RT Journal
A1 Li, Ran
A1 Gong, Mian
A1 Zhang, Xinmiao
A1 Wang, Fei
A1 Liu, Zhenyu
A1 Zhang, Lei
A1 Yang, Qimeng
A1 Xu, Yuan
A1 Xu, Mengsi
A1 Zhang, Huanhuan
A1 Zhang, Yunfeng
A1 Dai, Xuelei
A1 Gao, Yuanpeng
A1 Zhang, Zhuangbiao
A1 Fang, Wenwen
A1 Yang, Yuta
A1 Fu, Weiwei
A1 Cao, Chunna
A1 Yang, Peng
A1 Ghanatsaman, Zeinab Amiri
A1 Negari, Niloufar Jafarpour
A1 Nanaei, Hojjat Asadollahpour
A1 Yue, Xiangpeng
A1 Song, Yuxuan
A1 Lan, Xianyong
A1 Deng, Weidong
A1 Wang, Xihong
A1 Pan, Chuanying
A1 Xiang, Ruidong
A1 Ibeagha-Awemu, Eveline M.
A1 Heslop-Harrison, Pat (J.S.)
A1 Rosen, Benjamin D.
A1 Lenstra, Johannes A.
A1 Gan, Shangquan
A1 Jiang, Yu
T1 A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes
JF Genome Research 
JO Genome Research 
YR 2023 
FD March 01 
VO 33 
IS 3 
SP 463 
OP 477 
DO 10.1101/gr.277372.12 
UL http://genome.cshlp.org/content/33/3/463.abstract 
AB Structural variations (SVs) are a major contributor to genetic diversity and phenotypic variations, but their prevalence and functions in domestic animals are largely unexplored. Here we generated high-quality genome assemblies for 15 individuals from genetically diverse sheep breeds using Pacific Biosciences (PacBio) high-fidelity sequencing, discovering 130.3 Mb nonreference sequences, from which 588 genes were annotated. A total of 149,158 biallelic insertions/deletions, 6531 divergent alleles, and 14,707 multiallelic variations with precise breakpoints were discovered. The SV spectrum is characterized by an excess of derived insertions compared to deletions (94,422 vs. 33,571), suggesting recent active LINE expansions in sheep. Nearly half of the SVs display low to moderate linkage disequilibrium with surrounding single-nucleotide polymorphisms (SNPs) and most SVs cannot be tagged by SNP probes from the widely used ovine 50K SNP chip. We identified 865 population-stratified SVs including 122 SVs possibly derived in the domestication process among 690 individuals from sheep breeds worldwide. A novel 168-bp insertion in the 5′ untranslated region (5′ UTR) of HOXB13 is found at high frequency in long-tailed sheep. Further genome-wide association study and gene expression analyses suggest that this mutation is causative for the long-tail trait. In summary, we have developed a panel of high-quality de novo assemblies and present a catalog of structural variations in sheep. Our data capture abundant candidate functional variations that were previously unexplored and provide a fundamental resource for understanding trait biology in sheep.