Evolutionary and Functional Features of Copy Number Variation in the Cattle Genome

Evolutionary and Functional Features of Copy Number Variation in the Cattle Genome

Genomic structural variations are an important source of genetic diversity. Copy number variations (CNVs), gains and losses of large regions of genomic sequence between individuals of a species, have been associated with a wide variety of phenotypic traits. However, in cattle, as well as many other...

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Main Authors: Keel, Brittney N., Lindholm-Perry, Amanda K., Snelling, Warren M.
Format: Online
Language:English
Published: Frontiers Media S.A. 2016
Online Access:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5118444/
id pubmed-5118444
recordtype oai_dc
spelling pubmed-51184442016-12-05 Evolutionary and Functional Features of Copy Number Variation in the Cattle Genome Keel, Brittney N. Lindholm-Perry, Amanda K. Snelling, Warren M. Genetics Genomic structural variations are an important source of genetic diversity. Copy number variations (CNVs), gains and losses of large regions of genomic sequence between individuals of a species, have been associated with a wide variety of phenotypic traits. However, in cattle, as well as many other species, relatively little is understood about CNV, including frequency of CNVs in the genome, sizes, and locations, chromosomal properties, and evolutionary processes acting to shape CNV. In this work, we focused on copy number variation in the bovine genome, with the aim to detect CNVs in Bos taurus coding sequence and explore potential evolutionary mechanisms shaping these CNV. We identified and characterized CNV regions by utilizing exome sequence from 175 influential sires used in the Germplasm Evaluation project, representing 10 breeds. We examined various evolutionary and functional aspects of these CNVs, including selective constraint on CNV-overlapped genes, centrality of CNV genes in protein-protein interaction networks, and tissue-specific expression of CNV genes. Patterns of CNV in the Bos taurus genome reveal that reduced functional constraint and mutational bias may play a prominent role in shaping this type of structural variation. Frontiers Media S.A. 2016-11-22 /pmc/articles/PMC5118444/ /pubmed/27920798 http://dx.doi.org/10.3389/fgene.2016.00207 Text en Copyright © 2016 Keel, Lindholm-Perry and Snelling. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
repository_type Open Access Journal
institution_category Foreign Institution
institution US National Center for Biotechnology Information
building NCBI PubMed
collection Online Access
language English
format Online
author Keel, Brittney N.
Lindholm-Perry, Amanda K.
Snelling, Warren M.
spellingShingle Keel, Brittney N.
Lindholm-Perry, Amanda K.
Snelling, Warren M.
Evolutionary and Functional Features of Copy Number Variation in the Cattle Genome
author_facet Keel, Brittney N.
Lindholm-Perry, Amanda K.
Snelling, Warren M.
author_sort Keel, Brittney N.
title Evolutionary and Functional Features of Copy Number Variation in the Cattle Genome
title_short Evolutionary and Functional Features of Copy Number Variation in the Cattle Genome
title_full Evolutionary and Functional Features of Copy Number Variation in the Cattle Genome
title_fullStr Evolutionary and Functional Features of Copy Number Variation in the Cattle Genome
title_full_unstemmed Evolutionary and Functional Features of Copy Number Variation in the Cattle Genome
title_sort evolutionary and functional features of copy number variation in the cattle genome
description Genomic structural variations are an important source of genetic diversity. Copy number variations (CNVs), gains and losses of large regions of genomic sequence between individuals of a species, have been associated with a wide variety of phenotypic traits. However, in cattle, as well as many other species, relatively little is understood about CNV, including frequency of CNVs in the genome, sizes, and locations, chromosomal properties, and evolutionary processes acting to shape CNV. In this work, we focused on copy number variation in the bovine genome, with the aim to detect CNVs in Bos taurus coding sequence and explore potential evolutionary mechanisms shaping these CNV. We identified and characterized CNV regions by utilizing exome sequence from 175 influential sires used in the Germplasm Evaluation project, representing 10 breeds. We examined various evolutionary and functional aspects of these CNVs, including selective constraint on CNV-overlapped genes, centrality of CNV genes in protein-protein interaction networks, and tissue-specific expression of CNV genes. Patterns of CNV in the Bos taurus genome reveal that reduced functional constraint and mutational bias may play a prominent role in shaping this type of structural variation.
publisher Frontiers Media S.A.
publishDate 2016
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5118444/
_version_ 1613736025772785664

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