Genome assembly and structural variations of Guyuan cattle

Guyuan cattle, a transitional breed between northern and central Chinese cattle, are known for their climbing ability and disease resistance. However, the genomic resources of indigenous Chinese cattle breeds, including Guyuan cattle, remain largely unexplored. We first assembled the Guyuan cattle genome, named Guyuan_Btau_1.0, using PacBio HiFi sequencing. Guyuan_Btau_1.0, with a total size of 2.86 Gb, was anchored to 30 chromosomes (29 autosomes plus one X), achieving a contig N50 of 85.27 Mb and a scaffold N50 of 107.67 Mb. Additionally, we sequenced the genomes of 10 Guyuan cattle using Oxford Nanopore sequencing, which detected 65,273 structural variations (SVs) with lengths of 40.37 Mb and 4,849 shared SVs with lengths of 3.15 Mb. Across the shared SVs, we identified, visualized, and validated a 1,290 bp deletion in the second intron of IGF2BP2 gene in the genomes of 10 Guyuan cattle relative to ARS-UCD1.2. Overall, this study enriches the genetic resource database of indigenous Chinese cattle and provides new foundational data for the breeding and genetic improvement of Guyuan cattle.