TY  - JOUR
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
Y1  - 2023/03/27 
JF  - Genome Research 
JO  - Genome Research 
DO  - 10.1101/gr.277372.122 
UR  - http://genome.cshlp.org/content/early/2023/03/27/gr.277372.122.abstract 
N2  - 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. 
ER  -