RT Journal
A1 Zhou, Yang
A1 Yang, Lv
A1 Han, Xiaotao
A1 Han, Jiazheng
A1 Hu, Yan
A1 Li, Fan
A1 Xia, Han
A1 Peng, Lingwei
A1 Boschiero, Clarissa
A1 Rosen, Benjamin D.
A1 Bickhart, Derek M.
A1 Zhang, Shujun
A1 Guo, Aizhen
A1 Van Tassell, Curtis P.
A1 Smith, Timothy P.L.
A1 Yang, Liguo
A1 Liu, George E.
T1 Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history
JF Genome Research 
JO Genome Research 
YR 2022 
FD August 01 
VO 32 
IS 8 
SP 1585 
OP 1601 
DO 10.1101/gr.276550.122 
UL http://genome.cshlp.org/content/32/8/1585.abstract 
AB A cattle pangenome representation was created based on the genome sequences of 898 cattle representing 57 breeds. The pangenome identified 83 Mb of sequence not found in the cattle reference genome, representing 3.1% novel sequence compared with the 2.71-Gb reference. A catalog of structural variants developed from this cattle population identified 3.3 million deletions, 0.12 million inversions, and 0.18 million duplications. Estimates of breed ancestry and hybridization between cattle breeds using insertion/deletions as markers were similar to those produced by single nucleotide polymorphism–based analysis. Hundreds of deletions were observed to have stratification based on subspecies and breed. For example, an insertion of a Bov-tA1 repeat element was identified in the first intron of the APPL2 gene and correlated with cattle breed geographic distribution. This insertion falls within a segment overlapping predicted enhancer and promoter regions of the gene, and could affect important traits such as immune response, olfactory functions, cell proliferation, and glucose metabolism in muscle. The results indicate that pangenomes are a valuable resource for studying diversity and evolutionary history, and help to delineate how domestication, trait-based breeding, and adaptive introgression have shaped the cattle genome.