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The fascinating and secret wild life of the budding yeast S. cerevisiae.

Liti G - Elife (2015)

Bottom Line: However, it wasn't until a decade ago that the scientific community started to realise how little was known about this yeast's ecology and natural history, and how this information was vitally important for interpreting its biology.Recent large-scale population genomics studies coupled with intensive field surveys have revealed a previously unappreciated wild lifestyle of S. cerevisiae outside the restrictions of human environments and laboratories.The recent discovery that Chinese isolates harbour almost twice as much genetic variation as isolates from the rest of the world combined suggests that Asia is the likely origin of the modern budding yeast.

View Article: PubMed Central - PubMed

Affiliation: Institute for Research on Cancer and Ageing of Nice, CNRS UMR 7284, INSERM U1081, University of Nice Sophia Antipolis, Nice, France.

ABSTRACT
The budding yeast Saccharomyces cerevisiae has been used in laboratory experiments for over a century and has been instrumental in understanding virtually every aspect of molecular biology and genetics. However, it wasn't until a decade ago that the scientific community started to realise how little was known about this yeast's ecology and natural history, and how this information was vitally important for interpreting its biology. Recent large-scale population genomics studies coupled with intensive field surveys have revealed a previously unappreciated wild lifestyle of S. cerevisiae outside the restrictions of human environments and laboratories. The recent discovery that Chinese isolates harbour almost twice as much genetic variation as isolates from the rest of the world combined suggests that Asia is the likely origin of the modern budding yeast.

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S. cerevisiae genome relationships and population structure.(A) A phylogenetic tree of S. cerevisiae isolates, adapted from (Wang et al., 2012). The main worldwide and Chinese lineages (denoted, CHN I-V) are highlighted. Lineages CHN-I, CHN-III, CHN-V were mostly isolated from Fagaceae trees in the rainforest of the tropical Hainan Island in the South China Sea. Lineages CHN-II and CHN-IV were isolated from temperate areas in north China (Shaanxi province and Beijing province, respectively). (B) Sequence similarity plots of the Y55 and SK1 laboratory strains showing the relationships to the five, worldwide genetically distinct lineages (listed on the right) along chromosome II. Similarity is defined as N/(D+1), where N is the number of positions in a chromosomal window and D is the number of those positions where the nucleotides differ. The genomes of both Y55 and SK1 are mostly derived from the West African lineage (red line). However, large blocks of the chromosome show drops in similarity to the West African lineage and higher similarity to other lineages. Y55 has three segments (0–50 kb, around 400 kb, from 650 kb to the right telomere) with high similarity to the Wine/European genome (yellow line). Likewise, SK1 has a large segment (650–750 kb) with higher similarity to the Sake lineage (light green line). This type of analysis has revealed the mosaic genome structure of many S. cerevisiae isolates (Liti et al., 2009). Image credit: Anders Bergström and Gianni Liti.DOI:http://dx.doi.org/10.7554/eLife.05835.005
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fig3: S. cerevisiae genome relationships and population structure.(A) A phylogenetic tree of S. cerevisiae isolates, adapted from (Wang et al., 2012). The main worldwide and Chinese lineages (denoted, CHN I-V) are highlighted. Lineages CHN-I, CHN-III, CHN-V were mostly isolated from Fagaceae trees in the rainforest of the tropical Hainan Island in the South China Sea. Lineages CHN-II and CHN-IV were isolated from temperate areas in north China (Shaanxi province and Beijing province, respectively). (B) Sequence similarity plots of the Y55 and SK1 laboratory strains showing the relationships to the five, worldwide genetically distinct lineages (listed on the right) along chromosome II. Similarity is defined as N/(D+1), where N is the number of positions in a chromosomal window and D is the number of those positions where the nucleotides differ. The genomes of both Y55 and SK1 are mostly derived from the West African lineage (red line). However, large blocks of the chromosome show drops in similarity to the West African lineage and higher similarity to other lineages. Y55 has three segments (0–50 kb, around 400 kb, from 650 kb to the right telomere) with high similarity to the Wine/European genome (yellow line). Likewise, SK1 has a large segment (650–750 kb) with higher similarity to the Sake lineage (light green line). This type of analysis has revealed the mosaic genome structure of many S. cerevisiae isolates (Liti et al., 2009). Image credit: Anders Bergström and Gianni Liti.DOI:http://dx.doi.org/10.7554/eLife.05835.005

Mentions: Population genomics has provided a powerful means by which to illuminate the evolutionary history of budding yeast. In initial genome sequencing studies, half of the S. cerevisiae strains sequenced fell into a number of distinct lineages (Figure 3A). Genetic variants within these lineages are mostly unique to a subpopulation and absent in others and evenly distributed across the genome (Liti et al., 2009). Variation in phenotype tends to follow population structure (Warringer et al., 2011). Some of these lineages are characteristic of distinct fermentation processes and might represent examples of domesticated breeds (Fay and Benavides, 2005; Schacherer et al., 2009). These strains do not strictly follow geographic boundaries, for example, wine strains from Europe, Australia, Chile and New Zealand share recent ancestry and reflect human migration history (Legras et al., 2007; Liti et al., 2009; Goddard et al., 2010; Dunn et al., 2012).10.7554/eLife.05835.005Figure 3.S. cerevisiae genome relationships and population structure.


The fascinating and secret wild life of the budding yeast S. cerevisiae.

Liti G - Elife (2015)

S. cerevisiae genome relationships and population structure.(A) A phylogenetic tree of S. cerevisiae isolates, adapted from (Wang et al., 2012). The main worldwide and Chinese lineages (denoted, CHN I-V) are highlighted. Lineages CHN-I, CHN-III, CHN-V were mostly isolated from Fagaceae trees in the rainforest of the tropical Hainan Island in the South China Sea. Lineages CHN-II and CHN-IV were isolated from temperate areas in north China (Shaanxi province and Beijing province, respectively). (B) Sequence similarity plots of the Y55 and SK1 laboratory strains showing the relationships to the five, worldwide genetically distinct lineages (listed on the right) along chromosome II. Similarity is defined as N/(D+1), where N is the number of positions in a chromosomal window and D is the number of those positions where the nucleotides differ. The genomes of both Y55 and SK1 are mostly derived from the West African lineage (red line). However, large blocks of the chromosome show drops in similarity to the West African lineage and higher similarity to other lineages. Y55 has three segments (0–50 kb, around 400 kb, from 650 kb to the right telomere) with high similarity to the Wine/European genome (yellow line). Likewise, SK1 has a large segment (650–750 kb) with higher similarity to the Sake lineage (light green line). This type of analysis has revealed the mosaic genome structure of many S. cerevisiae isolates (Liti et al., 2009). Image credit: Anders Bergström and Gianni Liti.DOI:http://dx.doi.org/10.7554/eLife.05835.005
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fig3: S. cerevisiae genome relationships and population structure.(A) A phylogenetic tree of S. cerevisiae isolates, adapted from (Wang et al., 2012). The main worldwide and Chinese lineages (denoted, CHN I-V) are highlighted. Lineages CHN-I, CHN-III, CHN-V were mostly isolated from Fagaceae trees in the rainforest of the tropical Hainan Island in the South China Sea. Lineages CHN-II and CHN-IV were isolated from temperate areas in north China (Shaanxi province and Beijing province, respectively). (B) Sequence similarity plots of the Y55 and SK1 laboratory strains showing the relationships to the five, worldwide genetically distinct lineages (listed on the right) along chromosome II. Similarity is defined as N/(D+1), where N is the number of positions in a chromosomal window and D is the number of those positions where the nucleotides differ. The genomes of both Y55 and SK1 are mostly derived from the West African lineage (red line). However, large blocks of the chromosome show drops in similarity to the West African lineage and higher similarity to other lineages. Y55 has three segments (0–50 kb, around 400 kb, from 650 kb to the right telomere) with high similarity to the Wine/European genome (yellow line). Likewise, SK1 has a large segment (650–750 kb) with higher similarity to the Sake lineage (light green line). This type of analysis has revealed the mosaic genome structure of many S. cerevisiae isolates (Liti et al., 2009). Image credit: Anders Bergström and Gianni Liti.DOI:http://dx.doi.org/10.7554/eLife.05835.005
Mentions: Population genomics has provided a powerful means by which to illuminate the evolutionary history of budding yeast. In initial genome sequencing studies, half of the S. cerevisiae strains sequenced fell into a number of distinct lineages (Figure 3A). Genetic variants within these lineages are mostly unique to a subpopulation and absent in others and evenly distributed across the genome (Liti et al., 2009). Variation in phenotype tends to follow population structure (Warringer et al., 2011). Some of these lineages are characteristic of distinct fermentation processes and might represent examples of domesticated breeds (Fay and Benavides, 2005; Schacherer et al., 2009). These strains do not strictly follow geographic boundaries, for example, wine strains from Europe, Australia, Chile and New Zealand share recent ancestry and reflect human migration history (Legras et al., 2007; Liti et al., 2009; Goddard et al., 2010; Dunn et al., 2012).10.7554/eLife.05835.005Figure 3.S. cerevisiae genome relationships and population structure.

Bottom Line: However, it wasn't until a decade ago that the scientific community started to realise how little was known about this yeast's ecology and natural history, and how this information was vitally important for interpreting its biology.Recent large-scale population genomics studies coupled with intensive field surveys have revealed a previously unappreciated wild lifestyle of S. cerevisiae outside the restrictions of human environments and laboratories.The recent discovery that Chinese isolates harbour almost twice as much genetic variation as isolates from the rest of the world combined suggests that Asia is the likely origin of the modern budding yeast.

View Article: PubMed Central - PubMed

Affiliation: Institute for Research on Cancer and Ageing of Nice, CNRS UMR 7284, INSERM U1081, University of Nice Sophia Antipolis, Nice, France.

ABSTRACT
The budding yeast Saccharomyces cerevisiae has been used in laboratory experiments for over a century and has been instrumental in understanding virtually every aspect of molecular biology and genetics. However, it wasn't until a decade ago that the scientific community started to realise how little was known about this yeast's ecology and natural history, and how this information was vitally important for interpreting its biology. Recent large-scale population genomics studies coupled with intensive field surveys have revealed a previously unappreciated wild lifestyle of S. cerevisiae outside the restrictions of human environments and laboratories. The recent discovery that Chinese isolates harbour almost twice as much genetic variation as isolates from the rest of the world combined suggests that Asia is the likely origin of the modern budding yeast.

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