title: Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies.
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.
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Mingzhou
authors.identifier: 0000-0001-8681-7684
authors.initials: M
authors.lastname: Li
authors.affiliation: Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Sciences, Chongqing 402460, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Chen
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.|Novogene Bioinformatics Institute, Beijing 100089, China.
authors.forename: Shilin
authors.initials: S
authors.lastname: Tian
authors.affiliation: Novogene Bioinformatics Institute, Beijing 100089, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Lin
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Qianzi
authors.initials: Q
authors.lastname: Tang
authors.affiliation: Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Xuming
authors.initials: X
authors.lastname: Zhou
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Diyan
authors.initials: D
authors.lastname: Li
authors.affiliation: Novogene Bioinformatics Institute, Beijing 100089, China.
authors.forename: Carol K L
authors.initials: CKL
authors.lastname: Yeung
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Tiandong
authors.initials: T
authors.lastname: Che
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Long
authors.initials: L
authors.lastname: Jin
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.|College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Yuhua
authors.initials: Y
authors.lastname: Fu
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Jideng
authors.initials: J
authors.lastname: Ma
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Xun
authors.initials: X
authors.lastname: Wang
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Anan
authors.initials: A
authors.lastname: Jiang
authors.affiliation: Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Sciences, Chongqing 402460, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Lan
authors.affiliation: Novogene Bioinformatics Institute, Beijing 100089, China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Pan
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Yingkai
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Sciences, Chongqing 402460, China.
authors.forename: Zonggang
authors.initials: Z
authors.lastname: Luo
authors.affiliation: Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Sciences, Chongqing 402460, China.
authors.forename: Zongyi
authors.initials: Z
authors.lastname: Guo
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Haifeng
authors.initials: H
authors.lastname: Liu
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Li
authors.initials: L
authors.lastname: Zhu
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Surong
authors.initials: S
authors.lastname: Shuai
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Guoqing
authors.initials: G
authors.lastname: Tang
authors.affiliation: Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Sciences, Chongqing 402460, China.
authors.forename: Jiugang
authors.initials: J
authors.lastname: Zhao
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Yanzhi
authors.initials: Y
authors.lastname: Jiang
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Lin
authors.initials: L
authors.lastname: Bai
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Shunhua
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Miaomiao
authors.initials: M
authors.lastname: Mai
authors.affiliation: College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Changchun
authors.initials: C
authors.lastname: Li
authors.affiliation: Novogene Bioinformatics Institute, Beijing 100089, China.
authors.forename: Dawei
authors.initials: D
authors.lastname: Wang
authors.affiliation: Sichuan Animal Science Academy, Chengdu 610066, China.
authors.forename: Yiren
authors.initials: Y
authors.lastname: Gu
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.|Department of Animal Science, Texas A&M University, College Station, Texas 77843, USA.
authors.forename: Guosong
authors.initials: G
authors.lastname: Wang
authors.affiliation: Novogene Bioinformatics Institute, Beijing 100089, China.
authors.forename: Hongfeng
authors.initials: H
authors.lastname: Lu
authors.affiliation: Novogene Bioinformatics Institute, Beijing 100089, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Li
authors.affiliation: Novogene Bioinformatics Institute, Beijing 100089, China.
authors.forename: Haihao
authors.initials: H
authors.lastname: Zhu
authors.affiliation: Novogene Bioinformatics Institute, Beijing 100089, China.
authors.forename: Zongwen
authors.initials: Z
authors.lastname: Li
authors.affiliation: Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Ming
authors.initials: M
authors.lastname: Li
authors.affiliation: Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Vadim N
authors.initials: VN
authors.lastname: Gladyshev
authors.affiliation: Novogene Bioinformatics Institute, Beijing 100089, China.
authors.forename: Zhi
authors.initials: Z
authors.lastname: Jiang
authors.affiliation: College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Shuhong
authors.initials: S
authors.lastname: Zhao
authors.affiliation: Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Sciences, Chongqing 402460, China.
authors.forename: Jinyong
authors.initials: J
authors.lastname: Wang
authors.affiliation: Novogene Bioinformatics Institute, Beijing 100089, China.
authors.forename: Ruiqiang
authors.initials: R
authors.lastname: Li
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Xuewei
authors.initials: X
authors.lastname: Li
mesh_terms: D000818:Animals; D020451:Contig Mapping / Q000379:methods* / Q000592:standards; D016678:Genome; D023281:Genomics / Q000379:methods* / Q000592:standards; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000592:standards; D013552:Swine / Q000235:genetics*