Data from: The genome of blue-capped cordon-bleu uncovers hidden diversity of LTR retrotransposons in zebra finch

Avian genomes have perplexed researchers by being conservative in both
size and rearrangements, while simultaneously holding the blueprints for a
massive species radiation during the last 65 My. Transposable elements
(TEs) in bird genomes are relatively scarce but have been implicated as
important hotspots for chromosomal inversions. In zebra finch (Taeniopygia
guttata), long terminal repeat (LTR) retrotransposons have proliferated
and are positively associated with chromosomal breakpoint regions. Here,
we present the genome, karyotype and transposons of blue-capped
cordon-bleu (Uraeginthus cyanocephalus), an African songbird that diverged
from zebra finch at the root of estrildid finches 10 Mya. This constitutes
the third linked-read sequenced genome assembly and fourth in-depth
curated TE library of any bird. Exploration of TE diversity on this brief
evolutionary timescale constitutes a considerable increase in resolution
for avian TE biology and allowed us to uncover 4.5 Mb more LTR
retrotransposons in the zebra finch genome. In blue-capped cordon-bleu, we
likewise observed a recent LTR accumulation indicating that this is a
shared feature of Estrildidae. Curiously, we discovered 25 new endogenous
retrovirus-like LTR retrotransposon families of which at least 21 are
present in zebra finch but were previously undiscovered. This highlights
the importance of studying close relatives of model organisms.