Dataset Information

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.

SUBMITTER: Li M

PROVIDER: S-EPMC5411780 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature

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

Li Mingzhou M Chen Lei L Tian Shilin S Lin Yu Y Tang Qianzi Q Zhou Xuming X Li Diyan D Yeung Carol K L CKL Che Tiandong T Jin Long L Fu Yuhua Y Ma Jideng J Wang Xun X Jiang Anan A Lan Jing J Pan Qi Q Liu Yingkai Y Luo Zonggang Z Guo Zongyi Z Liu Haifeng H Zhu Li L Shuai Surong S Tang Guoqing G Zhao Jiugang J Jiang Yanzhi Y Bai Lin L Zhang Shunhua S Mai Miaomiao M Li Changchun C Wang Dawei D Gu Yiren Y Wang Guosong G Lu Hongfeng H Li Yan Y Zhu Haihao H Li Zongwen Z Li Ming M Gladyshev Vadim N VN Jiang Zhi Z Zhao Shuhong S Wang Jinyong J Li Ruiqiang R Li Xuewei X

Genome research 20160919 5

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 (<i>Sus scrofa</i>), we generated de novo assemblies of nine geographically and phenotypically representative pigs from ...[more]

PMID: 27646534

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Project description:BackgroundPrevious studies exploring sequence variation in the model legume, Medicago truncatula, relied on mapping short reads to a single reference. However, read-mapping approaches are inadequate to examine large, diverse gene families or to probe variation in repeat-rich or highly divergent genome regions. De novo sequencing and assembly of M. truncatula genomes enables near-comprehensive discovery of structural variants (SVs), analysis of rapidly evolving gene families, and ultimately, construction of a pan-genome.ResultsGenome-wide synteny based on 15 de novo M. truncatula assemblies effectively detected different types of SVs indicating that as much as 22% of the genome is involved in large structural changes, altogether affecting 28% of gene models. A total of 63 million base pairs (Mbp) of novel sequence was discovered, expanding the reference genome space for Medicago by 16%. Pan-genome analysis revealed that 42% (180 Mbp) of genomic sequences is missing in one or more accession, while examination of de novo annotated genes identified 67% (50,700) of all ortholog groups as dispensable - estimates comparable to recent studies in rice, maize and soybean. Rapidly evolving gene families typically associated with biotic interactions and stress response were found to be enriched in the accession-specific gene pool. The nucleotide-binding site leucine-rich repeat (NBS-LRR) family, in particular, harbors the highest level of nucleotide diversity, large effect single nucleotide change, protein diversity, and presence/absence variation. However, the leucine-rich repeat (LRR) and heat shock gene families are disproportionately affected by large effect single nucleotide changes and even higher levels of copy number variation.ConclusionsAnalysis of multiple M. truncatula genomes illustrates the value of de novo assemblies to discover and describe structural variation, something that is often under-estimated when using read-mapping approaches. Comparisons among the de novo assemblies also indicate that different large gene families differ in the architecture of their structural variation.

Dataset Information

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

Publications

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

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