Genome sequencing and assembly of feral chickens in the wild of Sulawesi, Indonesia

文献类型： 外文期刊

第一作者： Ashari, Hidayat

作者： Ashari, Hidayat;Han, Jian-Lin;Ashari, Hidayat;Ashari, Hidayat;Liu, Li-Sheng;Cai, Zheng-Fei;Xie, Guo-Li;Yin, Ting-Ting;Zhang, Ya-Ping;Peng, Min-Sheng;Liu, Li-Sheng;Cai, Zheng-Fei;Xie, Guo-Li;Yin, Ting-Ting;Zhang, Ya-Ping;Peng, Min-Sheng;Liu, Li-Sheng;Cai, Zheng-Fei;Yin, Ting-Ting;Zhang, Ya-Ping;Peng, Min-Sheng;Dagong, Muhammad Ihsan Andi;Cai, Zheng-Fei

作者机构：

关键词： admixture; chicken; feralization; genome; red jungle fowl; structural variations

期刊名称：ANIMAL GENETICS （ 影响因子：2.1； 五年影响因子：2.5 ）

ISSN： 0268-9146

年卷期： 2025 年 56 卷 1 期

页码：

收录情况： SCI

摘要： 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 similar to 45x ultra-long Oxford Nanopore Technology reads and similar to 28x 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.

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