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Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts

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Bioinformatics: from nucleotids to networks (N2N)
Abstract
The evolutionary history of the characters underlying the adaptation of microorganisms to food and biotechnological uses is poorly understood. We undertook comparative genomics to investigate evolutionary relationships of the dairy yeast Geotrichum candidum within Saccharomycotina. Surprisingly, a remarkable proportion of genes showed discordant phylogenies, clustering with the filamentous fungus subphylum (Pezizomycotina), rather than the yeast subphylum (Saccharomycotina), of the Ascomycota. These genes appear not to be the result of Horizontal Gene Transfer (HGT), but to have been specifically retained by G. candidum after the filamentous fungiyeasts split concomitant with the yeasts' genome contraction. We refer to these genes as SRAGs (Specifically Retained Ancestral Genes), having been lost by all or nearly all other yeasts, and thus contributing to the phenotypic specificity of lineages. SRAG functions include lipases consistent with a role in cheese making and novel endoglucanases associated with degradation of plant material. Similar gene retention was observed in three other distantly related yeasts representative of this ecologically diverse subphylum. The phenomenon thus appears to be widespread in the Saccharomycotina and argues that, alongside neo-functionalization following gene duplication and HGT, specific gene retention must be recognized as an important mechanism for generation of biodiversity and adaptation in yeasts.
Keywords
SACCHAROMYCES-CEREVISIAE EC1118, MULTIPLE SEQUENCE ALIGNMENT, TAXONOMICALLY RESTRICTED GENES, SCALE PHYLOGENETIC ANALYSES, GEOTRICHUM-CANDIDUM STRAINS, COMPARATIVE GENOMICS, INTERSPECIES HYBRIDIZATION, DEBARYOMYCES-HANSENII, HEMIASCOMYCETOUS YEASTS, MAXIMUM-LIKELIHOOD

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Citation

Please use this url to cite or link to this publication:

Chicago
Morel, Guillaume, Lieven Sterck, Dominique Swennen, Marina Marcet-Houben, Djamila Onesime, Anthony Levasseur, Noémie Jacques, et al. 2015. “Differential Gene Retention as an Evolutionary Mechanism to Generate Biodiversity and Adaptation in Yeasts.” Scientific Reports 5.
APA
Morel, G., Sterck, L., Swennen, D., Marcet-Houben, M., Onesime, D., Levasseur, A., Jacques, N., et al. (2015). Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts. SCIENTIFIC REPORTS, 5.
Vancouver
1.
Morel G, Sterck L, Swennen D, Marcet-Houben M, Onesime D, Levasseur A, et al. Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts. SCIENTIFIC REPORTS. 2015;5.
MLA
Morel, Guillaume, Lieven Sterck, Dominique Swennen, et al. “Differential Gene Retention as an Evolutionary Mechanism to Generate Biodiversity and Adaptation in Yeasts.” SCIENTIFIC REPORTS 5 (2015): n. pag. Print.
@article{6918030,
  abstract     = {The evolutionary history of the characters underlying the adaptation of microorganisms to food and biotechnological uses is poorly understood. We undertook comparative genomics to investigate evolutionary relationships of the dairy yeast Geotrichum candidum within Saccharomycotina. Surprisingly, a remarkable proportion of genes showed discordant phylogenies, clustering with the filamentous fungus subphylum (Pezizomycotina), rather than the yeast subphylum (Saccharomycotina), of the Ascomycota. These genes appear not to be the result of Horizontal Gene Transfer (HGT), but to have been specifically retained by G. candidum after the filamentous fungiyeasts split concomitant with the yeasts' genome contraction. We refer to these genes as SRAGs (Specifically Retained Ancestral Genes), having been lost by all or nearly all other yeasts, and thus contributing to the phenotypic specificity of lineages. SRAG functions include lipases consistent with a role in cheese making and novel endoglucanases associated with degradation of plant material. Similar gene retention was observed in three other distantly related yeasts representative of this ecologically diverse subphylum. The phenomenon thus appears to be widespread in the Saccharomycotina and argues that, alongside neo-functionalization following gene duplication and HGT, specific gene retention must be recognized as an important mechanism for generation of biodiversity and adaptation in yeasts.},
  articleno    = {11571},
  author       = {Morel, Guillaume and Sterck, Lieven and Swennen, Dominique and Marcet-Houben, Marina and Onesime, Djamila and Levasseur, Anthony and Jacques, No{\'e}mie and Mallet, Sandrine and Couloux, Arnaux and Labadie, Karine and Amselem, Jo{\"e}lle and Beckerich, Jean-Marie and Henrissat, Bernard and Van de Peer, Yves and Wincker, Patrick and Souciet, Jean-Luc and Gabald{\'o}n, Toni and Tinsley, Colin R and Casaregola, Serge},
  issn         = {2045-2322},
  journal      = {SCIENTIFIC REPORTS},
  keyword      = {SACCHAROMYCES-CEREVISIAE EC1118,MULTIPLE SEQUENCE ALIGNMENT,TAXONOMICALLY RESTRICTED GENES,SCALE PHYLOGENETIC ANALYSES,GEOTRICHUM-CANDIDUM STRAINS,COMPARATIVE GENOMICS,INTERSPECIES HYBRIDIZATION,DEBARYOMYCES-HANSENII,HEMIASCOMYCETOUS YEASTS,MAXIMUM-LIKELIHOOD},
  language     = {eng},
  pages        = {17},
  title        = {Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts},
  url          = {http://dx.doi.org/10.1038/srep11571},
  volume       = {5},
  year         = {2015},
}

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