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Finding single copy genes out of sequenced genomes for multilocus phylogenetics in non-model fungi

hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorFEAU, Nicolas
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorDECOURCELLE, Thibaut
hal.structure.identifierInteractions Arbres-Microorganismes [IAM]
dc.contributor.authorHUSSON, Claude
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorDESPREZ LOUSTAU, Marie Laure
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorDUTECH, Christian Cyril
dc.date.accessioned2022-10-12T12:51:42Z
dc.date.available2022-10-12T12:51:42Z
dc.date.issued2011
dc.identifier.issn1932-6203
dc.identifier.urihttps://oskar-bordeaux.fr/handle/20.500.12278/157350
dc.description.abstractEnHistorically, fungal multigene phylogenies have been reconstructed based on a small number of commonly used genes. The availability of complete fungal genomes has given rise to a new wave of model organisms that provide large number of genes potentially useful for building robust gene genealogies. Unfortunately, cross-utilization of these resources to study phylogenetic relationships in the vast majority of non-model fungi (i.e. “orphan” species) remains an unexamined question. To address this problem, we developed a method coupled with a program named “PHYLORPH” (PHYLogenetic markers for ORPHans). The method screens fungal genomic databases (107 fungal genomes fully sequenced) for single copy genes that might be easily transferable and well suited for studies at low taxonomic levels (for example, in species complexes) in non-model fungal species. To maximize the chance to target genes with informative regions, PHYLORPH displays a graphical evaluation system based on the estimation of nucleotide divergence relative to substitution type. The usefulness of this approach was tested by developing markers in four non-model groups of fungal pathogens. For each pathogen considered, 7 to 40% of the 10–15 best candidate genes proposed by PHYLORPH yielded sequencing success. Levels of polymorphism of these genes were compared with those obtained for some genes traditionally used to build fungal phylogenies (e.g. nuclear rDNA, β-tubulin, γ-actin, Elongation factor EF-1α). These genes were ranked among the best-performing ones and resolved accurately taxa relationships in each of the four non-model groups of fungi considered. We envision that PHYLORPH will constitute a useful tool for obtaining new and accurate phylogenetic markers to resolve relationships between closely related non-model fungal species.
dc.language.isoen
dc.publisherPublic Library of Science
dc.title.enFinding single copy genes out of sequenced genomes for multilocus phylogenetics in non-model fungi
dc.typeArticle de revue
dc.identifier.doi10.1371/journal.pone.0018803
dc.subject.halSciences du Vivant [q-bio]/Biologie cellulaire
bordeaux.journalPLoS ONE
bordeaux.page17 p.
bordeaux.volume6
bordeaux.hal.laboratoriesBioGeCo (Biodiversité Gènes & Communautés) - UMR 1202*
bordeaux.issue4
bordeaux.institutionUniversité de Bordeaux
bordeaux.institutionINRAE
bordeaux.peerReviewedoui
hal.identifierhal-02651218
hal.version1
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02651218v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=PLoS%20ONE&rft.date=2011&rft.volume=6&rft.issue=4&rft.spage=17%20p.&rft.epage=17%20p.&rft.eissn=1932-6203&rft.issn=1932-6203&rft.au=FEAU,%20Nicolas&DECOURCELLE,%20Thibaut&HUSSON,%20Claude&DESPREZ%20LOUSTAU,%20Marie%20Laure&DUTECH,%20Christian%20Cyril&rft.genre=article


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