Hooded crow genome assembly (PacBio long reads + BioNano optical maps + DoveTail HiC maps)

Structural variation (SV) is an important component of 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 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.