A near complete genome for goat genetic and genomic research

• DOI: 10.1186/s12711-021-00668-5
• Publication Date: 2021-09-10T18:03:04Z
• Authors: Ran Li; Peng Yang; Xuelei Dai; Hojjat Asadollahp...; Wenwen Fang; Zhirui Yang; Yudong Cai; Zhuqing Zheng; Xihong Wang; Yu Jiang
• Keywords: Male; 2. Zero hunger; Genome; Goats; 0206 medical engineering; Genomics; 02 engineering and technology; QH426-470; SF1-1100; Chromosomes, Mammalian; Polymorphism, Single Nucleotide; Animal culture; Dairying; Genetics; Animals; Research Article

Abstract Background Goat, one of the first domesticated livestock, is a worldwide important species both culturally and economically. The current goat reference genome, known as ARS1, is reported as the first nonhuman genome assembly using 69× PacBio sequencing. However, ARS1 suffers from incomplete X chromosome and highly fragmented Y chromosome scaffolds.

Results Here, we present a very high-quality de novo genome assembly, Saanen_v1, from a male Saanen dairy goat, with the first goat Y chromosome scaffold based on 117× PacBio long-read sequencing and 118× Hi-C data. Saanen_v1 displays a high level of completeness thanks to the presence of centromeric and telomeric repeats at the proximal and distal ends of two-thirds of the autosomes, and a much reduced number of gaps (169 vs. 773). The completeness and accuracy of the Saanen_v1 genome assembly are also evidenced by more assembled sequences on the chromosomes (2.63 Gb for Saanen_v1 vs. 2.58 Gb for ARS1), a slightly increased mapping ratio for transcriptomic data, and more genes anchored to chromosomes. The eight putative large assembly errors (1 to ~ 7 Mb each) found in ARS1 were amended, and for the first time, the substitution rate of this ruminant Y chromosome was estimated. Furthermore, sequence improvement in Saanen_v1, compared with ARS1, enables us to assign the likely correct positions for 4.4% of the single nucleotide polymorphism (SNP) probes in the widely used GoatSNP50 chip.

Conclusions The updated goat genome assembly including both sex chromosomes (X and Y) and the autosomes with high-resolution quality will serve as a valuable resource for goat genetic research and applications.