Article

Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae.

Stanford Genome Technology Center, 855 California Avenue, Palo Alto, CA 94304, USA.
Proceedings of the National Academy of Sciences (Impact Factor: 9.81). 02/2005; 102(4):1092-7. DOI: 10.1073/pnas.0409159102
Source: PubMed

ABSTRACT By using the maximum likelihood method, we made a genome-wide comparison of the evolutionary rates in the lineages leading to the laboratory strain (S288c) and a wild strain (YJM789) of Saccharomyces cerevisiae and found that genes in the laboratory strain tend to evolve faster than in the wild strain. The pattern of elevated evolution suggests that relaxation of selection intensity is the dominant underlying reason, which is consistent with recurrent bottlenecks in the S. cerevisiae laboratory strain population. Supporting this conclusion are the following observations: (i) the increases in nonsynonymous evolutionary rate occur for genes in all functional categories; (ii) most of the synonymous evolutionary rate increases in S288c occur in genes with strong codon usage bias; (iii) genes under stronger negative selection have a larger increase in nonsynonymous evolutionary rate; and (iv) more genes with adaptive evolution were detected in the laboratory strain, but they do not account for the majority of the increased evolution. The present discoveries suggest that experimental and possible industrial manipulations of the laboratory strain of yeast could have had a strong effect on the genetic makeup of this model organism. Furthermore, they imply an evolution of laboratory model organisms away from their wild counterparts, questioning the relevancy of the models especially when extensive laboratory cultivation has occurred. In addition, these results shed light on the evolution of livestock and crop species that have been under human domestication for years.

0 Followers
 · 
122 Views
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Studies on beetle/tree fungal symbionts typically characterize the ecological and geographic distributions of the fungal populations. There is limited understanding of the genome-wide evolutionary processes that act within and between species as such fungi adapt to different environments, leading to physiological differences and reproductive isolation. Here we assess genomic evidence for such evolutionary processes by extending our recent work on Grosmannia clavigera, which is vectored by the mountain pine beetle and jeffrey pine beetle. We report the genome sequences of an additional eleven G. clavigera sensu lato strains from the two known sibling species, Grosmannia sp. (Gs) and G. clavigera (Gc). The twelve fungal genomes are structurally similar, showing large-scale synteny within and between species. We identified 103,430 single nucleotide variations (SNVs) that separated the Grosmannia strains into divergent Gs and Gc clades, and further divided each of these clades into two subclades, one of which may represent an additional species. Comparing variable genes between these lineages, we identified truncated genes and potential pseudogenes, as well as seven genes that show evidence of positive selection. As these variable genes are involved in secondary metabolism and in detoxifying or utilizing host-tree defense chemicals (e.g. polyketide synthases, oxidoreductases, monooxygenases), their variants may reflect adaptation to the specific chemistries of the host trees Pinus contorta, P. ponderosa, and P. jeffreyi. This work provides a comprehensive resource for developing informative markers for landscape population genomics of these ecologically and economically important fungi, and an approach that could be extended to other beetle-tree associated fungi.
    Molecular Biology and Evolution 03/2014; DOI:10.1093/molbev/msu102 · 14.31 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The African cultivated rice (Oryza glaberrima) was domesticated in West Africa 3,000 years ago. Although less cultivated than the Asian rice (O. sativa), O. glaberrima landraces often display interesting adaptation to rustic environment (e.g., drought). Here, using RNA-seq technology we were able to compare more than 12,000 transcripts between 9 O. glaberrima, 10 wild O. barthii and one O. meridionalis individuals. With a synonymous nucleotide diversity πs = 0.0006 per site, O. glaberrima appears as the least genetically diverse crop grass ever documented. Using Approximate Bayesian Computation, we estimated that O. glaberrima experienced a severe bottleneck during domestication. This demographic scenario almost fully accounts for the pattern of genetic diversity across O. glaberrima genome as we detected very few outliers regions where positive selection may have further impacted genetic diversity. Moreover, the large excess of derived non-synonymous substitution that we detected suggests that the O. glaberrima population suffered from the “cost of domestication”. In addition, we used this genome-scale dataset to demonstrate that (i) O. barthii genetic diversity is positively correlated with recombination rate and negatively with gene density; (ii) expression level is negatively correlated with evolutionary constraint and (iii) one region on chromosome 5 (position 4-6 Mb) exhibits a clear signature of introgression with a yet unidentified Oryza species. This work represents the first genome-wide survey of the African rice genetic diversity and paves the way for further comparison between the African and the Asian rice, notably regarding the genetics underlying domestication traits.This article is protected by copyright. All rights reserved.
    Molecular Ecology 03/2014; DOI:10.1111/mec.12738 · 5.84 Impact Factor
  • Journal of Biosciences 09/2014; 39(4):605-7. DOI:10.1007/s12038-014-9441-0 · 1.94 Impact Factor

Full-text (2 Sources)

Download
25 Downloads
Available from
May 22, 2014