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Structural variant detection by large-scale sequencing reveals new evolutionary evidence on breed divergence between Chinese and European pigs Open Access

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Author or creator
Zhao, Pengju
Li, Junhui
Kang, Huimin
Wang, Haifei
Fan, Ziyao
Yin, Zongjun
Wang, Jiafu
Zhang, Qin
Wang, Zhiquan
Liu, Jian-Feng
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Subject/Keyword
Impact
Mechanisms
Provide Insight
Gene-Expression
Copy Number Variation
Architecture
DNA
Human Genome
Nucleotide
Paired-End
Type of item
Journal Article (Published)
Language
English
Place
Time
Description
In this study, we performed a genome-wide SV detection among the genomes of thirteen pigs from diverse Chinese and European originated breeds by next genetation sequencing, and constrcuted a single-nucleotide resolution map involving 56,930 putative SVs. We firstly identified a SV hotspot spanning 35 Mb region on the X chromosome specifically in the genomes of Chinese originated individuals. Further scrutinizing this region by large-scale sequencing data of extra 111 individuals, we obtained the confirmatory evidence on our initial finding. Moreover, thirty five SV-related genes within the hotspot region, being of importance for reproduction ability, rendered significant different evolution rates between Chinese and European originated breeds. The SV hotspot identified herein offers a novel evidence for assessing phylogenetic relationships, as well as likely explains the genetic difference of corresponding phenotypes and features, among Chinese and European pig breeds. Furthermore, we employed various SVs to infer genetic structure of individuls surveyed. We found SVs can clearly detect the difference of genetic background among individuals. This clues us that genome-wide SVs can capture majority of geneic variation and be applied into cladistic analyses. Characterizing whole genome SVs demonstrated that SVs are significantly enriched/depleted with various genomic features.
Date created
2016
DOI
doi:10.7939/R3J67995Q
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Attribution 4.0 International
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Zhao, Pengju, Li, Junhui, Kang, Huimin, Wang, Haifei, Fan, Ziyao, Yin, Zongjun, Wang, Jiafu, Zhang, Qin, Wang, Zhiquan, & Liu, Jian-Feng. (2016). Structural variant detection by large-scale sequencing reveals new evolutionary evidence on breed divergence between Chinese and European pigs. Scientific Reports, 6, [15].  http://dx.doi.org/10.1038/srep18501

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File title: Structural Variant Detection by Large-scale Sequencing Reveals New Evolutionary Evidence on Breed Divergence between Chines ..⸩㸾൥湤潢樍㐶㜠〠潢樍㰼⽄⡎假当剅偟卒䕐ㄸ㔰ㄮ楮摤㩁湣桯爠ㄶ㘺ㄶ㘩⽓⽇潔漾㸍敮摯扪ഴ㘸‰扪഼㰯䄠㔲ㄠ〠刯䍯畮琠㄰⽆楲獴‵㈲‰⁒⽌慳琠㔲㌠〠刯乥硴‴㤷‰⁒⽐慲敮琠㐶㘠〠刯呩瑬攨Results
File title: Structural Variant Detection by Large-scale Sequencing Reveals New Evolutionary Evidence on Breed Divergence between Chinese and European Pigs
File author: Pengju Zhao
Page count: 15
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