Ashari Hidayat, Liu Li-Sheng, Dagong Muhammad Ihsan Andi, Cai Zheng-Fei, Xie Guo-Li, Yin Ting-Ting, Zhang Ya-Ping, Han Jian-Lin, Peng Min-Sheng
CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
Graduate School of Chinese Academy of Agriculture Sciences (CAAS), Beijing, China.
Anim Genet. 2025 Feb;56(1):e13497. doi: 10.1111/age.13497.
The feralization of domestic chicken makes the conservation and management of red jungle fowl (Gallus gallus) more complicated and challenging. We collected two Sulawesi feral chickens, located east of the Wallace Line, for whole-genome sequencing and de novo genome assembly. Phylogenetic and f4-statistics analyses indicated that the Sulawesi feralized domestic chickens (G. g. domesticus) received gene flow from G. g. gallus. We integrated ~45× ultra-long Oxford Nanopore Technology reads and ~28× PacBio HiFi reads to generate a de novo genome assembly of a female Sulawesi feral chicken (GGsula) with a contig N50 of 19.88 Mbp. We characterized structural variations in GGsula, and found some were related to nervous system. Our study provides the first genome assembly of feral chickens, which is a unique genomic resource to explore the process of chicken domestication and feralization.
家鸡的野化使得红原鸡（原鸡）的保护和管理变得更加复杂且具有挑战性。我们收集了两只位于华莱士线以东的苏拉威西岛野化家鸡，用于全基因组测序和从头基因组组装。系统发育分析和f4统计分析表明，苏拉威西岛野化家鸡（原鸡指名亚种）从原鸡那里获得了基因流。我们整合了约45倍的超长牛津纳米孔技术读数和约28倍的PacBio HiFi读数，以生成一只雌性苏拉威西岛野化家鸡（GGsula）的从头基因组组装，其重叠群N50为19.88兆碱基对。我们对GGsula中的结构变异进行了表征，发现其中一些与神经系统有关。我们的研究提供了首个野化家鸡的基因组组装，这是探索家鸡驯化和野化过程的独特基因组资源。
