Discovery and population genomics of structural variation in a songbird genus

Matthias H. Weissensteiner (), Ignas Bunikis, Ana Catalán, Kees-Jan Francoijs, Ulrich Knief, Wieland Heim, Valentina Peona, Saurabh D. Pophaly, Fritz J. Sedlazeck, Alexander Suh, Vera M. Warmuth and Jochen B. W. Wolf ()
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Matthias H. Weissensteiner: Uppsala University
Ignas Bunikis: Uppsala University, BMC
Ana Catalán: LMU Munich
Kees-Jan Francoijs: BioNanoGenomics
Ulrich Knief: LMU Munich
Wieland Heim: University of Münster
Valentina Peona: Uppsala University
Saurabh D. Pophaly: LMU Munich
Fritz J. Sedlazeck: Human Genome Sequencing Center at Baylor College of Medicine
Alexander Suh: Uppsala University
Vera M. Warmuth: LMU Munich
Jochen B. W. Wolf: Uppsala University

Nature Communications, 2020, vol. 11, issue 1, 1-11

Abstract: Abstract 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.

Date: 2020
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-17195-4

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DOI: 10.1038/s41467-020-17195-4

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