Structural and Functional Annotation
We performed the structural annotation with BRAKER 2.1.2
(https://github.com/Gaius-Augustus/BRAKER) (–etpmode) using data from
both the Cory’s shearwater proteome (Feng et al., 2020), and the RNA-Seq
data generated in this work. Since the inclusion of RNA-Seq data
appeared detrimental, we excluded this piece of information to perform
the final annotation using the soft-masked genome with BRAKER 2.1.2
(–prg=gth –trainFromGth).
We made the functional annotation of the predicted genes using a
similarity-based approach. We determined the protein domains with
InterProScan 5.31-70.0 (Jones et al., 2014), used BLASTP (Altschul,
Gish, Miller, Myers, & Lipman, 1990; Camacho et al., 2009) (-evalue
1e-5; -max_target_seqs 10) against the Swiss-Prot database (Boutet et
al., 2016) and the Cory’s shearwater and the Zebra finch reference
(UP000007754) proteomes. Transcripts were annotated in the same manner.
We also annotated the ncRNAs using cmscan from INFERNAL 1.1.2 (Nawrocki,
Kolbe, & Eddy, 2009) with the covariance models (CMs) from the Rfam
14.1 database, and tRNA genes using tRNAscan-SE 2.0.5 (Chan & Lowe,
2019).