TY  - JOUR
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
Y1  - 2017/05/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 865 
EP  - 874 
DO  - 10.1101/gr.207456.116 
VL  - 27 
IS  - 5 
UR  - http://genome.cshlp.org/content/27/5/865.abstract 
N2  - 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. 
ER  -