is positive in the context and lamellae (Garnica et al. 2005;Soop et al. 2019 Currently included sections: Variegati. Description: Basidiomata medium-to large-sized, agaricoid (phlegmacioid), development type ± stipitocarpic. Pileus 3.5-10 cm, at first hemispherical then plano-convex; surface rimy at least when young: red-brown, darker from the centre; viscid to glutinous, with some hygrophanous spots. Lamellae crowded, adnexed to emarginate, greyish white to pale grey. Stipe 5-15 cm long, 1-1.5 cm wide at the apex, up to 2 cm at the base; cylindrical, clavate to bulbous, bulb marginate or not; silky-fibrillose, white, dry. Universal veil at first white, later pink to purplish pink, forming a thin sheet or some girdles on the 1/3 lowest part of the stipe. Context white. Odour in lamellae indistinct. KOH reaction negative. Basidiospores 6-8 × 3-4 μm, amygdaloid-fusoid, smooth to finely verrucose. Cystidia absent. Pileipellis duplex, hypoderm present.

Ecology and Distribution:
In the Northern Hemisphere with coniferous (Pinaceae) and more rarely with deciduous trees (Fagaceae).
Notes: The most characteristic features of this monotypic boreal subgenus are the initially white universal veil that becomes pinkish with age and small, almost smooth amygdaloid-fusoid spores. In addition, the basidiomata are medium-to large-sized, the development type is ± stipitocarpic and the pileipellis has a well-developed hypoderm. The pileus is red-brown, and the stipe is white. Our phylogenetic analysis also suggests that T. sect. Turmales could be included in this subgenus, but the relationship is not wellsupported. Section Turmales includes morphologically similar species with small (< 9 μm long), amygdaloid-fusoid, finely verrucose spores, and in at least one species of the section, C. turmalis, the mycelium becomes rose-coloured after exposure to air. Etymology: Derived from the word volva, that many species of this genus have, and the generic name Cortinarius.
Description: Basidiomata small-to rather small-sized, agaricoid (phlegmacioid) or rarely sequestrate, development type pileocarpic. Pileus 1.5-6 cm, at first hemispherical, then low convex to almost plane, yellow, ochraceous, ochraceous brown, orange-brown, olive brown to greenish, dry or viscid. Lamellae medium crowded to almost crowded, adnate, at first very pale brownish grey, later pale greyish brown. Stipe 3-8.5 cm long, 0.4-1.2 cm wide at the apex, cylindrical, with a bulbous base (up to 2.5 cm), with silky fibrillose surface, white, pale yellow, or pale greenish. Universal veil white or ochraceous, in some species with orange spots, often forming a volva at the base of the stipe. Context in most species white with ochraceous, greenish or brownish tints, in some species context in pileus brown. Odour in lamellae indistinct. Chemical reactions: context of the bulb turns red with ammonia Soop et al. 2019). Basidiospores 7-11.5 × 4-6.5 μm, citriform to amygdaloid, rarely ellipsoid, finely to strongly verrucose. Cystidia (cheilocystidia) balloon-shaped, present in some species. Pileipellis duplex, hypoderm developed.

3
Ecology and Distribution: In the Southern Hemisphere with species of Nothofagaceae.
Notes: This small genus is only known from the Southern Hemispheric Nothofagaceae forests. Members of this group can easily be identified in the field by the small and Phlegmacium-like basidiomata with a bulbous stipe, and the universal veil that in most species forms a distinct volva at the base of the stipe. Typical are also citriform to amygdaloid, rarely ellipsoid basidiospores and pileipellis duplex. A few species have balloon-shaped cheilocystidia. For a recent morphogenetic revision of C. sect. Thaumasti see Liimatainen et al. (2020b).

Which criteria make a good genus?
The primary criterion for recognizing a taxonomic rank such as genus is a natural, monophyletic group of species that is supported, for a given phylogenetic analysis. However, the rank and what other criteria should be used to delimit it are more or less subjective. Ultimately, the aim is to find a community consensus for practical solution to describing diversity. At least in species-rich fungal groups, monophyletic clades with good support often exist at different nested levels for a given phylogeny and there are, therefore, multiple ways in which generic limits could be drawn.
A genus is usually also defined by its morphological, chemical, or ecological characteristics that distinguish it from its relatives. Our proposed classification is largely inline with circumscription of other genera in the same order based on a combination of phylogenetic, morphological, chemical, and ecological traits. Although a universal set of objective criteria is not realistic for classifying all life with its multitudes of variation, the objective of achieving both coherence and practicality in recognizing evolutionary uniqueness of the generic rank within a higher taxon could be applied at approximately the same level of inclusiveness. This ideal exists not only because a basic assumption is that a certain taxonomic rank reflects a level of cohesion around a similar set of traits and phylogenetic patterns, but also because in practice it makes comparisons between different genera across different groups of organisms (e.g., in ecological, evolutionary, and conservation studies) more meaningful.
One additional aspect to take into consideration when delimiting genera is the amount of diversity to be included. Within reason, monotypic genera should be avoided, since the general aim of classification above the species level is to group closely related units together towards increasingly larger units, so that each taxonomic level, with cumulative inclusiveness, would deliver information that is something more than the previous unit. In practise, however, monotypic entities are hard to completely avoid since some clades are just less diverse than others. On the opposite end, if made possible by the other criteria above, we also try to avoid overly diverse entities in which we run out of infrageneric taxonomic ranks, i.e., subgenera and sections, to classify the distinct monophyletic groups identified within the genus. When delimiting genera, we aim to find a balance between the number of genera and the amount of diversity they include.
The trend in fungal taxonomy, after the introduction of molecular tools, has in many cases been towards smaller and natural genera (e.g., Buyck et al. 2008, Sánchez-García et al. 2014). The work is still ongoing and it would be important that all genera would go through the same re-evaluation so that, in the end, we would be applying a similar set of criteria for recognizing genera across higher fungal taxa. This process has and will, without a doubt, lead to nomenclatural changes, but the end result should be improvement-a natural, more meaningful, and stable classification that will provide a good framework for understanding and classifying fungal diversity in an evolutionary context.

Current delimitation of the genus Cortinarius and associated problems
The size of genus Cortinarius with thousands of species and tremendous morphological variation among them have contributed to a poor understanding of their true diversity and evolutionary relationships. Even at local scales, Cortinarius has often been too diverse to manage accurately as a whole and taxonomists have tended to specialize on certain groups. For example, in Funga Nordica (Niskanen et al. 2008) Cortinarius is the only genus in which different authors have written different subkeys of the genus.
The idea of splitting the genus Cortinarius into several genera is not a new one. Based on morphological data, different genera-i.e., Dermocybe, Phlegmacium, and Rozites-have been recognized in the past (e.g., Moser 1960;Moser and Horak 1975). The main issue with all previous classifications, however, has been that they were either unnatural or keeping them would have led to the splitting of the genus into far too many, upractical entities. Alternative solutions on how to divide the genus into natural units have not been possible until now, because the phylogenetic studies done so far have not been able to resolve the deeper nodes of the phylogeny, beyond the section level (e.g., Peintner et al 2004;Garnica et al. 2005;Soop et al. 2019).
If we look at how the current situation lines with other families in the suborder Agaricineae, the ectomycorrhizal family Inocybaceae provides a good point of reference for a comparison. It is a species-rich family, around 2600 species are recognized based on ITS sequence data using an SH threshold of 1.5% in UNITE (2021). Before its most recent molecular revisions (Matheny and Bougher 2006;Alvarado et al. 2010;Matheny et al. 2020), it used to be a monotypic family including one genus, Inocybe. Now, the family is delimited into seven genera based on morpho-genetic data. If the current system to delimit genus Cortinarius is neither practical nor does it align well with comparable genera in the suborder, the reasonable conclusion would be to split the genus. It is hard to see a reason, other than keeping nomenclatoric stability, to maintain Cortinarius as a single genus.

New classification proposed and justification for the new generic delimitations
Here we propose the classification of family Cortinariaceae into ten genera-Aureonarius, Austrocortinarius, Calonarius, Cortinarius, Cystinarius, Hygronarius, Mystinarius, Phlegmacium, Thaxterogaster, and Volvanariusbased on the phylogenomic analysis of 75 single-copy nuclear orthologs from 19 species, complemented with a wider 5-locus analysis of 245 recognized species. There are names already in existance for the three largest genera, as well as three to eleven generic level synonyms. Where several names of a genus are possible, the most ancient synonym must be chosen (Art. 11.4, 52.1), which explains why a name like Thaxterogaster now applies to a large taxon with only some gastroid members. Seven genera are described as new to science. The position of Stephanopus within suborder Agaricineae, for which no sequence data exist, remains to be studied. The genera have been delimited (i) to be the largest monophyletic units with statistical support, (ii) to be supported by morphological traits, (iii) to facilitate classification of Cortinariaceae diversity into infrageneric ranks, (iv) to avoid oversplitting, and (v) to be in line with other genera of gilled macrofungi.
To strike a balance between the number of genera and the amount of morphological and species diversity they include, a few exceptions to the principles above have been made. For example, we propose that the small telamonioid subgenus Carbonella should be included in an otherwise rather uniform genus Phlegmacium, because treating Carbonella as a separate genus would have required the division of the genus Phlegmacium into four separate genera. Also, the genus Cortinarius s. str. has been kept as one unit, rather than further split it into several smaller genera, even though morphologically it still is quite a variable genus (and six out of eleven entities currently recognized as subgenera already have a generic level name), because many relationships still remain unresolved and many species are not currently included in any well-supported group.
Based just on monophyly, the phylogeny would have allowed us to propose also other solutions for the generic classification within family Cortinariaceae. We could have delimited just two genera, Thaxterogaster and Cortinarius, but that would not have led to any major taxonomic improvements that accurately capture the morphological variation contained within a single genus. Also, having five genera-Thaxterogaster, Hygronarius, Austrocortinarius, Cortinarius, and Phlegmacium-could have been an option. However, in this scenario, the species-rich genera Phlegmacium and Calochroi, as well as the smaller Aureonarius, Cystinarius, and Mystinarius (all entities with morphological characteristics that make them easily distinguishable from one another) would have been grouped together.
All genera recognized have a combination of morphological traits that distinguish them from their closely related taxa. The smaller genera are more uniform morphologically and thus more easily defined and recognized. Additionally, one of the four species-rich genera, Calonarius, is also morphologically very uniform. However, the three largest genera contain clades that differ morphologically from the others within that genus. This broadens the infrageneric variation and affects the diagnostic value of the generic descriptions, although the vast majority of the species in those genera can still be distinguished based on morphology from members of other genera.
An estimation of the species diversity in the ten putative genera of Cortinariaceae is given in Table 3. Genus Cortinarius s. str. still remains the largest genus in the family, with ≥ 2000 species estimated worldwide, classified into eleven subgenera and more than a hundred sections. In the Northern Hemisphere, the next most species-rich genera are Phlegmacium (four subgenera, 15 sections) and Calonarius (three subgenera), while in the Southern Hemisphere (where Calonarius does not occur and where the diversity of Phlegmacium is low) the second largest genus is Thaxterogaster (six subgenera, 18 sections). All these three genera are estimated to have more than or ~ 200 species. The remaining six genera are smaller, containing ≤ 25 species.
Thus, how does the suggested delimitation of genera compare to other groups of gilled fungi? When comparing our proposal to the new Inocybaceae classification the new proposal and its justifcation are very similar. In both cases, after careful examination of global morpho-genetic data, the previously monotypic family has been divided into several genera to better recognize and communicate the amount of morphological, ecological, and biological diversity observed within each of them. We propose four larger and six smaller genera, whereas the current framework for Inocybaceae includes four larger (> 50 species) and three smaller genera of which one is monotypic. In both cases the genus on which the family name is based remains the largest one with hundreds of species. The refined classification will be more practical to use for comparative studies and is more appropriate for conservation studies and for identification of diversity hotspots than the previous, more inclusive one .
When comparing the sizes of the four most species-rich genera-Cortinarius, Phlegmacium, Thaxterogaster, and Calonarius-to other genera of gilled fungi, the new classification still retains the size signature of the old classification, only now with more segregated units that are better refined. Because comparison at a global scale is challenging since, for many genera, data are still lacking and/or can be strongly biased, and because local keys or checklists from the most intensively studied areas of the world can provide a better basis for a more accurate comparison, we here use species numbers from Funga Nordica (Niskanen et al. 2008) to give an idea of the sizes of the new genera. Based on the proposed classification, Cortinarius would still be at least the second largest genus (206 species) after Entoloma (232 species) in Northern Europe and, most likely even remain the largest when all species from the region are recorded. The size of Calonarius (~ 80 species) would be equal with Psathyrella, while the size of Phlegmacium (~ 60 species) with Tricholoma and the size of Thaxterogaster (~ 30 species) with Amanita although for the latter the comparison does not strictly apply, since Thaxterogaster has its centre of the diversity in the Southern Hemisphere and, globally, the size of this genus is equal to that of Phlegmacium.
To maintain nomenclatural stability as much as possible, we have kept the currently accepted sectional framework that has been created based on molecular data. In addition, the new generic names have been designed to have the same ending -narius as in Cortinarius, to keep the species epithets as they currently are, whenever possible.
In ecological and conservation studies, the go-to operational taxonomic unit is the species rank. Under current usage, the next rank used is the genus level, since no information on infrageneric ranks are associated with a name in fungal DNA barcoding databases. Therefore, the new classification proposed here will benefit ecological and other research by providing more biologically relevant categories. For example, the recognition of genus Calonarius, with many rare representatives that have narrow ecological preferences, will help highlight its uniqueness. Moreover, this classification will also advance communication of conservation priorities, as many of the species in Calonarius are included on national red lists across Europe (e.g. Stoltze and Pihl 1998; SLU Artdatabanken 2020) with C. meinhardii also making it into the global red list (Brandrud 2019). Having Calonarius as a separate genus will help draw focus into this group and provide a tool to better recognize it by ecologists and conservation biologists.

Previous phylogenetic studies in Cortinariaceae
Genera recognized in this study have also been recovered in the two previous multi-gene studies of Cortinariaceae that included data from the RPB1 region, in addition to the traditionally used ITS and LSU regions (Garnica et al. 2016;Soop et al 2019). Garnica et al. (2016) recognized the following clades: Phlegmacioid clade 1 (= Phlegmacium), Phlegmacioid clade 2 (= Thaxterogaster), Phlegmacioid clade 3 (= Calonarius), Renidentes (= Hygronarius), and Coleopodes (= Volvanarius). Also, Aureonarius, Cortinarius, Cystinarius, and Mystinarius were included in their analysis and formed their own respective clades, although they were not named in the tree. The only genus not represented in this earlier study is Austrocortinarius, but it was included in the phylogeny of Soop et al. (2019), which also recovered the same clades inferred by Garnica et al. (2016). Although many lineages in Garnica et al. (2016) received good support, they were unsupported in the analysis of Soop et al. (2019) and, therefore, were not recognized as formally named taxa.
The phylogenies based on ITS and LSU alone can recover the proposed genera to some extent, but these two gene regions do not suffice to resolve all of the infrafamilial relationships correctly. Particularly, they fail in recovering the monophyly of genera Cortinarius s. str. and Aureonarius (Garnica et al. 2005;Stensrud et al. 2014). Rather, the ITS and LSU regions are most suitable for shallow level classification, i.e., species and sections. To get a better idea on the higher level classification of Cortinariaceae, at least RPB1 would be needed, in addition to ITS and LSU. For optimal resolution, genome-wide data should be used.

How does the new proposed classification differ from the existing one?
Moving from one to ten genera is a big change, but our proposal is not a large leap in circumscribing the known diversity. First, most of the diversity belongs to four large genera, Cortinarius (species-rich in the Northern and Southern Hemispheres), Phlegmacium (species-rich in the Northern Hemisphere, but far fewer species in the Southern Hemisphere), Thaxterogaster (species-rich in the Southern Hemisphere, but far fewer species in the Northern Hemisphere) and Calonarius (restricted to the Northern Hemisphere). Secondly, most of the species-level diversity remains within genus Cortinarius s. str., which includes most of the species with telamonioid, cortinarioid (including dermocyboid and leprocyboid) or myxacioid habits, and all species with rozitoid or cuphocyboid habits (Table 3). Third, except for Aureonarius and Hygronarius, the small genera Austrocortinarius, Cystinarius, Mystinarius, and Volvanarius have long been enigmatic and difficult to confidently place within the previous classifications based on morphological traits only.
The main difference to the previous classification is the transfer of most phlegmacioid species to three separate genera: Phlegmacium, Calonarius, and Thaxterogaster. Of these, Calonarius is the easiest one to distinguish based solely on morphology. It has been recognized as a separate lineage from very early phylogenetic studies onwards (Peintner et al. 2004;Garnica et al. 2005) and several molecular studies have focused on it (e.g., Frøslev et al. 2007;Garnica et al. 2009Garnica et al. , 2011 (Peintner et al. 2001;Nouhra et al. 2021). Although most of them belong to either Cortinarius or Thaxterogaster, they are found in all four of the largest Cortinariaceae genera (Cortinarius, Phlegmacium, Calonarius, and Thaxterogaster), as well as in the small genus Volvanarius.

Infrageneric classification
Our main goal for this study, was to produce a revised generic framework for family Cortinariaceae based on a robust phylogeny derived from genomic data. Futhermore, a base for subgeneric classification is also proposed by recognizing clades with strong to full support, while indicating the possible limits of the already existing subgenera. In some genera, i.e., Aureonarius and Phlegmacium, for which single-copy gene data from a wide range of species already exist, all species were placed in moderately to fully supported groups (Fig. 2). Elsewhere, e.g., the two species-rich genera Cortinarius and Thaxterogaster, further multi-gene studies will be needed to clarify the infrageneric relationships and, at present, only the morphologically and genetically most distinct groups are here recognized. A total of 30 subgenera are recognized of which 10 are here described as new to science.
For the most species-rich genus, Cortinarius, 11 subgenera and 130 sections are currently recognized, although most of these sections (80) belong to the most species-rich subgenus of Cortinariaceae, C. subgen. Telamonia. Morphological variation in the genus is broad but correlates rather well with the phylogeny. The vast majority of cortinarioid (dermocyboid, leprocyboid) and telamonioid species are placed in the strongly supported (BS 97%) crown group of Cortinarius. The group includes the cortinarioid subgenera Dermocybe, Leprocybe, and Orellani, and the telamonioid subgenera Iodolentes, Illumini, and Telamonia, plus several sections and species whose relationships were not wellresolved (Fig. 2). The small phlegmacioid subgenus Infracti and the New Zealand endemic C. pholiotellus form a fully supported (BS 100%) sister group to the crown group. Leading to this crown clade, we find a grade comprised mainly myxacioid, rozitoid, cuphocypoid, and sequestrate species, together with C. sect. Anomali, which was previously placed in C. subgen. Telamonia. Tentative limits of the previously described subgenera are marked in the tree (Fig. 2). Subgenus Cortinarius, which includes the type species of the genus C. violaceus, is tentatively placed in an unsupported clade sister to all other Cortinarius species. It is a morphologically unique group characterized by dark purple to blackish-purple species with dry velvety-squamulose pileus and cheilocystidia (Harrower et al. 2015a, b).
In the genus Phlegmacium, four subgenera and 22 sections are recognized. The subgenera are all moderately to fully supported in the phylogenetic analysis and are also supported by morphological traits. The two large groups, P. subgen. Phlegmacium and P. subgen. Bulbopodium, are 1 3 characterized by different basidiomata development types: the basidiomata of Phlegmacium are stipitocarpic and those of Bulbopodium pileocarpic. The small subgenus Cyanicium includes species with bluish to violet (brownish)grey basidiomata and reddening context. They are phlegmacioid in appearance but have previously also been placed in Telamonia and Sericeocybe . Also, Carbonella is placed with moderate support in genus Phlegmacium in our analysis. It differs from all other lineages of Phlegmacium by having telamonioid basidiomata and is thus recognized here as its own subgenus.
Thaxterogaster includes phlegmacioid, myxacioid and a few telamonioid species. At present, five new subgenera, in addition to the autonym, are proposed to describe the morphologically most distinct units and to serve as anchors for further studies. Twenty-eight sections are recognized. More sampling of species from the Southern Hemisphere is needed to better understand the infrageneric relationships and evolution of the genus.
In Calonarius, three subgenera and 11 sections are recognized. In the smaller genera Aureonarius, Cystinarius, and Hygronarius, two subgenera are recognized for each genus, and this division is also supported by morphological traits. In Austrocortinarius, Mystinarius, and Volvanarius, which only contain a few species, no further infrageneric classification is proposed.

Fungariomics
Two approaches were used to create genomic data for our phylogenomic study: shallow WGS and targeted capture sequencing. For the shallow WGS, the goal was to produce sufficient sequence data representative of the whole genome to assemble into contiguous sequences and then fish our targets from the resulting assemblies. For the targeted capture sequencing, the baits are first designed for the chosen targets, then genomic libraries of chosen samples are enriched, via in solution hybridization with our baits, so that only the targets will be sequenced. We wanted to compare the performance of these two methods in fungi, for which the genome size is relatively small and thus producing low cost WGS data is possible.
Results obtained from targeted capture sequencing were remarkably better than those achieved via shallow WGS. With targeted capture sequencing, over 85% of the 75 targets used for the phylogenomics analysis were recovered, for nine out of 11 specimens. Whereas with WGS, the same percentage was only achieved for three out of nine specimens. The same specimen of Cystinarius crassus was processed with both methods and 33% of the targets were recovered with WGS, compared to 99% with targeted capture sequencing. The advantage of the targeted capture sequencing approach is that only the targeted regions of the systematic group studied are sequenced whereas in WGS the whole genome is sequenced, including possible contaminants present in the basidiomata collected from the wild or gained during the preservation process (Dentinger et al. 2016). Thus, prior knowledge of the genome size of the studied species might help optimize the number of specimens to be pooled for WGS; although, even then, some of the capacity might be lost to sequencing accompanying organisms. Somewhat better results could potentially have also been achieved by improved assembly quality through assembly refinement and it could also be possible that differences in the preservation state and molecular processing of sampled Cortinariaceae species might as well have had some impact in the results (Brewer et al. 2019;Forrest et al. 2019). However, a thorough comparison and evaluation of the effects of these different factors to the success rate is beyond the scope of this study and overall, they would not entirely explain the differences observed in performance.
The age of the fungarium specimens sampled ranged from one to 21 year for the WGS and from four to 13 year for the targeted capture sequencing. Targeted capture sequencing studies in plants have used herbarium specimens ~ 50-200 years old (Brewer et al. 2019;Shee et al. 2020), and even thousands of years old aDNA in archaeogenomic studies (Kistler et al. 2020). Therefore, targeted capture sequencing is also a very promising approach for fungariomics and provides a way to unlock the full potential of specimens stored in fungaria worldwide for phylogenetic analysis. In our study we generated genomic libraries with medium sized inserts, which we chose to sequence in a MiSeq using the Nano chemistry (250 × 250 bp), due to the small number of specimens processed in total. However, especially for the older specimens, where the DNA is likely to be more degraded, the Illumina platforms (i.e., HiSeq, NextSeq, NovaSeq), taking shorter sized fragments as template, would be more suitable.
Our results join the existing evidence  showing that targeted capture sequencing provides a cost-efficient approach (Hale et al. 2020) to produce data for phylogenomic analyses for species-rich groups, like Cortinariaceae, in which one can use the same set of baits for a large range of species (e.g., see Liu et al. 2019, mosses;Johnson et al. 2019, angiosperms;or Widhelm et al. 2021, peltigeralean lichens). The initial bait design and capture reactions add costs compared to the WGS and therefore the latter approach can be more appropriate for smaller taxonomic groups, unless an enrichment panel is already available. It is difficult to provide a precise threshold on the number of species for which targeted capture sequencing becomes cheaper than WGS in fungi, since costs of genomic data are in constant flux and costs also depend on the genome size and intended sequencing coverage, as well as the number of baits to be included in the enrichment panel. Nonetheless, to give some idea of the difference in volume between these two methods, for Cortinariaceae we estimated that about ~ 200 specimens could be pooled into a single Illumina MiSeq 2 × 300 bp paired end run, when using targeted capture sequencing, compared to five to six specimens in total for the WGS approach. On the other hand, in some cases it might be justified to choose the WGS approach for other reasons, e.g., its potential added value of providing data on other genomic features or other loci, not included for a given enrichment panel, for analyses at different taxonomic levels.

Conclusions
This study is the first family revision in Agaricales based on genomic data and hopefully many others will soon follow. We have come a long way from the time of Fries when all gilled fungi were in one genus, Agaricus (Fries 1821). Since then, mycologists have, in most cases, created smaller and smaller genera due to the increased understanding of the diversity and enhanced ability to collect data of the organisms for taxonomic studies. The same phenomenon has happened in plants and animals. The genus Cortinarius has been an especially difficult group for taxonomists, because it includes an enormous amount of morphological and species diversity. While there have been previous efforts to divide the genus into more manageable, practical, and natural units, none have achieved a natural classification for the whole group. Our proposed classification for Cortinariaceae is more equilevant to contemporary concepts in other genera of gilled fungi and we hope that our framework will be more user-friendly, facilitating the identification, conservation and ecological studies on these fascinating organisms.