RT Journal
A1 Li, Mingzhou
A1 Chen, Lei
A1 Tian, Shilin
A1 Lin, Yu
A1 Tang, Qianzi
A1 Zhou, Xuming
A1 Li, Diyan
A1 Yeung, Carol K.L.
A1 Che, Tiandong
A1 Jin, Long
A1 Fu, Yuhua
A1 Ma, Jideng
A1 Wang, Xun
A1 Jiang, Anan
A1 Lan, Jing
A1 Pan, Qi
A1 Liu, Yingkai
A1 Luo, Zonggang
A1 Guo, Zongyi
A1 Liu, Haifeng
A1 Zhu, Li
A1 Shuai, Surong
A1 Tang, Guoqing
A1 Zhao, Jiugang
A1 Jiang, Yanzhi
A1 Bai, Lin
A1 Zhang, Shunhua
A1 Mai, Miaomiao
A1 Li, Changchun
A1 Wang, Dawei
A1 Gu, Yiren
A1 Wang, Guosong
A1 Lu, Hongfeng
A1 Li, Yan
A1 Zhu, Haihao
A1 Li, Zongwen
A1 Li, Ming
A1 Gladyshev, Vadim N.
A1 Jiang, Zhi
A1 Zhao, Shuhong
A1 Wang, Jinyong
A1 Li, Ruiqiang
A1 Li, Xuewei
T1 Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies
JF Genome Research 
JO Genome Research 
YR 2017 
FD May 01 
VO 27 
IS 5 
SP 865 
OP 874 
DO 10.1101/gr.207456.116 
UL http://genome.cshlp.org/content/27/5/865.abstract 
AB Uncovering genetic variation through resequencing is limited by the fact that only sequences with similarity to the reference genome are examined. Reference genomes are often incomplete and cannot represent the full range of genetic diversity as a result of geographical divergence and independent demographic events. To more comprehensively characterize genetic variation of pigs (Sus scrofa), we generated de novo assemblies of nine geographically and phenotypically representative pigs from Eurasia. By comparing them to the reference pig assembly, we uncovered a substantial number of novel SNPs and structural variants, as well as 137.02-Mb sequences harboring 1737 protein-coding genes that were absent in the reference assembly, revealing variants left by selection. Our results illustrate the power of whole-genome de novo sequencing relative to resequencing and provide valuable genetic resources that enable effective use of pigs in both agricultural production and biomedical research.