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

Guillaume Morel, Lieven Sterck (UGent) , Dominique Swennen, Marina Marcet-Houben, Djamila Onesime, Anthony Levasseur, Noémie Jacques, Sandrine Mallet, Arnaux Couloux, Karine Labadie, et al.
(2015) SCIENTIFIC REPORTS. 5.
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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

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MLA
Morel, Guillaume, et al. “Differential Gene Retention as an Evolutionary Mechanism to Generate Biodiversity and Adaptation in Yeasts.” SCIENTIFIC REPORTS, vol. 5, 2015, doi:10.1038/srep11571.
APA
Morel, G., Sterck, L., Swennen, D., Marcet-Houben, M., Onesime, D., Levasseur, A., … Casaregola, S. (2015). Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts. SCIENTIFIC REPORTS, 5. https://doi.org/10.1038/srep11571
Chicago author-date
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. https://doi.org/10.1038/srep11571.
Chicago author-date (all authors)
Morel, Guillaume, Lieven Sterck, Dominique Swennen, Marina Marcet-Houben, Djamila Onesime, Anthony Levasseur, Noémie Jacques, Sandrine Mallet, Arnaux Couloux, Karine Labadie, Joëlle Amselem, Jean-Marie Beckerich, Bernard Henrissat, Yves Van de Peer, Patrick Wincker, Jean-Luc Souciet, Toni Gabaldón, Colin R Tinsley, and Serge Casaregola. 2015. “Differential Gene Retention as an Evolutionary Mechanism to Generate Biodiversity and Adaptation in Yeasts.” SCIENTIFIC REPORTS 5. doi:10.1038/srep11571.
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.
IEEE
[1]
G. Morel et al., “Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts,” SCIENTIFIC REPORTS, vol. 5, 2015.
@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, Noémie and Mallet, Sandrine and Couloux, Arnaux and Labadie, Karine and Amselem, Joëlle and Beckerich, Jean-Marie and Henrissat, Bernard and Van de Peer, Yves and Wincker, Patrick and Souciet, Jean-Luc and Gabaldón, Toni and Tinsley, Colin R and Casaregola, Serge}},
  issn         = {{2045-2322}},
  journal      = {{SCIENTIFIC REPORTS}},
  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}},
  language     = {{eng}},
  pages        = {{17}},
  title        = {{Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts}},
  url          = {{http://doi.org/10.1038/srep11571}},
  volume       = {{5}},
  year         = {{2015}},
}
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