Similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencing
Abstract Background Whole genome re-sequencing data from dogs and wolves are now commonly used to study how natural and artificial selection have shaped the patterns of genetic diversity. Single nucleotide polymorphisms, microsatellites and variants in mitochondrial DNA have been interrogated for li...
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doaj-02734fe3325045ee863c35aca91a87462020-11-24T22:01:47ZengBMCBMC Genomics1471-21642017-12-0118111510.1186/s12864-017-4318-xSimilar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencingAitor Serres-Armero0Inna S. Povolotskaya1Javier Quilez2Oscar Ramirez3Gabriel Santpere4Lukas F. K. Kuderna5Jessica Hernandez-Rodriguez6Marcos Fernandez-Callejo7Daniel Gomez-Sanchez8Adam H. Freedman9Zhenxin Fan10John Novembre11Arcadi Navarro12Adam Boyko13Robert Wayne14Carles Vilà15Belen Lorente-Galdos16Tomas Marques-Bonet17IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la SalutIBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la SalutIBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la SalutIBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la SalutIBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la SalutIBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la SalutIBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la SalutCNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST)IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la SalutUCLA, Department of Ecology and Evolutionary BiologyKey Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan UniversityUCLA, Department of Ecology and Evolutionary BiologyIBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la SalutCornell University, Department of Biological Statistics and Computational BiologyUCLA, Department of Ecology and Evolutionary BiologyEstación Biológica de Doñana EBD-CSIC, Department of Integrative EcologyIBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la SalutIBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la SalutAbstract Background Whole genome re-sequencing data from dogs and wolves are now commonly used to study how natural and artificial selection have shaped the patterns of genetic diversity. Single nucleotide polymorphisms, microsatellites and variants in mitochondrial DNA have been interrogated for links to specific phenotypes or signals of domestication. However, copy number variation (CNV), despite its increasingly recognized importance as a contributor to phenotypic diversity, has not been extensively explored in canids. Results Here, we develop a new accurate probabilistic framework to create fine-scale genomic maps of segmental duplications (SDs), compare patterns of CNV across groups and investigate their role in the evolution of the domestic dog by using information from 34 canine genomes. Our analyses show that duplicated regions are enriched in genes and hence likely possess functional importance. We identify 86 loci with large CNV differences between dogs and wolves, enriched in genes responsible for sensory perception, immune response, metabolic processes, etc. In striking contrast to the observed loss of nucleotide diversity in domestic dogs following the population bottlenecks that occurred during domestication and breed creation, we find a similar proportion of CNV loci in dogs and wolves, suggesting that other dynamics are acting to particularly select for CNVs with potentially functional impacts. Conclusions This work is the first comparison of genome wide CNV patterns in domestic and wild canids using whole-genome sequencing data and our findings contribute to study the impact of novel kinds of genetic changes on the evolution of the domestic dog.http://link.springer.com/article/10.1186/s12864-017-4318-xCopy number variationDog genomicsEvolutionDomestication |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Aitor Serres-Armero Inna S. Povolotskaya Javier Quilez Oscar Ramirez Gabriel Santpere Lukas F. K. Kuderna Jessica Hernandez-Rodriguez Marcos Fernandez-Callejo Daniel Gomez-Sanchez Adam H. Freedman Zhenxin Fan John Novembre Arcadi Navarro Adam Boyko Robert Wayne Carles Vilà Belen Lorente-Galdos Tomas Marques-Bonet |
spellingShingle |
Aitor Serres-Armero Inna S. Povolotskaya Javier Quilez Oscar Ramirez Gabriel Santpere Lukas F. K. Kuderna Jessica Hernandez-Rodriguez Marcos Fernandez-Callejo Daniel Gomez-Sanchez Adam H. Freedman Zhenxin Fan John Novembre Arcadi Navarro Adam Boyko Robert Wayne Carles Vilà Belen Lorente-Galdos Tomas Marques-Bonet Similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencing BMC Genomics Copy number variation Dog genomics Evolution Domestication |
author_facet |
Aitor Serres-Armero Inna S. Povolotskaya Javier Quilez Oscar Ramirez Gabriel Santpere Lukas F. K. Kuderna Jessica Hernandez-Rodriguez Marcos Fernandez-Callejo Daniel Gomez-Sanchez Adam H. Freedman Zhenxin Fan John Novembre Arcadi Navarro Adam Boyko Robert Wayne Carles Vilà Belen Lorente-Galdos Tomas Marques-Bonet |
author_sort |
Aitor Serres-Armero |
title |
Similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencing |
title_short |
Similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencing |
title_full |
Similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencing |
title_fullStr |
Similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencing |
title_full_unstemmed |
Similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencing |
title_sort |
similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencing |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2017-12-01 |
description |
Abstract Background Whole genome re-sequencing data from dogs and wolves are now commonly used to study how natural and artificial selection have shaped the patterns of genetic diversity. Single nucleotide polymorphisms, microsatellites and variants in mitochondrial DNA have been interrogated for links to specific phenotypes or signals of domestication. However, copy number variation (CNV), despite its increasingly recognized importance as a contributor to phenotypic diversity, has not been extensively explored in canids. Results Here, we develop a new accurate probabilistic framework to create fine-scale genomic maps of segmental duplications (SDs), compare patterns of CNV across groups and investigate their role in the evolution of the domestic dog by using information from 34 canine genomes. Our analyses show that duplicated regions are enriched in genes and hence likely possess functional importance. We identify 86 loci with large CNV differences between dogs and wolves, enriched in genes responsible for sensory perception, immune response, metabolic processes, etc. In striking contrast to the observed loss of nucleotide diversity in domestic dogs following the population bottlenecks that occurred during domestication and breed creation, we find a similar proportion of CNV loci in dogs and wolves, suggesting that other dynamics are acting to particularly select for CNVs with potentially functional impacts. Conclusions This work is the first comparison of genome wide CNV patterns in domestic and wild canids using whole-genome sequencing data and our findings contribute to study the impact of novel kinds of genetic changes on the evolution of the domestic dog. |
topic |
Copy number variation Dog genomics Evolution Domestication |
url |
http://link.springer.com/article/10.1186/s12864-017-4318-x |
work_keys_str_mv |
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