The genomic architecture of segmental duplications and associated copy number variants in dogs RID E-6420-2011
Structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of segmental duplications and associated copy number variants (CNVs) in the modern domesticated dog, Canis familiaris, which exhibits considera...
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Online Access: | http://hdl.handle.net/11586/56519 https://doi.org/10.1101/gr.084715.108 |
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ftunivbari:oai:ricerca.uniba.it:11586/56519 2024-04-14T08:12:04+00:00 The genomic architecture of segmental duplications and associated copy number variants in dogs RID E-6420-2011 Nicholas TJ Cheng Z Mealey K Eichler EE Akey JM VENTURA, MARIO Nicholas, Tj Cheng, Z Ventura, Mario Mealey, K Eichler, Ee Akey, Jm 2009 http://hdl.handle.net/11586/56519 https://doi.org/10.1101/gr.084715.108 eng eng info:eu-repo/semantics/altIdentifier/wos/WOS:000263847500014 volume:19 issue:3 firstpage:491 lastpage:499 numberofpages:9 journal:GENOME RESEARCH http://hdl.handle.net/11586/56519 doi:10.1101/gr.084715.108 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-61849144443 info:eu-repo/semantics/article 2009 ftunivbari https://doi.org/10.1101/gr.084715.108 2024-03-21T18:11:14Z Structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of segmental duplications and associated copy number variants (CNVs) in the modern domesticated dog, Canis familiaris, which exhibits considerable morphological, physiological, and behavioral variation. Through computational analyses of the publicly available canine reference sequence, we estimate that segmental duplications comprise similar to 4.21% of the canine genome. Segmental duplications overlap 841 genes and are significantly enriched for specific biological functions such as immunity and defense and KRAB box transcription factors. We designed high-density tiling arrays spanning all predicted segmental duplications and performed aCGH in a panel of 17 breeds and a gray wolf. In total, we identified 3583 CNVs, similar to 68% of which were found in two or more samples that map to 678 unique regions. CNVs span 429 genes that are involved in a wide variety of biological processes such as olfaction, immunity, and gene regulation. Our results provide insight into mechanisms of canine genome evolution and generate a valuable resource for future evolutionary and phenotypic studies. Article in Journal/Newspaper gray wolf Università degli Studi di Bari Aldo Moro: CINECA IRIS Genome Research 19 3 491 499 |
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Università degli Studi di Bari Aldo Moro: CINECA IRIS |
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ftunivbari |
language |
English |
description |
Structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of segmental duplications and associated copy number variants (CNVs) in the modern domesticated dog, Canis familiaris, which exhibits considerable morphological, physiological, and behavioral variation. Through computational analyses of the publicly available canine reference sequence, we estimate that segmental duplications comprise similar to 4.21% of the canine genome. Segmental duplications overlap 841 genes and are significantly enriched for specific biological functions such as immunity and defense and KRAB box transcription factors. We designed high-density tiling arrays spanning all predicted segmental duplications and performed aCGH in a panel of 17 breeds and a gray wolf. In total, we identified 3583 CNVs, similar to 68% of which were found in two or more samples that map to 678 unique regions. CNVs span 429 genes that are involved in a wide variety of biological processes such as olfaction, immunity, and gene regulation. Our results provide insight into mechanisms of canine genome evolution and generate a valuable resource for future evolutionary and phenotypic studies. |
author2 |
Nicholas, Tj Cheng, Z Ventura, Mario Mealey, K Eichler, Ee Akey, Jm |
format |
Article in Journal/Newspaper |
author |
Nicholas TJ Cheng Z Mealey K Eichler EE Akey JM VENTURA, MARIO |
spellingShingle |
Nicholas TJ Cheng Z Mealey K Eichler EE Akey JM VENTURA, MARIO The genomic architecture of segmental duplications and associated copy number variants in dogs RID E-6420-2011 |
author_facet |
Nicholas TJ Cheng Z Mealey K Eichler EE Akey JM VENTURA, MARIO |
author_sort |
Nicholas TJ |
title |
The genomic architecture of segmental duplications and associated copy number variants in dogs RID E-6420-2011 |
title_short |
The genomic architecture of segmental duplications and associated copy number variants in dogs RID E-6420-2011 |
title_full |
The genomic architecture of segmental duplications and associated copy number variants in dogs RID E-6420-2011 |
title_fullStr |
The genomic architecture of segmental duplications and associated copy number variants in dogs RID E-6420-2011 |
title_full_unstemmed |
The genomic architecture of segmental duplications and associated copy number variants in dogs RID E-6420-2011 |
title_sort |
genomic architecture of segmental duplications and associated copy number variants in dogs rid e-6420-2011 |
publishDate |
2009 |
url |
http://hdl.handle.net/11586/56519 https://doi.org/10.1101/gr.084715.108 |
genre |
gray wolf |
genre_facet |
gray wolf |
op_relation |
info:eu-repo/semantics/altIdentifier/wos/WOS:000263847500014 volume:19 issue:3 firstpage:491 lastpage:499 numberofpages:9 journal:GENOME RESEARCH http://hdl.handle.net/11586/56519 doi:10.1101/gr.084715.108 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-61849144443 |
op_doi |
https://doi.org/10.1101/gr.084715.108 |
container_title |
Genome Research |
container_volume |
19 |
container_issue |
3 |
container_start_page |
491 |
op_container_end_page |
499 |
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1796309812146864128 |