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Genome skimming and plastid microsatellite profiling of alder trees (Alnus spp., Betulaceae): phylogenetic and phylogeographical prospects

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Abstract

Alders (Alnus spp.) represent keystone species trees of riparian and mountainous habitats of the northern hemisphere. Previous genetic studies have suggested a complex intrageneric diversification with numerous events of interspecific hybridization and polyploidization. Here, we first aim to test the present taxonomical treatment of Alnus by generating phylogenetic hypotheses based on plastid and nuclear data obtained from species belonging to the three main alder subgenera (Alnus, Alnobetula, and Clethropsis). A genome-skimming strategy was used to assemble the complete plastome and the nuclear ribosomal DNA cluster of 22 Eurasian and American alder individuals. Phylogenies based on these data strongly support an early diverging subgenus Alnobetula, while members of the subgenus Clethropsis do not constitute a monophyletic clade and are embedded within the subgenus Alnus. Incongruent topologies also sustain reticulate evolution within this group. Our results thus suggest considering the subgenera Clethropsis and Alnus within the same taxonomical unit. Our second aim is to test for the utility of highly variable plastid markers (microsatellites) to investigate the phylogeographic patterns of Eurasian alder species. Fifty-two polymorphic plastid microsatellite markers were developed and tested on 33 populations of the subgenus Alnus in western Eurasia. On average, 4.3 alleles per locus were revealed in 131 individuals of Alnus glutinosa, allowing the identification of 30 chlorotypes (multiloci profiles). Strong phylogeographic signals and recurrent cytoplasmic captures between co-occurring species are revealed, demonstrating that our plastid microsatellite profiling method is suitable for tracing the post-glacial spread of maternal lineages among alder species. All these results finally support the use of nuclear genomic regions for species identification and of plastid markers for phylogeographic aspects and origin certification in genetic resource management.

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Acknowledgments

We thank L. Csiba and F. Forest (Jodrell Laboratory) for samples of the living collection of Royal Botanic Gardens (Kew, Richmond) and DNA extractions, R. Etienne and A. Gasc (EDB) for the help in plant genotyping, B. Grosso (EDB) for the conservation of dried specimens, and A. Roy and B. Durrington for English corrections. We deeply thank Pr. G. Nakhutsrishvili and Dr. A. Jorjadze (Tbilisi Botanical Garden and Institute of Botany), J. Bastenaire and A. Latrille (Institut Français de Georgie), L. Gogava and D. Sincu (Romanian Academy of Science), T. Manilova (Ceske Budejovice University), S. Ravera (Roma Botanical Garden), M. Dosmann (Arnold Arboretum of Harvard University), J.P. Gibson, C. Ehardt and S. Rice (University of Oklahoma), J.A. Bérubé (Université Laval), A. Bellino, D. Puntillo and L. Hugot (Conservatoire Botanique National de Corse), P. Jargeat, D. Badr, C. del Rio, and M. Gardes (EDB), for their helpful support in the field.

Funding

All authors are members of the Laboratoire Evolution & Diversité Biologique (EDB) part of the LABEX entitled TULIP managed by Agence Nationale de la Recherche (ANR-10-LABX-0041). We also acknowledge an Investissement d’Avenir grant of the Agence Nationale de la Recherche (CEBA: ANR-10-LABX-25-01) and an EC2CO MicrobiEn grant (ECosphère COntinentale et CÔtière, Microbiologie ENvironnementale, “Coévolution et phylogéographie des mutualismes aulne-microorganismes”). CVDP and GB were funded by the Regional Council Midi-Pyrenees (AAP 13053637, 2014-EDB-UT3-DOCT). This study also received support from the PhyloAlps project, with the help of M. Boleda and A. Iribar O. Bouchez from the Genopole in Toulouse (INRA) helped with the Illumina sequencing.

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  1. CNRS, UPS, ENSFEA, IRD, Laboratoire Evolution & Diversité Biologique, UMR 5174, 310624, Toulouse, France

    Hervé Gryta, Céline Van de Paer, Sophie Manzi, Hélène Holota, Mélanie Roy & Guillaume Besnard

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  1. Hervé Gryta
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  2. Céline Van de Paer
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  3. Sophie Manzi
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  4. Hélène Holota
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Contributions

HG and GB conceived the initial project; SM, HH, and GB did the lab work; HG, MR, and GB collected plants; HG, CVDP, and GB analyzed data; HG and GB wrote the paper; and all authors commented and approved the final version of the manuscript.

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Correspondence to Hervé Gryta or Guillaume Besnard.

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Additional information

Communicated by P. Ingvarsson

Data archiving statement

All newly assembled chloroplast genomes and nuclear ribosomal clusters are available in the NCBI nucleotide database under accession nos. MF136495to MF136538. The cpSSR dataset is provided in the Supporting Information (Table S3).

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Gryta, H., Van de Paer, C., Manzi, S. et al. Genome skimming and plastid microsatellite profiling of alder trees (Alnus spp., Betulaceae): phylogenetic and phylogeographical prospects. Tree Genetics & Genomes 13, 118 (2017). https://doi.org/10.1007/s11295-017-1204-2

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