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Structural variation during dog domestication: insights from gray wolf and dhole genomes

National Science Review 2019年第1期6卷 110-122页

作者： Guo-Dong Wang Xiu-Juan Shao Bing Bai Junlong Wang Xiaobo Wang Xue Cao Yan-Hu Liu Xuan Wang Ting-Ting Yin Shao-Jie Zhang Yan Lu Zechong Wang Lu Wang Wenming Zhao Bing Zhang Jue Ruan Ya-Ping Zhang State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Agricultural Genomics Institute Chinese Academy of Agricultural Sciences Medical Faculty Kunming University of Science and Technology Department of Pediatrics the First People's Hospital of Yunnan Province College of Pharmacology Soochow University Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province Kunming Institute of ZoologyChinese Academy of Sciences Department of Laboratory Animal Science Kunming Medical University Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education Yunnan University Kunming College of Life Science University of Chinese Academy of Sciences Beijing Zoo Core Genomic Facility Beijing Institute of GenomicsChinese Academy of Sciences

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 ***, 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 AKR1 B1(Aldo-Keto Reductase Family 1 Member B) transcript. Transcriptome analysis reveals a high level of expression of the new AKR1 B1 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.

关键词： dog domestication genome assembly structural variation gray wolf dhole

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