Abstract
Yeasts belonging to the Saccharomyces genus play an important role in human-driven fermentations. The species S. cerevisiae has been widely studied because it is the dominant yeast in most fermentations and it has been widely used as a model eukaryotic organism. Recently, other species of the Saccharomyces genus are gaining interest to solve the new challenges that the fermentation industry are facing. One of these species is S. kudriavzevii, which exhibits interesting physiological properties compared to S. cerevisiae, such as a better adaptation to grow at low temperatures, a higher glycerol synthesis and lower ethanol production. The aim of this study is to understand the molecular basis behind these phenotypic differences of biotechnological interest by using a species-based comparative genomics approach. In this work, we sequenced, assembled and annotated two new genomes of S. kudriavzevii. We used a combination of different statistical methods to identify functional divergence, signatures of positive selection and acceleration of substitution rates at specific amino acid sites of proteins in S. kudriavzevii when compared to S. cerevisiae, and vice versa. We provide a list of candidate genes in which positive selection could be acting during the evolution of both S. cerevisiae and S. kudriavzevii clades. Some of them could be related to certain important differences in metabolism previously reported by other authors such us DAL3 and ARO4, involved in nitrogen assimilation and amino acid biosynthesis. In addition, three of those genes (FBA1, ZIP1, and RQC2) showed accelerated evolutionary rates in Sk branch. Finally, genes of the riboflavin biosynthesis were also among those genes with a significant higher rate of nucleotide substitution and those proteins have amino acid positions contributing to functional divergence.
Highlights
How species have adapted to new environments by the action of natural selection shaping their genomes is a key question in modern biology since Charles Darwin proposed the theory of natural selection to explain the origin of adaptations
As representatives of S. kudriavzevii (Sk), we included four complete genome assemblies from strains of different origins. Those from strains NBRC 1802 and ZP 591 were publicly available from a previous study (Scannell et al, 2011) and the other two, corresponding to strains isolated from oak bark samples taken in different locations of Spain, were sequenced, de novo assembled and annotated for the present study
Saccharomyces kudriavzevii is a species from the Saccharomyces genus isolated from natural environments such as tree barks and decayed leaves (Boynton and Greig, 2014)
Summary
How species have adapted to new environments by the action of natural selection shaping their genomes is a key question in modern biology since Charles Darwin proposed the theory of natural selection to explain the origin of adaptations. Saccharomyces kudriavzevii and S. cerevisiae Comparative Genomics most natural populations contain enough genetic variation, generated by mutation, to respond to any sort of selection, and explained adaptation as the gradual evolution resulting from changes in the frequencies of the genetic variants acted upon by natural selection. As deleterious mutations are removed by purifying selection, most genetic variation, both within-species polymorphisms and between-species divergence, is the result of the action of genetic drift, with a negligible contribution of the rare beneficial mutations fixed by positive selection (Kimura, 1983). According to Michael Lynch (2007), p. 375): “the nonadaptive force of random genetic drift set the stage for future paths of adaptive evolution in novel ways that would not otherwise be possible.”
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
