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

Xuefeng 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.

The 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.

Our 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.