Project Description

Structural rearrangements (inversions, translocations, transpositions, and large insertions, deletions and duplications) hold a key role in promoting and maintaining genetic variation with broad implications in genome instability, speciation, functional innovation and disease susceptibility. However, our understanding of their evolutionary dynamics remains limited due to insufficient resolution and accuracy in characterizing complex events with short-read sequencing. The incomplete reference genome assemblies of many organisms further exacerbate this problem, especially in repetitive and highly variable regions such as subtelomeres and chromosome-ends.

The applications of long-read sequencing technology in several recent studies have proved to be quite successful in detecting and resolving structural rearrangements, even for complex genomic regions (Chaisson et al. Nature 2014; Zapata et al. PNAS 2016; Dong et al. PNAS 2016). Here we take this to the next level, by applying long-read sequencing technology to the population level by sequencing 12 representative strains from the partially domesticated yeast Saccharomyces cerevisiae and its closest wild relative Saccharomyces paradoxus. This allowed us to systematically discover structural rearrangements based on complete genome assemblies. Furthermore, for the first time, we explicitly partitioned nuclear chromosomes into cores, subtelomeres and chromosome-ends, which allows us to assess their respective structural dynamics accordingly. In particular, instead of relying on the current subtelomere definition that treats all chromosomes indiscriminately (e.g. 20~30 kb from chromosome-ends in yeasts), we proposed a chromosome-specific subtelomere definition based on synteny conservation. Crucially, this effectively captured the dynamic nature of subtelomeres. Our high-resolution analysis of structural rearrangements across different chromosome partitions within a well-defined phylogenetic framework uncovered striking contrasts in genome dynamics between domesticated and wild yeasts – revealing the influence of human activities on structural genome evolution.

Impact Statement

The striking contrasts of structural genome dynamics between domesticated and wild yeasts reveal the influence of human activities on genome evolution.

Keywords

yeast, structural rearrangement, subtelomere, evolution, genome

Research Organisms

Saccharomyces cerevisiae and Saccharomyces paradoxus