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Genome Res. 2017 May;27(5):865-874. doi: 10.1101/gr.207456.116. Epub 2016 Sep 19.

Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies.

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Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Sciences, Chongqing 402460, China.
Novogene Bioinformatics Institute, Beijing 100089, China.
Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.
College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
Sichuan Animal Science Academy, Chengdu 610066, China.
Department of Animal Science, Texas A&M University, College Station, Texas 77843, USA.
Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.


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.

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