A new high-quality genome assembly and annotation for the threatened Florida Scrub-Jay (Aphelocoma coerulescens)

• Published in: G3 : genes - genomes - genetics 2024-09, Vol.14 (12)
• Main Authors: Romero, Faye G, Beaudry, Felix E G, Hovmand Warner, Eyvind, Nguyen, Tram N, Fitzpatrick, John W, Chen, Nancy
• Format: Article
• Language: English
• Subjects: Genome Report
• ISSN: 2160-1836; 2160-1836
• DOI: 10.1093/g3journal/jkae232

Abstract The Florida Scrub-Jay (Aphelocoma coerulescens), a federally Threatened, cooperatively breeding bird, is an emerging model system in evolutionary biology and ecology. Extensive individual-based monitoring and genetic sampling for decades has yielded a wealth of data, allowing for the detailed study of social behavior, demography, and population genetics of this natural population. Here, we report a linkage map and a chromosome-level genome assembly and annotation for a female Florida Scrub-Jay made with long-read sequencing technology, chromatin conformation data, and the linkage map. We constructed a linkage map comprising 4,468 SNPs that had 34 linkage groups and a total sex-averaged autosomal genetic map length of 2446.78 cM. The new genome assembly is 1.33 Gb in length, consisting of 33 complete or near-complete autosomes and the sex chromosomes (ZW). This highly contiguous assembly has an NG50 of 68 Mb and a Benchmarking Universal Single-Copy Orthologs completeness score of 97.1% with respect to the Aves database. The annotated gene set has a Benchmarking Universal Single-Copy Orthologs transcriptome completeness score of 95.5% and 17,964 identified protein-coding genes, 92.5% of which have associated functional annotations. This new, high-quality genome assembly and linkage map of the Florida Scrub-Jay provides valuable tools for future research into the evolutionary dynamics of small, natural populations of conservation concern. Romero et al. present a new high-quality genome assembly and annotation for the Florida Scrub-Jay (Aphelocoma coerulescens), a Federally Threatened bird species. In comparison to other genome assemblies of this species, the authors’ assembly is the first one generated using long-read sequencing technology and from a female individual. They also constructed the first linkage map for this species. The authors’ genome assembly is highly contiguous and is of similar quality to other bird genome assemblies.