A Highly Contiguous Genome Assembly for the Wrentit (Chamaea Fasciata), the Sole Representative of the Babbler Radiation in the Americas

Abstract

The wrentit (Chamaea fasciata) is a chaparral and scrub specialist bird found from coastal Oregon to northern Baja California. We generated a draft reference assembly for the species using PacBio HiFi long read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project (CCGP). Sequenced reads were assembled into 1342 scaffolds totaling 1.19 Gb in length. A contig N50 of 4.5 Mb, scaffold N50 of 73.3 Mb, and BUSCO completeness score of 96.8% indicate that the wrentit genome is a highly contiguous assembly in line with other high quality avian assemblies. An annotation of the assembly identified 16 821 protein-coding genes. We detected a translocation between chromosome 4A of the zebra finch to the Z chromosome of the wrentit. This translocation has previously been identified as a neo-sex chromosome shared across the superfamily Sylvioidea. Finally, we found a negative correlation between transposable element richness and gene density across the genome, but a positive relationship between GC content and gene density. This reference will serve as an essential resource for studies on the biogeography, local adaptation, and conservation genetics of this iconic species of California's chaparral.

Keywords: California conservation genomics project; Paradoxornithidae; chaparral; neo-sex chromosome; transposable elements.