@article{Li01052017,
author = {Li, Mingzhou and Chen, Lei and Tian, Shilin and Lin, Yu and Tang, Qianzi and Zhou, Xuming and Li, Diyan and Yeung, Carol K.L. and Che, Tiandong and Jin, Long and Fu, Yuhua and Ma, Jideng and Wang, Xun and Jiang, Anan and Lan, Jing and Pan, Qi and Liu, Yingkai and Luo, Zonggang and Guo, Zongyi and Liu, Haifeng and Zhu, Li and Shuai, Surong and Tang, Guoqing and Zhao, Jiugang and Jiang, Yanzhi and Bai, Lin and Zhang, Shunhua and Mai, Miaomiao and Li, Changchun and Wang, Dawei and Gu, Yiren and Wang, Guosong and Lu, Hongfeng and Li, Yan and Zhu, Haihao and Li, Zongwen and Li, Ming and Gladyshev, Vadim N. and Jiang, Zhi and Zhao, Shuhong and Wang, Jinyong and Li, Ruiqiang and Li, Xuewei}, 
title = {Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies},
volume = {27}, 
number = {5}, 
pages = {865-874}, 
year = {2017}, 
doi = {10.1101/gr.207456.116}, 
abstract ={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.}, 
URL = {http://genome.cshlp.org/content/27/5/865.abstract}, 
eprint = {http://genome.cshlp.org/content/27/5/865.full.pdf+html}, 
journal = {Genome Research} 
}