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Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication
BACKGROUND: Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of the dog domestication process, we conducted whole-genome sequence analysis of...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7057629/ https://www.ncbi.nlm.nih.gov/pubmed/32131720 http://dx.doi.org/10.1186/s12864-020-6619-8 |
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author | Amiri Ghanatsaman, Zeinab Wang, Guo-Dong Asadollahpour Nanaei, Hojjat Asadi Fozi, Masood Peng, Min-Sheng Esmailizadeh, Ali Zhang, Ya-Ping |
author_facet | Amiri Ghanatsaman, Zeinab Wang, Guo-Dong Asadollahpour Nanaei, Hojjat Asadi Fozi, Masood Peng, Min-Sheng Esmailizadeh, Ali Zhang, Ya-Ping |
author_sort | Amiri Ghanatsaman, Zeinab |
collection | PubMed |
description | BACKGROUND: Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of the dog domestication process, we conducted whole-genome sequence analysis of three wolves and three dogs from Iran which covers the eastern part of the Fertile Crescent located in Southwest Asia where the independent domestication of most of the plants and animals has been documented and also high haplotype sharing between wolves and dog breeds has been reported. RESULTS: Higher diversity was found within the wolf genome compared with the dog genome. A total number of 12.45 million SNPs were detected in all individuals (10.45 and 7.82 million SNPs were identified for all the studied wolves and dogs, respectively) and a total number of 3.49 million small Indels were detected in all individuals (3.11 and 2.24 million small Indels were identified for all the studied wolves and dogs, respectively). A total of 10,571 copy number variation regions (CNVRs) were detected across the 6 individual genomes, covering 154.65 Mb, or 6.41%, of the reference genome (canFam3.1). Further analysis showed that the distribution of deleterious variants in the dog genome is higher than the wolf genome. Also, genomic annotation results from intron and intergenic regions showed that the proportion of variations in the wolf genome is higher than that in the dog genome, while the proportion of the coding sequences and 3′-UTR in the dog genome is higher than that in the wolf genome. The genes related to the olfactory and immune systems were enriched in the set of the structural variants (SVs) identified in this work. CONCLUSIONS: Our results showed more deleterious mutations and coding sequence variants in the domestic dog genome than those in wolf genome. By providing the first Iranian dog and wolf variome map, our findings contribute to understanding the genetic architecture of the dog domestication. |
format | Online Article Text |
id | pubmed-7057629 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-70576292020-03-10 Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication Amiri Ghanatsaman, Zeinab Wang, Guo-Dong Asadollahpour Nanaei, Hojjat Asadi Fozi, Masood Peng, Min-Sheng Esmailizadeh, Ali Zhang, Ya-Ping BMC Genomics Research Article BACKGROUND: Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of the dog domestication process, we conducted whole-genome sequence analysis of three wolves and three dogs from Iran which covers the eastern part of the Fertile Crescent located in Southwest Asia where the independent domestication of most of the plants and animals has been documented and also high haplotype sharing between wolves and dog breeds has been reported. RESULTS: Higher diversity was found within the wolf genome compared with the dog genome. A total number of 12.45 million SNPs were detected in all individuals (10.45 and 7.82 million SNPs were identified for all the studied wolves and dogs, respectively) and a total number of 3.49 million small Indels were detected in all individuals (3.11 and 2.24 million small Indels were identified for all the studied wolves and dogs, respectively). A total of 10,571 copy number variation regions (CNVRs) were detected across the 6 individual genomes, covering 154.65 Mb, or 6.41%, of the reference genome (canFam3.1). Further analysis showed that the distribution of deleterious variants in the dog genome is higher than the wolf genome. Also, genomic annotation results from intron and intergenic regions showed that the proportion of variations in the wolf genome is higher than that in the dog genome, while the proportion of the coding sequences and 3′-UTR in the dog genome is higher than that in the wolf genome. The genes related to the olfactory and immune systems were enriched in the set of the structural variants (SVs) identified in this work. CONCLUSIONS: Our results showed more deleterious mutations and coding sequence variants in the domestic dog genome than those in wolf genome. By providing the first Iranian dog and wolf variome map, our findings contribute to understanding the genetic architecture of the dog domestication. BioMed Central 2020-03-04 /pmc/articles/PMC7057629/ /pubmed/32131720 http://dx.doi.org/10.1186/s12864-020-6619-8 Text en © The Author(s). 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. 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 in a credit line to the data. |
spellingShingle | Research Article Amiri Ghanatsaman, Zeinab Wang, Guo-Dong Asadollahpour Nanaei, Hojjat Asadi Fozi, Masood Peng, Min-Sheng Esmailizadeh, Ali Zhang, Ya-Ping Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication |
title | Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication |
title_full | Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication |
title_fullStr | Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication |
title_full_unstemmed | Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication |
title_short | Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication |
title_sort | whole genome resequencing of the iranian native dogs and wolves to unravel variome during dog domestication |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7057629/ https://www.ncbi.nlm.nih.gov/pubmed/32131720 http://dx.doi.org/10.1186/s12864-020-6619-8 |
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