RT Journal Article
SR Electronic
T1 <em>De Novo</em> Assembly of the Northern Cardinal (<em>Cardinalis cardinalis</em>) Genome Reveals Candidate Regulatory Regions for Sexually Dichromatic Red Plumage Coloration
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.05.12.092080
DO 10.1101/2020.05.12.092080
A1 Simon Yung Wa Sin
A1 Lily Lu
A1 Scott V. Edwards
YR 2020
UL http://biorxiv.org/content/early/2020/05/14/2020.05.12.092080.abstract
AB Northern cardinals (Cardinalis cardinalis) are common, mid-sized passerines widely distributed in North America. As an iconic species with strong sexual dichromatism, it has been the focus of extensive ecological and evolutionary research, yet genomic studies investigating the evolution of genotype–phenotype association of plumage coloration and dichromatism are lacking. Here we present a new, highly contiguous assembly for C. cardinalis. We generated a 1.1 Gb assembly comprised of 4,762 scaffolds, with a scaffold N50 of 3.6 Mb, a contig N50 of 114.4 kb and a longest scaffold of 19.7 Mb. We identified 93.5% complete and single-copy orthologs from an Aves dataset using BUSCO, demonstrating high completeness of the genome assembly. We annotated the genomic region comprising the CYP2J19 gene, which plays a pivotal role in the red coloration in birds. Comparative analyses demonstrated non-exonic regions unique to the CYP2J19 gene in passerines and a long insertion upstream of the gene in C. cardinalis. Transcription factor binding motifs discovered in the unique insertion region in C. cardinalis suggest potential androgen-regulated mechanisms underlying sexual dichromatism. Pairwise Sequential Markovian Coalescent (PSMC) analysis of the genome reveals fluctuations in historic effective population size between 100,000–250,000 in the last 2 millions years, with declines concordant with the beginning of the Pleistocene epoch and Last Glacial Period. This draft genome of C. cardinalis provides an important resource for future studies of ecological, evolutionary, and functional genomics in cardinals and other birds.Competing Interest StatementThe authors have declared no competing interest.