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

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.

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Publication Details

Journal
Animal Genetics
Published
2024-12-22
DOI
https://doi.org/10.1111/age.13497
Citations
2
Primary Topic
Livestock and Poultry Management
Type
article
Field-Weighted Citation Impact
0.68

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article

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

Min‐Sheng Peng, Lisheng Liu, Jianlin Han, Tingting Yin et al.
2 citations
Animal Genetics
Livestock and Poultry Management
0.68
article

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

Min‐Sheng Peng, Lisheng Liu, Jianlin Han, Tingting Yin, Muhammad Ihsan Andi Dagong, Hidayat Ashari, Zheng‐Fei Cai, Yaping Zhang, Guoli Xie
article en
2 citations

Abstract

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.

Animal GeneticsVol. 56(1)
Kunming Institute of Zoology (CN), Yunnan University (CN), Chinese Academy of Sciences (CN), Chinese Academy of Agricultural Sciences (CN), University of Chinese Academy of Sciences (CN), National Research and Innovation Agency (ID), Hasanuddin University (ID)
National Natural Science Foundation of China, Yunnan Provincial Science and Technology Department, National Key Research and Development Program of China
Life in Land
Openalex Percentile: Top 30%
Livestock and Poultry Management
0.68
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Genome sequencing and assembly of feral chickens in the wild of Sulawesi, Indonesia — Min‐Sheng Peng, Lisheng Liu, et al. · Animal Genetics (2024) | TGRS Research Map | TGRS