Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies
- Mingzhou Li1,9,
- Lei Chen2,9,
- Shilin Tian1,3,9,
- Yu Lin3,9,
- Qianzi Tang1,9,
- Xuming Zhou4,9,
- Diyan Li1,
- Carol K.L. Yeung3,
- Tiandong Che1,
- Long Jin1,
- Yuhua Fu1,5,
- 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 Wang1,7,
- Hongfeng Lu3,
- Yan Li3,
- Haihao Zhu3,
- Zongwen Li3,
- Ming Li8,
- Vadim N. Gladyshev4,
- Zhi Jiang3,
- Shuhong Zhao5,
- Jinyong Wang2,
- Ruiqiang Li3 and
- Xuewei Li1
- 1Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China;
- 2Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Sciences, Chongqing 402460, China;
- 3Novogene Bioinformatics Institute, Beijing 100089, China;
- 4Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA;
- 5College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
- 6Sichuan Animal Science Academy, Chengdu 610066, China;
- 7Department of Animal Science, Texas A&M University, College Station, Texas 77843, USA;
- 8Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Corresponding authors: mingzhou.li{at}sicau.edu.cn, kingyou{at}vip.sina.com, lirq{at}novogene.cn, xuewei.li{at}sicau.edu.cn
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↵9 These authors contributed equally to this work.
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.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.207456.116.
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Freely available online through the Genome Research Open Access option.
- Received March 23, 2016.
- Accepted September 16, 2016.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
