Structural variation during dog domestication: insights from gray wolf and dhole genomes
Several processes like phenotypic evolution, disease susceptibility and environmental adaptations, which fashion the domestication of animals, are largely attributable to structural variations (SVs) in the genome. Here, we present high-quality draft genomes of the gray wolf (Canis lupus) and dhole (...
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ftpubmed:oai:pubmedcentral.nih.gov:8291444 2023-05-15T15:50:40+02:00 Structural variation during dog domestication: insights from gray wolf and dhole genomes Wang, Guo-Dong Shao, Xiu-Juan Bai, Bing Wang, Junlong Wang, Xiaobo Cao, Xue Liu, Yan-Hu Wang, Xuan Yin, Ting-Ting Zhang, Shao-Jie Lu, Yan Wang, Zechong Wang, Lu Zhao, Wenming Zhang, Bing Ruan, Jue Zhang, Ya-Ping 2019-01 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8291444/ https://doi.org/10.1093/nsr/nwy076 en eng Oxford University Press http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8291444/ http://dx.doi.org/10.1093/nsr/nwy076 © The Author(s) 2018. Published by Oxford University Press on behalf of China Science Publishing & Media Ltd. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com CC-BY CC-BY-NC Natl Sci Rev Molecular Biology & Genetics Text 2019 ftpubmed https://doi.org/10.1093/nsr/nwy076 2021-10-24T00:23:21Z Several processes like phenotypic evolution, disease susceptibility and environmental adaptations, which fashion the domestication of animals, are largely attributable to structural variations (SVs) in the genome. Here, we present high-quality draft genomes of the gray wolf (Canis lupus) and dhole (Cuon alpinus) with scaffold N50 of 6.04 Mb and 3.96 Mb, respectively. Sequence alignment comprising genomes of three canid species reveals SVs specific to the dog, particularly 16 315 insertions, 2565 deletions, 443 repeats, 16 inversions and 15 translocations. Functional annotation of the dog SVs associated with genes indicates their enrichments in energy metabolisms, neurological processes and immune systems. Interestingly, we identify and verify at population level an insertion fully covering a copy of the AKR1B1 (Aldo-Keto Reductase Family 1 Member B) transcript. Transcriptome analysis reveals a high level of expression of the new AKR1B1 copy in the small intestine and liver, implying an increase in de novo fatty acid synthesis and antioxidant ability in dog compared to gray wolf, likely in response to dietary shifts during the agricultural revolution. For the first time, we report a comprehensive analysis of the evolutionary dynamics of SVs during the domestication step of dogs. Our findings demonstrate that retroposition can birth new genes to facilitate domestication, and affirm the importance of large-scale genomic variants in domestication studies. Text Canis lupus gray wolf PubMed Central (PMC) National Science Review 6 1 110 122 |
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Molecular Biology & Genetics |
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Molecular Biology & Genetics Wang, Guo-Dong Shao, Xiu-Juan Bai, Bing Wang, Junlong Wang, Xiaobo Cao, Xue Liu, Yan-Hu Wang, Xuan Yin, Ting-Ting Zhang, Shao-Jie Lu, Yan Wang, Zechong Wang, Lu Zhao, Wenming Zhang, Bing Ruan, Jue Zhang, Ya-Ping Structural variation during dog domestication: insights from gray wolf and dhole genomes |
topic_facet |
Molecular Biology & Genetics |
description |
Several processes like phenotypic evolution, disease susceptibility and environmental adaptations, which fashion the domestication of animals, are largely attributable to structural variations (SVs) in the genome. Here, we present high-quality draft genomes of the gray wolf (Canis lupus) and dhole (Cuon alpinus) with scaffold N50 of 6.04 Mb and 3.96 Mb, respectively. Sequence alignment comprising genomes of three canid species reveals SVs specific to the dog, particularly 16 315 insertions, 2565 deletions, 443 repeats, 16 inversions and 15 translocations. Functional annotation of the dog SVs associated with genes indicates their enrichments in energy metabolisms, neurological processes and immune systems. Interestingly, we identify and verify at population level an insertion fully covering a copy of the AKR1B1 (Aldo-Keto Reductase Family 1 Member B) transcript. Transcriptome analysis reveals a high level of expression of the new AKR1B1 copy in the small intestine and liver, implying an increase in de novo fatty acid synthesis and antioxidant ability in dog compared to gray wolf, likely in response to dietary shifts during the agricultural revolution. For the first time, we report a comprehensive analysis of the evolutionary dynamics of SVs during the domestication step of dogs. Our findings demonstrate that retroposition can birth new genes to facilitate domestication, and affirm the importance of large-scale genomic variants in domestication studies. |
format |
Text |
author |
Wang, Guo-Dong Shao, Xiu-Juan Bai, Bing Wang, Junlong Wang, Xiaobo Cao, Xue Liu, Yan-Hu Wang, Xuan Yin, Ting-Ting Zhang, Shao-Jie Lu, Yan Wang, Zechong Wang, Lu Zhao, Wenming Zhang, Bing Ruan, Jue Zhang, Ya-Ping |
author_facet |
Wang, Guo-Dong Shao, Xiu-Juan Bai, Bing Wang, Junlong Wang, Xiaobo Cao, Xue Liu, Yan-Hu Wang, Xuan Yin, Ting-Ting Zhang, Shao-Jie Lu, Yan Wang, Zechong Wang, Lu Zhao, Wenming Zhang, Bing Ruan, Jue Zhang, Ya-Ping |
author_sort |
Wang, Guo-Dong |
title |
Structural variation during dog domestication: insights from gray wolf and dhole genomes |
title_short |
Structural variation during dog domestication: insights from gray wolf and dhole genomes |
title_full |
Structural variation during dog domestication: insights from gray wolf and dhole genomes |
title_fullStr |
Structural variation during dog domestication: insights from gray wolf and dhole genomes |
title_full_unstemmed |
Structural variation during dog domestication: insights from gray wolf and dhole genomes |
title_sort |
structural variation during dog domestication: insights from gray wolf and dhole genomes |
publisher |
Oxford University Press |
publishDate |
2019 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8291444/ https://doi.org/10.1093/nsr/nwy076 |
genre |
Canis lupus gray wolf |
genre_facet |
Canis lupus gray wolf |
op_source |
Natl Sci Rev |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8291444/ http://dx.doi.org/10.1093/nsr/nwy076 |
op_rights |
© The Author(s) 2018. Published by Oxford University Press on behalf of China Science Publishing & Media Ltd. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
op_rightsnorm |
CC-BY CC-BY-NC |
op_doi |
https://doi.org/10.1093/nsr/nwy076 |
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National Science Review |
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6 |
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110 |
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122 |
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1766385658675331072 |