Discovery and population genomics of structural variation in a songbird genus.

Weissensteiner MH, Bunikis I, Catalán A, Francoijs KJ, Knief U, Heim W, Peona V, Pophaly SD, Sedlazeck FJ, Suh A, Warmuth VM, Wolf JBW

Nat Commun 11 (1) 3403 [2020-07-07; online 2020-07-07]

Structural variation (SV) constitutes an important type of genetic mutations providing the raw material for evolution. Here, we uncover the genome-wide spectrum of intra- and interspecific SV segregating in natural populations of seven songbird species in the genus Corvus. Combining short-read (N = 127) and long-read re-sequencing (N = 31), as well as optical mapping (N = 16), we apply both assembly- and read mapping approaches to detect SV and characterize a total of 220,452 insertions, deletions and inversions. We exploit sampling across wide phylogenetic timescales to validate SV genotypes and assess the contribution of SV to evolutionary processes in an avian model of incipient speciation. We reveal an evolutionary young (~530,000 years) cis-acting 2.25-kb LTR retrotransposon insertion reducing expression of the NDP gene with consequences for premating isolation. Our results attest to the wealth and evolutionary significance of SV segregating in natural populations and highlight the need for reliable SV genotyping.

Bioinformatics Compute and Storage [Service]

NGI Uppsala (SNP&SEQ Technology Platform) [Service]

NGI Uppsala (Uppsala Genome Center) [Collaborative]

National Genomics Infrastructure [Collaborative]

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PubMed 32636372

DOI 10.1038/s41467-020-17195-4

Crossref 10.1038/s41467-020-17195-4

pii: 10.1038/s41467-020-17195-4
pmc: PMC7341801
Dryad: 10.5061/dryad.ns1rn8ppj