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

TitleDiscovery and population genomics of structural variation in a songbird genus.
Publication TypeJournal Article
Year of Publication2020
AuthorsWeissensteiner, MH, Bunikis, I, Catalán, A, Francoijs, K-J, Knief, U, Heim, W, Peona, V, Pophaly, SD, Sedlazeck, FJ, Suh, A, Warmuth, VM, Wolf, JBW
JournalNat Commun
Date Published2020 Jul 07
KeywordsAnimals, Chromosome Inversion, Gene Deletion, Genetic Variation, Genetics, Population, Genome, Genomic Structural Variation, Genotype, Phylogeny, Polymorphism, Single Nucleotide, Retroelements, Sequence Analysis, DNA, Songbirds

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.

Alternate JournalNat Commun
PubMed ID32636372
PubMed Central IDPMC7341801
Grant ListUM1 HG008898 / HG / NHGRI NIH HHS / United States

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