Evidence map›Paper›PMID 42163097›Full record

ArticleBMC genomics2026

Chromosome-level genome assembly of Xuefeng Black-bone chicken and comparative genomics analysis.

Songchang Guo, Jingzhe Huang, Qiongtao Zi, Peng Li, Lingyun He, Xi He, Haihan Zhang, Donghua Li, Meichun Li, Xiangyong Qu and 1 more

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Article in BMC genomics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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5 · Who and what money

Authors and funding

11 authors.

Songchang GuoCollege of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, 410128, China.
Jingzhe HuangCollege of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, 410128, China.
Qiongtao ZiCollege of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, 410128, China.
Peng LiCollege of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, 410128, China.
Lingyun HeHuaihua Animal Husbandry and Fishery Affairs Center, Huaihua, Hunan, 418000, China.
Xi HeCollege of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, 410128, China.
Haihan ZhangCollege of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, 410128, China.
Donghua LiCollege of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, 450002, China.
Meichun LiHunan Yunfeifeng Agricultural Co. Ltd., Huaihua, Hunan, 418200, China.
Xiangyong QuCollege of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, 410128, China.
Changqing HeCollege of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, 410128, China. 2681633710@qq.com.

Funding

Hunan Agriculture Research System HARS-06National Natural Science Foundation of China 32072711Yuelushan Laboratory Seed Industry Special Project YLS-2025-ZY02025
6 · The paper itself

Abstract

backgroundXuefeng Black-bone chicken is a precious poultry variety for its characteristic traits, high-economic value and medicinal diet value. However, the genomic information for the Xuefeng Black-bone chicken was still lacking, which have hindered the identification of genetic variants underlying its distinctive traits and impeded the implementation of genomic selection strategies in breeding programs. Therefore, we applied PacBio SMRT (Single Molecule Real-Time) sequencing, Illumina sequencing, Hi-C and RNA-seq to establish a high-contiguity reference genome for Xuefeng Black-bone chicken, achieving chromosome-level.

resultsThe de novo assembly yielded a 1.13 Gb genome, exhibiting contiguity metrics of 21.76 Mb (contig N50) and 83.79 Mb (scaffold N50), and comprised 40 pseudochromosomes. Merqury demonstrated a QV (Consensus quality value) score of 43.1876 and 96.7% BUSCO gene representation completeness. The genome of the Xuefeng Black-bone chicken contained about 18.48% repetitive sequences. The genomic annotation identified 20,146 protein-coding genes, of which 15,804 (78.45%) possessed functional characterization, and 1471 ncRNAs (non-coding RNAs) were also predicted. Comparative genomics analysis revealed 5,170,902 SNPs (single nucleotide polymorphisms) and 1127 SVs (structural variations) between Xuefeng Black-bone chicken genome and other chicken varieties genomes. These SVs were linked to 11,391 genes enriched in transcription by RNA polymerase II, heterocycle biosynthetic process, DNA binding, peroxisome and calcium signaling pathway, which mainly involved in the environmental adaption, stress resistance and immune system.

conclusionsOur assembly of the Xuefeng Black-bone chicken genome was high quality and the genome will provide more resources and insights into the unique characteristics study of the chicken, which will enhance our understanding and guide the breeding work better.

Indexed as

ChickensChromosomesGenomeGenomicsAnimalsHigh-Throughput Nucleotide SequencingMolecular Sequence AnnotationPolymorphism, Single NucleotideComparative genomics analysisGenome annotationGenome assemblyXuefeng Black-bone chicken

Identifiers

PMID42163097
PMCPMC13419013

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