Rapid genome functional annotation pipeline anchored to the House sparrow (Passer domesticus, Linnaeus 1758) genome reannotation

Abstract

House sparrow (Passer domesticus) is an important avian model for both laboratory and field-based studies of evolutionary genetics, development, neurobiology, physiology, behavior, and ecology. The current annotation of theP. domesticusgenome is available at Ensembl Rapid Release site, which currently only focuses on gene set building. Here, we provide the first functional reannotation of theP. domesticusgenome based on enrichment with intestinal Illumina RNA-Seq libraries. This revised annotation describes 38592 transcripts, compared to 23574 currently for Ensembl, and 14717 predicted protein-coding genes, with 96.4% complete Passeriformes lineage BUSCOs. A key improvement in this revised annotation is the definition of untranslated region (UTR) sequences, with 82.7% and 93.8% of transcripts containing 5′ and 3′ UTRs, respectively. Our reannotation highlights the benefits to genome annotation improvement when additional specific RNA-Seq data is available for analysis and rapid data throughput (>200 Mb h−1) is used