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A global analysis of CNVs in diverse yak populations using whole-genome resequencing

BACKGROUND: Genomic structural variation represents a source for genetic and phenotypic variation, which may be subject to selection during the environmental adaptation and population differentiation. Here, we described a genome-wide analysis of copy number variations (CNVs) in 16 populations of yak...

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Autores principales: Wang, Hui, Chai, Zhixin, Hu, Dan, Ji, Qiumei, Xin, Jinwei, Zhang, Chengfu, Zhong, Jincheng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6339343/
https://www.ncbi.nlm.nih.gov/pubmed/30658572
http://dx.doi.org/10.1186/s12864-019-5451-5
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author Wang, Hui
Chai, Zhixin
Hu, Dan
Ji, Qiumei
Xin, Jinwei
Zhang, Chengfu
Zhong, Jincheng
author_facet Wang, Hui
Chai, Zhixin
Hu, Dan
Ji, Qiumei
Xin, Jinwei
Zhang, Chengfu
Zhong, Jincheng
author_sort Wang, Hui
collection PubMed
description BACKGROUND: Genomic structural variation represents a source for genetic and phenotypic variation, which may be subject to selection during the environmental adaptation and population differentiation. Here, we described a genome-wide analysis of copy number variations (CNVs) in 16 populations of yak based on genome resequencing data and CNV-based cluster analyses of these populations. RESULTS: In total, we identified 51,461 CNV events and defined 3174 copy number variation regions (CNVRs) that covered 163.8 Mb (6.2%) of yak genome with more “loss” events than both “gain” and “both” events, and we confirmed 31 CNVRs in 36 selected yaks using quantitative PCR. Of the total 163.8 Mb CNVR coverage, a 10.8 Mb region of high-confidence CNVRs directly overlapped with the 52.9 Mb of segmental duplications, and we confirmed their uneven distributions across chromosomes. Furthermore, functional annotation indicated that the CNVR-harbored genes have a considerable variety of molecular functions, including immune response, glucose metabolism, and sensory perception. Notably, some of the identified CNVR-harbored genes associated with adaptation to hypoxia (e.g., DCC, MRPS28, GSTCD, MOGAT2, DEXI, CIITA, and SMYD1). Additionally, cluster analysis, based on either individuals or populations, showed that the CNV clustering was divided into two origins, indicating that some yak CNVs are likely to arisen independently in different populations and contribute to population difference. CONCLUSIONS: Collectively, the results of the present study advanced our understanding of CNV as an important type of genomic structural variation in yak, and provide a useful genomic resource to facilitate further research on yak evolution and breeding. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5451-5) contains supplementary material, which is available to authorized users.
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spelling pubmed-63393432019-01-23 A global analysis of CNVs in diverse yak populations using whole-genome resequencing Wang, Hui Chai, Zhixin Hu, Dan Ji, Qiumei Xin, Jinwei Zhang, Chengfu Zhong, Jincheng BMC Genomics Research Article BACKGROUND: Genomic structural variation represents a source for genetic and phenotypic variation, which may be subject to selection during the environmental adaptation and population differentiation. Here, we described a genome-wide analysis of copy number variations (CNVs) in 16 populations of yak based on genome resequencing data and CNV-based cluster analyses of these populations. RESULTS: In total, we identified 51,461 CNV events and defined 3174 copy number variation regions (CNVRs) that covered 163.8 Mb (6.2%) of yak genome with more “loss” events than both “gain” and “both” events, and we confirmed 31 CNVRs in 36 selected yaks using quantitative PCR. Of the total 163.8 Mb CNVR coverage, a 10.8 Mb region of high-confidence CNVRs directly overlapped with the 52.9 Mb of segmental duplications, and we confirmed their uneven distributions across chromosomes. Furthermore, functional annotation indicated that the CNVR-harbored genes have a considerable variety of molecular functions, including immune response, glucose metabolism, and sensory perception. Notably, some of the identified CNVR-harbored genes associated with adaptation to hypoxia (e.g., DCC, MRPS28, GSTCD, MOGAT2, DEXI, CIITA, and SMYD1). Additionally, cluster analysis, based on either individuals or populations, showed that the CNV clustering was divided into two origins, indicating that some yak CNVs are likely to arisen independently in different populations and contribute to population difference. CONCLUSIONS: Collectively, the results of the present study advanced our understanding of CNV as an important type of genomic structural variation in yak, and provide a useful genomic resource to facilitate further research on yak evolution and breeding. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5451-5) contains supplementary material, which is available to authorized users. BioMed Central 2019-01-18 /pmc/articles/PMC6339343/ /pubmed/30658572 http://dx.doi.org/10.1186/s12864-019-5451-5 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Wang, Hui
Chai, Zhixin
Hu, Dan
Ji, Qiumei
Xin, Jinwei
Zhang, Chengfu
Zhong, Jincheng
A global analysis of CNVs in diverse yak populations using whole-genome resequencing
title A global analysis of CNVs in diverse yak populations using whole-genome resequencing
title_full A global analysis of CNVs in diverse yak populations using whole-genome resequencing
title_fullStr A global analysis of CNVs in diverse yak populations using whole-genome resequencing
title_full_unstemmed A global analysis of CNVs in diverse yak populations using whole-genome resequencing
title_short A global analysis of CNVs in diverse yak populations using whole-genome resequencing
title_sort global analysis of cnvs in diverse yak populations using whole-genome resequencing
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6339343/
https://www.ncbi.nlm.nih.gov/pubmed/30658572
http://dx.doi.org/10.1186/s12864-019-5451-5
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