A highly contiguous genome assembly for the wrentit (Chamaea fasciata), the sole representative of the babbler radiation in the Americas

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. Sequenced reads were assembled into 1342 scaffolds totaling 1.19 gigabase in length. A contig N50 of 4.5 Mb, scaffold N50 of 73.3 Mb, and Benchmarking Universal Single-Copy Orthologs 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 guanine-cytosine 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.