Repeat annotation
We generated a de novo repeat library of the genome with
RepeatModeler – 1.0.11 (Smit, Hubley, & Green,) on scaffolds
>100 kbp. This library was combined with all avian and
ancestral consensus repeats from Dfam_Consensus-20181026 (Storer,
Hubley, Rosen, Wheeler, & Smit, 2021), RepBase-20181026 (Jurka et al.,
2005) and the repeat annotation of the Cory’s shearwater
(Calonectris borealis ) (Feng et al., 2020), which represents the
most closely related sequenced genome. Redundancies among libraries were
removed with the script ReannTE_MergeFasta.pl
(https://github.com/4ureliek/ReannTE).
We then ran RepeatMasker 4.0.7 (Smit et al.,) using the combined library
as a reference, with the following parameters: -xsmall -e ncbi -s
-gccalc -no_is -gff.