Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

Daniel C. Jeffares, Clemency Jolly, Mimoza Hoti, Doug Speed, Liam Shaw, Charalampos Rallis, Francois Balloux, Christophe Dessimoz, Jürg Bähler, Fritz J. Sedlazeck
  • Nature Communications, January 2017, Nature Publishing Group
  • DOI: 10.1038/ncomms14061

What is it about?

In this manuscript we describe the discovery and analysis of structural variants (SVs) in a comprehensive worldwide sample of fission yeast strains. We proceeded by identifying a high-quality catalogue of SVs and then describing their effects on multiple quantitative traits, gene expression and intrinsic reproductive isolation. In particular, three insights with broad implications stand out: First, we observe that different types of SVs have dramatically different biological consequences: while duplications and deletions are shown to play a key role in explaining quantitative traits, they have no detectable impact on reproductive isolation. Conversely, translocations and inversions are shown to have significant effects on intrinsic reproductive isolation, but much weaker effects on quantitative traits. Second, we demonstrate that SVs are responsible for 19% of trait variance on average, and contribute close to 100% of the heritable variation in three winemaking traits, which may be under recent strong selection. We show that when heritability is estimated without SVs data, much of their impact will be wrongly ascribed to SNPs. Third, we show that duplications are often transient: they can vary even within near-clonal populations, and these duplications produce un-buffered stoichiometric changes in gene expression. This raises the tantalising prospect that such transient duplications might provide a mechanism for rapid adaptation to environmental changes. By conducting GWAS using SVs, we identify a clear example of this phenomenon: we locate a transient duplication that is associated with resistance to the Brefeldin A antibiotic.

Why is it important?

Our study reaffirms our previous finding that S. pombe is a powerful and relevant model for understanding the complexities of heritable variation (Nature Genetics 47:235–241, 2015). The analysis will have particular appeal to the fission and budding yeast research communities, particularly those describing population genetics, evolution and quantative variation. More broadly, this work extends the current understanding of the effects of structural variation within genomes. By quantifying their effects on a large number of quantitative traits, and showing how the same set of variants affect on reproductive isolation we illustrate the variety and strengths of their effects. Our results have clear similarities and relevance to the population genetics and the effects of structural variation in the human genome (eg: the 1000 genomes project analysis of SVs, Nature 526:75–81, 2015), and less detailed studies of other mammalian and plant genomes. Our analysis has consequences for readers interested in heritable variation, GWAS analyses (which typically ignore SVs), and evolutionary biology (reproductive isolation, trait variation, and adaptation). The bioinformatics community will find use in the novel “SURVIVOR” open source software for consensus SVs calling, introduced as part of this paper and available at https://github.com/fritzsedlazeck/SURVIVOR

Perspectives

Dr Christophe Dessimoz
Universite de Lausanne

We wrote a blog post on the story behind the paper here: http://lab.dessimoz.org/blog/2017/02/08/sex-alcohol-and-structural-variants-in-fission-yeast

Read Publication

http://dx.doi.org/10.1038/ncomms14061

The following have contributed to this page: Fritz Sedlazeck, Dr Daniel C Jeffares, Dr Christophe Dessimoz, and Professor Jurg Bahler