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Journal Articles Scientific Reports Year : 2015

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

Lieven Sterck
Dominique Swennen
  • Function : Author
Marina Marcet-Houben
  • Function : Author
Anthony Levasseur
Noémie Jacques
  • Function : Author
Sandrine Mallet
  • Function : Author
Arnaux Couloux
  • Function : Author
Karine Labadie
Joëlle Amselem
  • Function : Author
Bernard Henrissat
  • Function : Author
  • PersonId : 833340
Yves van de Peer
Patrick Wincker
Jean-Luc Souciet
  • Function : Author
Toni Gabaldón
Colin Tinsley
  • Function : Author

Abstract

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 fungi–yeasts 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.

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Biodiversity

Dates and versions

hal-03274350 , version 1 (30-06-2021)

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Guillaume Morel, Lieven Sterck, Dominique Swennen, Marina Marcet-Houben, Djamila Onesime, et al.. Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts. Scientific Reports, 2015, 5 (1), ⟨10.1038/srep11571⟩. ⟨hal-03274350⟩

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