Genome assembly and transcriptomic analyses reveal important genes for avian migration

Migratory behaviour is a variable characteristic in many free-living birds. The white-crowned sparrow, Zonotrichia leucophrys, is a passerine bird with a wide distribution and variation in migratory behaviour, which has historically acted as a model species in studies on avian ecology, physiology and behaviour. We have generated a high-quality genome of the white-crowned sparrow, along with RNA-seq data from across different tissues and life history stages. By using PacBio and OmniC sequencing data we assembled 31 chromosomes in complete scaffolds along with other, unplaced, scaffolds. We comprehensively compared the gene expression profile across different stages of the breeding cycle in both sexes. Genes important in different tissues were identified, including genes critical for reproductive behaviours. For instance, the gonadal expression difference of gene ZP3 was significantly different in reproductively active individuals, while the CGA gene was identified in hypothalamus, suggesting differences in gonadotropin expression. The genome assembly and the transcriptomic profile offers an important resource for the research community in understanding avian genome biology and development, and provides a genomic basis for understanding avian migration.