A high-quality genome assembly and annotation of the dark-eyed junco Junco hyemalis, a recently diversified songbird

The dark-eyed junco (Junco hyemalis) is one of the most common passerines of North America, and has served as a model organism in studies related to ecophysiology, behavior and evolutionary biology for over a century. It is composed of at least six distinct, geographically structured forms of recent evolutionary origin, presenting remarkable variation in phenotypic traits, migratory behavior and habitat. Here we report a high-quality genome assembly and annotation of the dark-eyed junco generated using a combination of shotgun libraries and proximity ligation ChicagoTM and Dovetail Hi-CTM libraries. The final assembly is ∼1.03 Gb in size, with 98.3% of the sequence located in 30 full or nearly full chromosome scaffolds, and with a N50/L50 of 71,3 Mb/5 scaffolds. We identified 19,026 functional genes combining gene prediction and similarity approaches, of which 15,967 were associated to GO terms. The genome assembly and the set of annotated genes yielded 95.4% and 96.2% completeness scores, respectively, when compared with the BUSCO avian dataset. This new assembly for J. hyemalis provides a valuable resource for genome evolution analysis, and for identifying functional genes involved in adaptive processes and speciation.