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

By D. Jeffares, Clemency Jolly, M. Hoti, Doug Speed, L. Shaw, C. Rallis, François Balloux, Christophe Dessimoz, J. Bähler, Fritz J. Sedlazeck. Nature Communications, 2017

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Large structural variations (SVs) within genomes are more challenging to identify than smaller genetic variants but may substantially contribute to phenotypic diversity and evolution. We analyse the effects of SVs on gene expression, quantitative traits and intrinsic reproductive isolation in the yeast Schizosaccharomyces pombe. We establish a high-quality curated catalogue of SVs in the genomes of a worldwide library of S. pombe strains, including duplications, deletions, inversions and translocations. We show that copy number variants (CNVs) show a variety of genetic signals consistent with rapid turnover. These transient CNVs produce stoichiometric effects on gene expression both within and outside the duplicated regions. CNVs make substantial contributions to quantitative traits, most notably intracellular amino acid concentrations, growth under stress and sugar utilization in winemaking, whereas rearrangements are strongly associated with reproductive isolation. Collectively, these findings have broad implications for evolution and for our understanding of quantitative traits including complex human diseases. Fission yeastSchizosaccharomyces pombe has diverse traits. Jeffares et al. characterize large copy number variations (CNVs) and rearrangements in S. pombe, and show that CNVs are transient with effects on quantitative traits and gene expression, whereas rearrangements influence intrinsic reproductive isolation.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ce5b2371030d51ebbcc89a307d97347a854ccd86

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Citations in the corpus

Piercing the dark matter: bioinformatics of long-range sequencing and mapping (2018, background): “One strategy is to use a consensus approach to improve sensitivity (for example, MetaSV 82 ) or limit the false discovery rate (for example, SURVIVOR 64 ).”
Major impacts of widespread structural variation on gene expression and crop improvement in tomato (2020, positive): “7, minimum distance of 1kbp, types must match, and a minimum length of 10bp) (Jeffares et al., 2017).”
Accurate detection of complex structural variations using single molecule sequencing (2017, positive): “Short-read approaches, however, have been reported as lacking sensitivity, with only 10% 17 to 70% 6,8 of SVs detected, very high (up to 89”
Detection of mosaic and population-level structural variants with Sniffles2 (2024, positive): “The genomic locus including the dosage-sensitive gene MECP2 at Xq28 is particularly susceptible to such genomic instability due to nearby inverted and direct orientation low-copy repeats (LCRs) 33–35 .”
Structural variant calling: the long and the short of it (2019, methodology): “MetaSV [64], Parliament2 [65], and SUR-VIVOR [10] have been reported to yield higher recall than a single caller, at the cost of moderately reduced precision.”
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome (2019, methodology): “An integrated callset was produced from the pbsv, Sniffles and paftools/ Canu callsets using SURVIVOR 53 and custom scripts.”