Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies
- Mingzhou Li1,9,
- Lei Chen2,
- Shilin Tian1,
- Yu Lin3,
- Qianzi Tang1,
- Xuming Zhou4,
- Diyan Li1,
- Carol KL Yeung3,
- Tiandong Che1,
- Long Jin1,
- Yuhua Fu1,
- Jideng Ma1,
- Xun Wang1,
- Anan Jiang1,
- Jing Lan2,
- Qi Pan3,
- Yingkai Liu1,
- Zonggang Luo2,
- Zongyi Guo2,
- Haifeng Liu1,
- Li Zhu1,
- Surong Shuai1,
- Guoqing Tang1,
- Jiugang Zhao2,
- Yanzhi Jiang1,
- Lin Bai1,
- Shunhua Zhang1,
- Miaomiao Mai1,
- Changchun Li5,
- Dawei Wang3,
- Yiren Gu6,
- Guosong Wang1,
- Hongfeng Lu3,
- Yan Li3,
- Haihao Zhu3,
- Zongwen Li3,
- Ming Li7,
- Vadim N. Gladyshev8,
- Zhi Jiang3,
- Shuhong Zhao5,
- Jinyong Wang2,
- Ruiqiang Li3 and
- Xuewei Li1
- 1 Sichuan Agricultural University;
- 2 Chongqing Academy of Animal Sciences;
- 3 Novogene Bioinformatics Institute;
- 4 Harvard Medical School;
- 5 Huazhong Agricultural University;
- 6 Sichuan Animal Science Academy;
- 7 Institute of Zoology, Chinese Academy of Sciences;
- 8 Brigham and Women's Hospital, Harvard Medical School
- ↵* Corresponding author; email: mingzhou.li{at}163.com
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, structural variations, as well as 137.02 Mb sequences harboring 1,737 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.
- Received March 23, 2016.
- Accepted September 16, 2016.
- Published by Cold Spring Harbor Laboratory Press
This manuscript is Open Access.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International license), as described at http://creativecommons.org/licenses/by-nc/4.0/.
