A near telomere-to-telomere gap-free genome assembly of the Chinese indigenous Guanling cattle

Background High-quality reference genomes are critical for elucidating the genetic architecture of complex traits in livestock. Conventional assemblies often contain gaps in repetitive regions, limiting the resolution of structural variation and regulatory elements. Telomere-to-telomere (T2T) assemblies enabled by PacBio HiFi, Oxford Nanopore ultra-long sequencing, and Hi-C provide gap-free chromosomal scaffolds. Although T2T genomes have been reported for humans and a limited number of cattle breeds, such resources remain unavailable for many indigenous breeds. Guanling cattle, an indigenous breed from southwestern China belonging to the southern Chinese cattle group and carrying mixed taurine and indicine ancestry, are known for high meat yield, protein content, and low fat, lack a complete reference genome, constraining studies of meat quality, adaptation, and conservation. Results By integrating PacBio HiFi, ONT ultra-long, and Hi-C data, we constructed a near T2T haplotype-collapsed genome assembly for Guanling cattle. The ~3.25 Gb assembly was anchored to 31 chromosomes, achieving a contig N50 of 111.67 Mb and leaving gaps only on the Y chromosome. The assembly showed excellent quality, with >99.9% read mapping rates, QV values exceeding 40, and 98.3% BUSCO completeness. Hi-C data revealed conserved three-dimensional chromatin organization, including A/B compartments, TADs, and chromatin loops. Genome annotation identified 56.74% repetitive elements, dominated by LINEs, and 1,157,450 SSRs enriched in A/T mononucleotides. We predicted 22,854 protein-coding genes, of which 99.7% were functionally annotated, along with a comprehensive set of non-coding RNAs. Comparative genomics uncovered a highly conserved bovine genome framework in Guanling cattle, with lineage-specific gene family dynamics and positive selection shaping adaptive divergence. Conclusions This near T2T assembly provides a high-quality genomic foundation for dissecting the genetic basis of superior meat quality, supporting precision breeding, evolutionary studies, and conservation of Guanling cattle. It also enriches indigenous bovine genomic resources and facilitates future pangenome analyses.