Large structural variations (SVs) in the genomes are harder to identify than smaller genetic variants, and so their effects have been studies far less intensively. However, they are increasingly suspected to be major contributors to phenotypic diversity, reproductive isolation, adaptation therefore to evolution.
Using genome sequences from a worldwide sample of 160 natural isolates of the fission yeast Schizosaccharomyces pombe, we created a high-quality, curated catalog of structural variations, including duplications, deletions, inversions and translocations. We described the effects of these variants on gene expression, their contributions to 53 quantitative traits, and their influence on intrinsic reproductive isolation.
We uncovered several interesting facets of structural variant biology. We found that copy number variants (CNVs) frequently segregate within closely related clonal populations and are in weak linkage with single nucleotide polymorphisms (SNPs), indicating rapid turnover. These transient CNVs produce stoichiometric effects on gene expression. SVs in general contribute an average of 19% of trait variance (SNPs contribute 30% on average), with the majority of this effect being due to CNVs. Variation in some traits, including our recently characterized winemaking traits were entirely due to the effects of structural variants, with no measureable contribution from SNPs. Rearrangements (inversions & translocations), in contrast contribute strongly to reproductive isolation, but little to trait variation. Collectively, these findings have broad implications for evolution and for our understanding of quantitative traits including complex human diseases.
A preprint of this research is available on bioRxiv, see: danieljeffares.com/publications/