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2017 ; 27
(5
): 865-874
Nephropedia Template TP
gab.com Text
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English Wikipedia
Comprehensive variation discovery and recovery of missing sequence in the pig
genome using multiple de novo assemblies
#MMPMID27646534
Li M
; Chen L
; Tian S
; Lin Y
; Tang Q
; Zhou X
; Li D
; Yeung CKL
; Che T
; Jin L
; Fu Y
; Ma J
; Wang X
; Jiang A
; Lan J
; Pan Q
; Liu Y
; Luo Z
; Guo Z
; Liu H
; Zhu L
; Shuai S
; Tang G
; Zhao J
; Jiang Y
; Bai L
; Zhang S
; Mai M
; Li C
; Wang D
; Gu Y
; Wang G
; Lu H
; Li Y
; Zhu H
; Li Z
; Li M
; Gladyshev VN
; Jiang Z
; Zhao S
; Wang J
; Li R
; Li X
Genome Res
2017[May]; 27
(5
): 865-874
PMID27646534
show ga
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.