Structural variation during dog domestication: insights from gray wolf and dhole genomes
Abstract 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) an...
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Oxford University Press (OUP)
2018
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Online Access: | http://dx.doi.org/10.1093/nsr/nwy076 http://academic.oup.com/nsr/article-pdf/6/1/110/38915183/nwy076.pdf |
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croxfordunivpr:10.1093/nsr/nwy076 2024-10-13T14:06:33+00:00 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 National Natural Science Foundation of China Chinese Academy of Sciences Youth Innovation Promotion Association Key Laboratory of Shenzhen 2018 http://dx.doi.org/10.1093/nsr/nwy076 http://academic.oup.com/nsr/article-pdf/6/1/110/38915183/nwy076.pdf en eng Oxford University Press (OUP) http://creativecommons.org/licenses/by/4.0/ National Science Review volume 6, issue 1, page 110-122 ISSN 2095-5138 2053-714X journal-article 2018 croxfordunivpr https://doi.org/10.1093/nsr/nwy076 2024-09-17T04:31:00Z Abstract 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. Article in Journal/Newspaper Canis lupus gray wolf Oxford University Press National Science Review 6 1 110 122 |
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Oxford University Press |
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croxfordunivpr |
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English |
description |
Abstract 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. |
author2 |
National Natural Science Foundation of China Chinese Academy of Sciences Youth Innovation Promotion Association Key Laboratory of Shenzhen |
format |
Article in Journal/Newspaper |
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 |
spellingShingle |
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 |
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 (OUP) |
publishDate |
2018 |
url |
http://dx.doi.org/10.1093/nsr/nwy076 http://academic.oup.com/nsr/article-pdf/6/1/110/38915183/nwy076.pdf |
genre |
Canis lupus gray wolf |
genre_facet |
Canis lupus gray wolf |
op_source |
National Science Review volume 6, issue 1, page 110-122 ISSN 2095-5138 2053-714X |
op_rights |
http://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.1093/nsr/nwy076 |
container_title |
National Science Review |
container_volume |
6 |
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1 |
container_start_page |
110 |
op_container_end_page |
122 |
_version_ |
1812812749281951744 |