A High-Quality Genome Assembly of the North American Song Sparrow, Melospiza melodia

Abstract

The song sparrow, Melospiza melodia, is one of the most widely distributed species of songbirds found in North America. It has been used in a wide range of behavioral and ecological studies. This species’ pronounced morphological and behavioral diversity across populations makes it a favorable candidate in several areas of biomedical research. We have generated a high-quality de novo genome assembly of M. melodia using Illumina short read sequences from genomic and in vitro proximity-ligation libraries. The assembled genome is 978.3 Mb, with a physical coverage of 24.9×, N50 scaffold size of 5.6 Mb and N50 contig size of 31.7 Kb. Our genome assembly is highly complete, with 87.5% full-length genes present out of a set of 4,915 universal single-copy orthologs present in most avian genomes. We annotated our genome assembly and constructed 15,086 gene models, a majority of which have high homology to related birds, Taeniopygia guttata and Junco hyemalis. In total, 83% of the annotated genes are assigned with putative functions. Furthermore, only ∼7% of the genome is found to be repetitive; these regions and other non-coding functional regions are also identified. The high-quality M. melodia genome assembly and annotations we report will serve as a valuable resource for facilitating studies on genome structure and evolution that can contribute to biomedical research and serve as a reference in population genomic and comparative genomic studies of closely related species.

A beginner’s guide to manual curation of transposable elements

“…Platt II et al [ 7 ] published, alongside their manuscript, a set of scripts and recommendations to aid the manual curation process [ 7 ] and these have been adopted by many others (refs [ 8 – 10 ] to name a few). More recently, Storer et al [ 11 ] published an excellent set of protocols and scripts to aid manual curation.…”

Maintenance of local adaptation despite gene flow in a coastal songbird

“…Fortunately, whole‐genome studies of the song sparrow have been recently made possible by the creation of an annotated reference genome for the species (Louha et al. 2020). In addition to better characterizing the genomic landscape of divergence between these subspecies, further assessment of adaptive traits and associating them with their underlying causal genetic variants will allow for a more robust understanding of how divergent selection maintains locally adapted populations despite gene flow.…”

“…As it did for a congeneric, coastally adapted subspecies, the coastal plain swamp sparrow (M. georgiana nigrescens; Deane-Coe et al 2018a,b), comprehensively identifying regions of the genome under divergent selection in the Atlantic song sparrow will require the use of whole-genome sequencing data. Fortunately, wholegenome studies of the song sparrow have been recently made possible by the creation of an annotated reference genome for the species (Louha et al 2020). In addition to better characterizing the genomic landscape of divergence between these subspecies, further assessment of adaptive traits and associating them with their underlying causal genetic variants will allow for a more robust understanding of how divergent selection maintains locally adapted populations despite gene flow.…”

Adaptive divergence in bill morphology and other thermoregulatory traits is facilitated by restricted gene flow in song sparrows on the California Channel Islands

“…The chromosomal-level zebra finch genome provides high quality positional and gene annotation information for aligned loci. Gene annotations are highly homologous between the recently developed scaffold-assembly song sparrow reference genome and zebra finch genome (Louha et al, 2020). The high quality chromosomal-level zebra finch reference genome allows us infer locus position across the avian genome with greater confidence compared to the scaffoldassembly song sparrow reference genome.…”