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Rapid identification of polymorphic sequences in non-model fungal species: the PHYLORPH method tested in Armillaria species

hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorDUTECH, Cyril
hal.structure.identifierSwiss Federal Institute for Forest, Snow and Landscape Research WSL
dc.contributor.authorPROSPERO, Simone
hal.structure.identifierSwiss Federal Institute for Forest, Snow and Landscape Research WSL
dc.contributor.authorHEINZELMANN, R.
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorFABREGUETTES, Olivier
hal.structure.identifierDepartment of Forest and Conservation Sciences, British Columbia
dc.contributor.authorFEAU, Nicolas
dc.date.accessioned2022-10-12T13:09:09Z
dc.date.available2022-10-12T13:09:09Z
dc.date.issued2016
dc.identifier.issn1437-4781
dc.identifier.urihttps://oskar-bordeaux.fr/handle/20.500.12278/157721
dc.description.abstractEnDevelopment of molecular markers for phylogenetic, population genetics and phylogeographic studies remains arduous in non-model species with low or no genomic resources. Sequencing the whole or a large part of the genome of the target species using next-generation sequencing technologies is considered a promising method, although it still needs a large investment in bioinformatics. To quickly find polymorphic markers in fungal species, we tested an alternative method, named PHYLORPH. This method allows users to quickly target polymorphic regions of single copy genes in fungi using public databases. We applied this method to Armillaria species, which are important fungal pathogens and saprophytes playing a central role in the dynamics of forest ecosystems worldwide. We isolated 32 single copy genes with numerous single nucleotide polymorphism (SNP) sites. A genetic analysis of two French populations validated the polymorphism of 80 among 92 SNPs tested, and seven of these sequences exactly reconstructed the known phylogenetic tree of four tested Armillaria species. These results confirmed that the PHYLORPH method is efficient to identify various markers at both the intra- and interspecific levels for fungal species with no or few previous genetic markers.
dc.language.isoen
dc.publisherWiley
dc.title.enRapid identification of polymorphic sequences in non-model fungal species: the PHYLORPH method tested in Armillaria species
dc.typeArticle de revue
dc.identifier.doi10.1111/efp.12256
dc.subject.halSciences du Vivant [q-bio]
bordeaux.journalForest Pathology
bordeaux.page298-308
bordeaux.volume46
bordeaux.hal.laboratoriesBioGeCo (Biodiversité Gènes & Communautés) - UMR 1202*
bordeaux.issue4
bordeaux.institutionUniversité de Bordeaux
bordeaux.institutionINRAE
bordeaux.peerReviewedoui
hal.identifierhal-02630717
hal.version1
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02630717v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Forest%20Pathology&rft.date=2016&rft.volume=46&rft.issue=4&rft.spage=298-308&rft.epage=298-308&rft.eissn=1437-4781&rft.issn=1437-4781&rft.au=DUTECH,%20Cyril&PROSPERO,%20Simone&HEINZELMANN,%20R.&FABREGUETTES,%20Olivier&FEAU,%20Nicolas&rft.genre=article


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