A highly contiguous genome assembly for the California quail (Callipepla californica)

The California quail (Callipepla californica) is an iconic native bird of scrub and oak woodlands in California and the Baja Peninsula of Mexico. Here, we report a draft reference assembly for the species generated from 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 321 scaffolds totaling 1.08 Gb in length. Assembly metrics indicate a highly contiguous and complete assembly with a contig N50 of 5.5 Mb, scaffold N50 of 19.4 Mb, and BUSCO completeness score of 96.5%. Transposable elements (TEs) occupy 16.5% of the genome, more than previous Odontophoridae quail assemblies but in line with estimates of TE content for recent long-read assemblies of chicken and Peking duck. Together these metrics indicate that the present assembly is more complete than prior reference assemblies generated for Odontophoridae quail. This reference will serve as an essential resource for studies on local adaptation, phylogeography, and conservation genetics in this species of significant biological and recreational interest.

Automated summary

This study presents a draft reference assembly for the California quail, based on PacBio HiFi long read and Omni-C chromatin-proximity sequencing data. The assembly is highly contiguous and complete, with a total length of 1.08 Gb and 321 scaffolds. Transposable elements occupy 16.5% of the genome, indicating a higher content compared to previous quail assemblies. This reference assembly will be valuable for investigating local adaptation, phylogeography, and conservation genetics in the California quail.