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Adaptive Gene Content and Allele Distribution Variations in the Wild and Domesticated Populations of Saccharomyces cerevisiae

Recent studies on population genomics of Saccharomyces cerevisiae have substantially improved our understanding of the genetic diversity and domestication history of the yeast. However, the origin of the domesticated population of S. cerevisiae and the genomic changes responsible for ecological adap...

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Autores principales: Han, Da-Yong, Han, Pei-Jie, Rumbold, Karl, Koricha, Anbessa Dabassa, Duan, Shou-Fu, Song, Liang, Shi, Jun-Yan, Li, Kuan, Wang, Qi-Ming, Bai, Feng-Yan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7925643/
https://www.ncbi.nlm.nih.gov/pubmed/33679656
http://dx.doi.org/10.3389/fmicb.2021.631250
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author Han, Da-Yong
Han, Pei-Jie
Rumbold, Karl
Koricha, Anbessa Dabassa
Duan, Shou-Fu
Song, Liang
Shi, Jun-Yan
Li, Kuan
Wang, Qi-Ming
Bai, Feng-Yan
author_facet Han, Da-Yong
Han, Pei-Jie
Rumbold, Karl
Koricha, Anbessa Dabassa
Duan, Shou-Fu
Song, Liang
Shi, Jun-Yan
Li, Kuan
Wang, Qi-Ming
Bai, Feng-Yan
author_sort Han, Da-Yong
collection PubMed
description Recent studies on population genomics of Saccharomyces cerevisiae have substantially improved our understanding of the genetic diversity and domestication history of the yeast. However, the origin of the domesticated population of S. cerevisiae and the genomic changes responsible for ecological adaption of different populations and lineages remain to be fully revealed. Here we sequenced 64 African strains from various indigenous fermented foods and forests in different African countries and performed a population genomic analysis on them combined with a set of previously sequenced worldwide S. cerevisiae strains representing the maximum genetic diversity of the species documented so far. The result supports the previous observations that the wild and domesticated populations of S. cerevisiae are clearly separated and that the domesticated population diverges into two distinct groups associated with solid- and liquid-state fermentations from a single ancestor. African strains are mostly located in basal lineages of the two domesticated groups, implying a long domestication history of yeast in Africa. We identified genes that mainly or exclusively occur in specific groups or lineages and genes that exhibit evident group or lineage specific allele distribution patterns. Notably, we show that the homing endonuclease VDE is generally absent in the wild but commonly present in the domesticated lineages of S. cerevisiae. The genes with group specific allele distribution patterns are mostly enriched in functionally similar or related fundamental metabolism processes, including the evolutionary conserved TOR signaling pathway.
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spelling pubmed-79256432021-03-04 Adaptive Gene Content and Allele Distribution Variations in the Wild and Domesticated Populations of Saccharomyces cerevisiae Han, Da-Yong Han, Pei-Jie Rumbold, Karl Koricha, Anbessa Dabassa Duan, Shou-Fu Song, Liang Shi, Jun-Yan Li, Kuan Wang, Qi-Ming Bai, Feng-Yan Front Microbiol Microbiology Recent studies on population genomics of Saccharomyces cerevisiae have substantially improved our understanding of the genetic diversity and domestication history of the yeast. However, the origin of the domesticated population of S. cerevisiae and the genomic changes responsible for ecological adaption of different populations and lineages remain to be fully revealed. Here we sequenced 64 African strains from various indigenous fermented foods and forests in different African countries and performed a population genomic analysis on them combined with a set of previously sequenced worldwide S. cerevisiae strains representing the maximum genetic diversity of the species documented so far. The result supports the previous observations that the wild and domesticated populations of S. cerevisiae are clearly separated and that the domesticated population diverges into two distinct groups associated with solid- and liquid-state fermentations from a single ancestor. African strains are mostly located in basal lineages of the two domesticated groups, implying a long domestication history of yeast in Africa. We identified genes that mainly or exclusively occur in specific groups or lineages and genes that exhibit evident group or lineage specific allele distribution patterns. Notably, we show that the homing endonuclease VDE is generally absent in the wild but commonly present in the domesticated lineages of S. cerevisiae. The genes with group specific allele distribution patterns are mostly enriched in functionally similar or related fundamental metabolism processes, including the evolutionary conserved TOR signaling pathway. Frontiers Media S.A. 2021-02-17 /pmc/articles/PMC7925643/ /pubmed/33679656 http://dx.doi.org/10.3389/fmicb.2021.631250 Text en Copyright © 2021 Han, Han, Rumbold, Koricha, Duan, Song, Shi, Li, Wang and Bai. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Han, Da-Yong
Han, Pei-Jie
Rumbold, Karl
Koricha, Anbessa Dabassa
Duan, Shou-Fu
Song, Liang
Shi, Jun-Yan
Li, Kuan
Wang, Qi-Ming
Bai, Feng-Yan
Adaptive Gene Content and Allele Distribution Variations in the Wild and Domesticated Populations of Saccharomyces cerevisiae
title Adaptive Gene Content and Allele Distribution Variations in the Wild and Domesticated Populations of Saccharomyces cerevisiae
title_full Adaptive Gene Content and Allele Distribution Variations in the Wild and Domesticated Populations of Saccharomyces cerevisiae
title_fullStr Adaptive Gene Content and Allele Distribution Variations in the Wild and Domesticated Populations of Saccharomyces cerevisiae
title_full_unstemmed Adaptive Gene Content and Allele Distribution Variations in the Wild and Domesticated Populations of Saccharomyces cerevisiae
title_short Adaptive Gene Content and Allele Distribution Variations in the Wild and Domesticated Populations of Saccharomyces cerevisiae
title_sort adaptive gene content and allele distribution variations in the wild and domesticated populations of saccharomyces cerevisiae
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7925643/
https://www.ncbi.nlm.nih.gov/pubmed/33679656
http://dx.doi.org/10.3389/fmicb.2021.631250
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