Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes

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• dc.contributor.author Gladieux, Pierre
• dc.contributor.author Ropars, Jeanne
• dc.contributor.author Badouin, Hélène
• dc.contributor.author Branca, Antoine
• dc.contributor.author Aguileta, Gabriela
• dc.contributor.author de Vienne, Damien M.
• dc.contributor.author Rodríguez de la Vega, Ricardo C.
• dc.contributor.author Branco, Sara
• dc.contributor.author Giraud, Tatiana
• dc.date.accessioned 2024-01-16T06:58:40Z
• dc.date.available 2024-01-16T06:58:40Z
• dc.date.issued 2013
• dc.description.abstract Fungi are ideal model organisms for dissecting the genomic bases of adaptive divergence in eukaryotes. They have simple morphologies and small genomes, occupy contrasting, well-identified ecological niches and tend to have short generation times, and many are amenable to experimental approaches. Fungi also display diverse lifestyles, from saprotrophs to pathogens or mutualists, and they play extremely important roles in both ecosystems and human activities, as wood decayers, mycorrhizal fungi, lichens, endophytes, plant and animal pathogens, and in fermentation or drug production. We review here recent insights into the patterns and mechanisms of adaptive divergence in fungi, including sources of divergence, genomic variation and, ultimately, speciation. We outline the various ecological sources of divergent selection and genomic changes, showing that gene loss and changes in gene expression and in genomic architecture are important adaptation processes, in addition to the more widely recognized processes of amino acid substitution and gene duplication. We also review recent findings regarding the interspecific acquisition of genomic variation and suggesting an important role for introgression, hybridization and horizontal gene transfers (HGTs). We show that transposable elements can mediate several of these genomic changes, thus constituting important factors for adaptation. Finally, we review the consequences of divergent selection in terms of speciation, arguing that genetic incompatibilities may not be as widespread as generally thought and that pleiotropy between adaptation and reproductive isolation is an important route of speciation in fungal pathogens.
• dc.description.sponsorship This work was supported by the ANR Grant 12-ADAP-0009-02-GANDALF and the ERC starting grant, GenomeFun 309403 to TG, the ANR FROMA-GEN Grant ANR-12-PDOC-0030 to AB, the National Science Foundation Grant DBI 1046115 to SB and Marie Curie postdoctoral fellowships to PG [FP7-PEOPLE-2010- IOF-No.273086], GA [FP7-PEOPLE-2010-IEF-No.274223] and RRDLV [FP7 COFUND PRES-SUD No. 246556]. We thank François Delmotte, Tobin Peever, the Mycology Laboratory BIOTEC and Jacques Guinberteau (INRA) for the pictures in Fig. 1.
• dc.format.mimetype application/pdf
• dc.identifier.citation Gladieux P, Ropars J, Badouin H, Branca A, Aguileta G, de Vienne DM, et al. Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes. Molecular Ecology. 2014 Feb;23(4):753-73. DOI: 10.1111/mec.12631
• dc.identifier.doi http://dx.doi.org/10.1111/mec.12631
• dc.identifier.issn 0962-1083
• dc.identifier.uri http://hdl.handle.net/10230/58707
• dc.language.iso eng
• dc.publisher Wiley
• dc.relation.ispartof Molecular Ecology. 2014 Feb;23(4):753-73
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/273086
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/274223
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/246556
• dc.rights © 2016 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Coccidioides
• dc.subject.keyword Competition
• dc.subject.keyword Effector
• dc.subject.keyword Gene regulation
• dc.subject.keyword Genetic incompatibilities
• dc.subject.keyword Genomic islands
• dc.subject.keyword Local adaptation
• dc.subject.keyword Neurospora
• dc.subject.keyword Penicillium
• dc.subject.keyword Positive selection
• dc.subject.keyword Saccharomyces
• dc.subject.keyword Yeast
• dc.title Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion