Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper

Wei Yin, Zong-ji Wang, Qi-ye Li, Jin-ming Lian, Yang Zhou, Bing-zheng Lu, Li-jun Jin, Peng-xin Qiu, Pei Zhang, Wen-bo Zhu, Bo Wen, Yi-jun Huang, Zhi-long Lin, Bi-tao Qiu, Xing-wen Su, Huan-ming Yang, Guo-jie Zhang, Guang-mei Yan () and Qi Zhou ()
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Wei Yin: Zhongshan School of Medicine, Sun Yat-sen University
Zong-ji Wang: Life Sciences Institute, The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, Zhejiang University
Qi-ye Li: China National Genebank, BGI-Shenzhen
Jin-ming Lian: China National Genebank, BGI-Shenzhen
Yang Zhou: China National Genebank, BGI-Shenzhen
Bing-zheng Lu: Zhongshan School of Medicine, Sun Yat-sen University
Li-jun Jin: China National Genebank, BGI-Shenzhen
Peng-xin Qiu: Zhongshan School of Medicine, Sun Yat-sen University
Pei Zhang: China National Genebank, BGI-Shenzhen
Wen-bo Zhu: Zhongshan School of Medicine, Sun Yat-sen University
Bo Wen: BGI-Shenzhen
Yi-jun Huang: Zhongshan School of Medicine, Sun Yat-sen University
Zhi-long Lin: BGI-Shenzhen
Bi-tao Qiu: China National Genebank, BGI-Shenzhen
Xing-wen Su: Zhongshan School of Medicine, Sun Yat-sen University
Huan-ming Yang: BGI-Shenzhen
Guo-jie Zhang: China National Genebank, BGI-Shenzhen
Guang-mei Yan: Zhongshan School of Medicine, Sun Yat-sen University
Qi Zhou: Life Sciences Institute, The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, Zhejiang University

Nature Communications, 2016, vol. 7, issue 1, 1-11

Abstract: Abstract Snakes have numerous features distinctive from other tetrapods and a rich history of genome evolution that is still obscure. Here, we report the high-quality genome of the five-pacer viper, Deinagkistrodon acutus, and comparative analyses with other representative snake and lizard genomes. We map the evolutionary trajectories of transposable elements (TEs), developmental genes and sex chromosomes onto the snake phylogeny. TEs exhibit dynamic lineage-specific expansion, and many viper TEs show brain-specific gene expression along with their nearby genes. We detect signatures of adaptive evolution in olfactory, venom and thermal-sensing genes and also functional degeneration of genes associated with vision and hearing. Lineage-specific relaxation of functional constraints on respective Hox and Tbx limb-patterning genes supports fossil evidence for a successive loss of forelimbs then hindlimbs during snake evolution. Finally, we infer that the ZW sex chromosome pair had undergone at least three recombination suppression events in the ancestor of advanced snakes. These results altogether forge a framework for our deep understanding into snakes’ history of molecular evolution.

Date: 2016
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DOI: 10.1038/ncomms13107

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