Abstract
Substantial difficulties in the morphological identification of phoma-like fungi, including Paraphoma spp., have resulted in poor understanding of the generic and species boundaries in this group of organisms. This study was devoted to the reidentification and taxonomic revision of phoma-like isolates derived from Convolvulaceae leaves collected from different geographical locations in Russia and territories of neighboring countries. The study was based primarily on sequencing phylogenetically informative loci (ITS, LSU, TUB, and RPB2) and on traditional morphological approaches. The resulting phylogenetic tree revealed three well-supported monophyletic clades, corresponding to three Paraphoma species. The new species Paraphoma melnikiae Gomzhina M. M. & Gasich E. L. was described, and a new taxonomic combination, Paraphoma convolvuli (Dearn. & House) Gomzhina M. M. & Gasich E. L., was established for Stagonospora convolvuli. Several isolates were preliminarily identified as Paraphoma cf. convolvuli and are likely new species of the genus Paraphoma, but this requires further verification.
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References
Alcalde MB (1952) Algunos micromicetos recollectades por el Prof. Caballero Segares en Valencia Anales del Jardin Botanico de Madrid 10:229–255
Boerema GH, de Gruyter J, Noordeloos ME, Hamers MEC (2004) Phoma identification manual. CABI Publishing
Bondartsev AS (1953) Polyporic mushrooms in the European USSR and Caucasus. AS USSR, Moscow, Leningrad
Boyle JS, Lew AM (1995) An inexpensive alternative to glassmilk for DNA purification. Trends Genet 11(8)
Chen Q, Jiang JR, Zhang GZ, Cai L, Crous PW (2015) Resolving the Phoma enigma. Studies in mycology 82: 137–217.
Crous PW, Wingfield MJ, Burgess TI et al (2017) Fungal planet description sheets: 558–624. Persoonia 38:240–384
de Gruyter J, Woudenberg JHC, Aveskamp MM, Verkley GJM, Groenewald JZ, Grous PW (2010) Systematic reappraisal of species in Phoma section Paraphoma, Pyrenochaeta and Pleurophoma. Mycologia 102(5):1066–1081
Defago G, Ammon HU, Cogán L, Draeger B, Greaves MP, Guntli D, Hoeke D, Klimes L, Lawrie J, Moënne-Loccoz Y, Nicolet B, Pfirter HA, Tabacchi R, Tóth P (2001) Towards the biocontrol of bindweeds with a mycoherbicide. BioControl 46:157–173
Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15
Gardes M, Bruns TD (1993) ITS primers with enhanced specificity for basidiomycetes – application to the identification of mycorrhizae and rusts. Mol Ecol 2:113–118
Guntli D, Pfirter HA, Moёnne-Loccoz Y, Défago G (1998) Stagonospora convolvuli LA39 for biocontrol of field bindweed infesting cotoneaster in a cemetery. HortScience 33(5):860–861
Heiny DK (1990) Phoma proboscis sp. nov. pathogenic on Convolvulus arvensis. Mycotaxon XXXVI(2):457–471
Heiny DK, Templeton GE (1991) Effects of spore concentration, temperature, and dew period on disease of field bindweed caused by Phoma proboscis. Phytopathology 81:905–909
Heiny DK, Templeton GE (1995) Method and compositions for the biological control of field bindweed. United States Patent 5391538
Liu YJ, Whelen S, Hall BD (1999) Phylogenetic relationships among ascomycetes: evidence from an RNA polymerase II subunit. Mol Biol Evol 16:1799–1808
Morgan-Jones G, White JF (1983) Studies in genus Phoma. III. Paraphoma, a new genus to accommodate Phoma radicina. Mycotaxon XVIII(1):57–65
Moslemi A, Ades PK, Groom T, Crous PW, Nicolas ME, Taylor PWJ (2016) Paraphoma crown rot of pyrethrum (Tanacetum cinerariifolium). Plant Dis:1–7
Moslemi A, Ades PK, Crous PW, Groom T, Scott JB, Nicolas ME, Taylor PWJ (2017) Paraphoma chlamydocopiosa sp. nov. and Paraphoma pye sp. nov., two new species associated with leaf and crown infection of pyrethrum. Plant Pathology:1–12
Nadtochiy IN (2008) Convolvulus arvensis. In: Afonin AN, Greene SL, Dzyubenko NI, Frolov AN. (ed) Interactive agricultural ecological atlas of Russia and neighboring countries: economic plants and their diseases, pests and weeds [online]. Available at: http://www.agroatlas.ru/en/content/related/Convolvulus_arvensis/
O’Donnell K, Cigelnik E (1997) Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous. Mol Phylogenet Evol 7:103–116
Ormeno-Nuñez J, Reeleder RD, Watson AK (1988a) A new species of Phomopsis recovered from field bindweed (Convolvulus arvensis. Can J Bot 66: 2228–2233
Ormeno-Nuñez J, Reeleder RD, Watson AK (1988b) A foliar disease of field bindweed (Convolvulus arvensis) caused by Phomopsis convolvulus. Plant Dis 72:338–342
Pfirter HA, Defago G (1998) The potential of Stagonospora sp. as a mycoherbicide for field bindweed. Biocontrol Sci Tech 8:93–101
Pfirter HA, Guntli D, Ruess M, Defago G (1999) Preservation, mass production and storage of Stagonospora convolvuli, a bioherbicide candidate for field bindweed (Convolvulus arvensis). BioControl 44:437–447
Poluektova E, Yu T, Sokornova S, Chisty L, Evidente A, Berestetskiy A (2018) Curvulin and Phaeosphaeride A from Paraphoma sp. VIZR 1.46 isolated from Cirsium arvense as potential herbicides. Molecules 23(11):2795
Punithalingam E (1982) Phomopsis ipomoeae-batatas. CMI Descriptions of Pathogenic Fungi and Bacteria 739:1–2
Quaedvlieg W, Verkley GJM, Shin H-D, Barreto RW, Alfenas AC, Swart WJ et al (2013) Sizing up Septoria. Stud Mycol 75:307–390
Rehner SA, Samuels GJ (1994) Taxonomy and phylogeny of Gliocladium analysed from nuclear large subunit ribosomal DNA sequences. Mycol Res 98:625–634
Saccardo PA (1895) Sylloge fungorum 11(3): 491–492
Saccardo PA (1931) Sylloge fungorum 25: 364–365
Saleh AA, Leslie JF (2004) Cephalosporium maydis is a distinct species in the Gaeumannomyces-Harpophora species complex. Mycologia 96(6):1294–1305
Samson RA, Hoekstra ES, Frisvad JC, Filtenborg O Introduction to food- and airborne fungi, 6th edn. Centraal bureau voor schimmel cultures, Utrecht 2000. ISBN-10: 9070351420
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74(12):5463–5467
Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690
Stetsov GY, Sadovnikova NN (2012) Convolvulus arvensis and it’s controlling. Agricultural department 2012 Available at: https://agrosektor.kz/agricultural-technologies/vyunok-polevoj-i-borba-s-nim.html
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 24:4876–4882
Vogelsang S, Watson AK, DiTommaso A (1998) Effect of moisture, inoculum production, and planting substrate on disease reaction of field bindweed (Convolvulus arvensis L.) to the fungal pathogen, Phomopsis convolvulus. Eur J Plant Pathol 104:253–262
Watson AK, Reeleder RD, Ormeno-Nuñez J (1993) Fungal herbicides. United States Patent 5212086
Wehmeyer LE (1946) Sudies on some fungi from northwestern Wyoming. II Fungi Imperfecti Mycologia 38: 306–330
White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR protocols: a guide to methods and applications. Academic Press, San Diego, pp 315–322
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This study was financially supported by the Russian Science Foundation, project 19-76-30005.
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Gomzhina, M.M., Gasich, E.L., Khlopunova, L.B. et al. Paraphoma species associated with Convolvulaceae. Mycol Progress 19, 185–194 (2020). https://doi.org/10.1007/s11557-020-01558-8
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DOI: https://doi.org/10.1007/s11557-020-01558-8