Freel Kelle C, Friedrich Anne, Sarilar Véronique, Devillers Hugo, Neuvéglise Cécile, Schacherer Joseph
Department of Genetics, Genomics and Microbiology, UMR7156, University of Strasbourg - CNRS, Strasbourg, France.
INRA, UMR1319 Micalis, Jouy-en-Josas, France AgroParisTech, UMR1319 Micalis, Jouy-en-Josas, France.
Genome Biol Evol. 2016 Jan 5;8(3):733-41. doi: 10.1093/gbe/evv262.
The gold standard in yeast population genomics has been the model organism Saccharomyces cerevisiae. However, the exploration of yeast species outside the Saccharomyces genus is essential to broaden the understanding of genome evolution. Here, we report the analyses of whole-genome sequences of nineisolates from the recently described yeast species Lachancea quebecensis. The genome of one isolate was assembled and annotated, and the intraspecific variability within L. quebecensis was surveyed by comparing the sequences from the eight other isolates to this reference sequence. Our study revealed that these strains harbor genomes with an average nucleotide diversity of π = 2 × 10(-3) which is slightly lower, although on the same order of magnitude, as that previously determined for S. cerevisiae (π = 4 × 10(-3)). Our results show that even though these isolates were all obtained from a relatively isolated geographic location, the same ecological source, and represent a smaller sample size than is available for S. cerevisiae, the levels of divergence are similar to those observed in this model species. This divergence is essentially linked to the presence of two distinct clusters delineated according to geographic location. However, even with relatively similar ranges of genome divergence, L. quebecensis has an extremely low global phenotypic variance of 0.062 compared with 0.59 previously determined in S. cerevisiae.
酵母群体基因组学的金标准一直是模式生物酿酒酵母。然而，探索酿酒酵母属以外的酵母物种对于拓宽对基因组进化的理解至关重要。在此，我们报告了对最近描述的酵母物种魁北克拉申酵母的九个分离株的全基因组序列分析。组装并注释了一个分离株的基因组，并通过将其他八个分离株的序列与该参考序列进行比较，对魁北克拉申酵母的种内变异性进行了调查。我们的研究表明，这些菌株的基因组平均核苷酸多样性π = 2×10⁻³，虽然与之前确定的酿酒酵母（π = 4×10⁻³）处于同一数量级，但略低。我们的结果表明，尽管这些分离株均来自相对孤立的地理位置、相同的生态来源，且样本量比酿酒酵母的样本量小，但分化水平与在该模式物种中观察到的相似。这种分化基本上与根据地理位置划分的两个不同聚类的存在有关。然而，即使基因组分化范围相对相似，魁北克拉申酵母的全球表型方差极低，为0.062，而之前在酿酒酵母中确定的为0.59。
