A high-definition view of functional genetic variation from natural yeast genomes..pdf (886.54 kB)
A high-definition view of functional genetic variation from natural yeast genomes
conference contribution
posted on 2015-10-28, 11:12 authored by A. Bergström, J. T. Simpson, F. Salinas, B. Barré, L. Parts, A. Zia, A. N. Nguyen Ba, A. M. Moses, Edward John Louis, V. Mustonen, J. Warringer, R. Durbin, G. LitiThe question of how genetic variation in a population influences phenotypic variation and evolution is of major importance in modern biology. Yet much is still unknown about the relative functional importance of different forms of genome variation and how they are shaped by evolutionary processes. Here we address these questions by population level sequencing of 42 strains from the budding yeast Saccharomyces cerevisiae and its closest relative S. paradoxus. We find that genome content variation, in the form of presence or absence as well as copy number of genetic material, is higher within S. cerevisiae than within S. paradoxus, despite genetic distances as measured in single-nucleotide polymorphisms being vastly smaller within the former species. This genome content variation, as well as loss-of-function variation in the form of premature stop codons and frameshifting indels, is heavily enriched in the subtelomeres, strongly reinforcing the relevance of these regions to functional evolution. Genes affected by these likely functional forms of variation are enriched for functions mediating interaction with the external environment (sugar transport and metabolism, flocculation, metal transport, and metabolism). Our results and analyses provide a comprehensive view of genomic diversity in budding yeast and expose surprising and pronounced differences between the variation within S. cerevisiae and that within S. paradoxus. We also believe that the sequence data and de novo assemblies will constitute a useful resource for further evolutionary and population genomics studies.
History
Citation
Molecular Biology and Evolution, 2014, 31 (4), pp. 872-888Author affiliation
/Organisation/COLLEGE OF MEDICINE, BIOLOGICAL SCIENCES AND PSYCHOLOGY/MBSP Non-Medical Departments/Department of GeneticsSource
United StatesVersion
- VoR (Version of Record)
Published in
Molecular Biology and EvolutionPublisher
Oxford University Press (OUP)eissn
1537-1719Copyright date
2014Available date
2015-10-28Publisher DOI
Publisher version
http://mbe.oxfordjournals.org/content/31/4/872Language
enAdministrator link
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Keywords
functional variationgenome evolutionloss-of-function variantspopulation genomicssubtelomeresyeastArsenitesDNA Copy Number VariationsDrug Resistance, FungalEvolution, MolecularGenes, FungalGenetic LinkageGenetic SpeciationGenome, FungalMolecular Sequence AnnotationMultigene FamilyPhylogenyPolymorphism, Single NucleotideSaccharomyces cerevisiaeSequence Analysis, DNASodium Compounds