De novo genome assembly of the red-legged partridge (Alectoris rufa)

Listed among the most popular small game species of western Europe, the red-legged partridge (Alectoris rufa, Galliformes) is also a species of major zootechnical interest. In this study, we generated a high-quality genome assembly (96× coverage; estimated genome size 1.19 Gb; N50 11,577 Mb; overall genome heterozygosity 0.0023; GC content 41.44%; no runs of homozigosity) – the first complete genome for the genus Alectoris – by utilising novel Linked-Reads 10X Chromium technology. We flagged 94.9% of single copy avian orthologs (7,913 single copy orthologs out of 8,338 proteins) relying on BUSCO (Benchmarking Universal Single-Copy Orthologs) analysis, while genome annotation allowed us to identify 21,589 protein coding genes which were assigned to 16,772 orthologs. A comparative approach based on publicly available and fully annotated avian genomes (i.e. domestic chicken Gallus gallus, Japanese quail Coturnix japonica and zebra finch Taeniopygia guttata), indicated that 201 gene families were unique to Alectoris. Enrichment analyses revealed their involvement in processes such as positive regulation of epithelial cell migration, viral genome integration and maturation. This novel genome will offer the opportunity to improve the poultry husbandry practices for this and related species by bettering our understanding of the physiological processes associated with disease resistance as well as egg and meat production.