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Aug 11, 2025;12 (1): 1399.

De novo genome assembly of Yanbian cattle using PacBio HiFi and Hi-C combined with RNA-seq data.

Wenwen Fang, Yang Cao, Yu Liu, Jian Wu, Lisheng Miao, Cheng Xiao, Xin Li, Aihui Lv, Yumin Zhao, Yang Cao
Author Information
  1. Wenwen Fang: Institute of Animal Husbandry and Veterinary Medicine, Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China), Gongzhuling, 136100, China. ORCID
  2. Yang Cao: Institute of Animal Husbandry and Veterinary Medicine, Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China), Gongzhuling, 136100, China.
  3. Yu Liu: Institute of Animal Husbandry and Veterinary Medicine, Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China), Gongzhuling, 136100, China.
  4. Jian Wu: Institute of Animal Husbandry and Veterinary Medicine, Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China), Gongzhuling, 136100, China.
  5. Lisheng Miao: Institute of Animal Husbandry and Veterinary Medicine, Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China), Gongzhuling, 136100, China.
  6. Cheng Xiao: Institute of Animal Husbandry and Veterinary Medicine, Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China), Gongzhuling, 136100, China.
  7. Xin Li: Institute of Animal Husbandry and Veterinary Medicine, Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China), Gongzhuling, 136100, China.
  8. Aihui Lv: Yanbian Livestock Development Corporation, Yanji, Jilin, 133000, China.
  9. Yumin Zhao: Institute of Animal Husbandry and Veterinary Medicine, Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China), Gongzhuling, 136100, China. zhaoym-02-12@vip.163.com.
  10. Yang Cao: Institute of Animal Husbandry and Veterinary Medicine, Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China), Gongzhuling, 136100, China. caoyang003@163.com.
PMID: 40789862 DOI: 10.1038/s41597-025-05689-z

Abstract

Yanbian cattle are a native cattle breed originating from the Yanbian Korean Autonomous Prefecture in Jilin Province, northeastern China. Developed over centuries through natural and artificial selection under cold climatic conditions, this breed is highly adapted to harsh environments, including low temperatures, rugged terrain, and sparse forage. Here, we constructed a high-quality chromosome-level genome assembly for Yanbian cattle using HiFi, Hi-C and RNA-seq data. The genome sequence was anchored to 30 chromosomes, with a total genome length of 2.8 Gb, a contig N50 of 86.41 Mb and a scaffold N50 of 111.08 Mb. Short-read data showed the average 99.56% mapping ratio to the assembly, validating base-level accuracy. Also, 93% complete BUSCOs verified the integrity of the assembled genome. 51.94% repetitive elements of the genome and 20,421 protein-coding genes were annotated. This Yanbian cattle genome serves as an indispensable resource for bovine genomic studies and local breed conservation, enabling both evolutionary insights and genetic characteristic analyses.

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MeSH Term

Animals
Cattle
Genome
RNA-Seq
China
Genomics
Molecular Sequence Annotation
Journal Article Dataset

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