We produced a high-quality de novo genome assembly of the red-legged partridge A. rufa, the first reference genome of its genus, by utilising novel 10× Chromium technology. The estimated genome size was 1.19 Gb with an overall genome heterozygosity of 0.0022; no runs of homozygosity were observed. In total, 21,589 protein coding genes were identified and assigned to 16,772 orthologs. Of these, 201 emerged as unique to Alectoris and were enriched for positive regulation of epithelial cell migration, viral genome integration and maturation. Using PSMC analysis, we inferred a major demographic decline commencing ~140,000 years ago, consistent with forest expansion and reduction of open habitats during the Eemian interglacial. Present-day populations exhibit the historically lowest genetic diversity. Besides implications for management and conservation, this genome also promises key insights into the physiology of these birds with a view to improving poultry husbandry practices.

我们利用新的 10× Chromium 技术制作了红腿鹧鸪A. rufa的高质量从头基因组组装，这是其属的第一个参考基因组。估计的基因组大小为 1.19 Gb，总基因组杂合度为 0.0022；没有观察到纯合子的运行。总共鉴定出 21,589 个蛋白质编码基因并分配给 16,772 个直系同源物。其中，201 种是Alectoris独有的，富含对上皮细胞迁移、病毒基因组的正调控整合和成熟。使用 PSMC 分析，我们推断大约 140,000 年前开始的主要人口下降，这与 Eemian 间冰期期间森林扩张和开放栖息地减少一致。当今的种群表现出历史上最低的遗传多样性。除了对管理和保护的影响外，该基因组还承诺对这些鸟类的生理学有重要见解，以改善家禽饲养实践。