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Nat Commun. 2016 Oct 6;7:13107. doi: 10.1038/ncomms13107.

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

Yin W1, Wang ZJ2,3,4,5, Li QY3,4,6, Lian JM3, Zhou Y3, Lu BZ7, Jin LJ3, Qiu PX7, Zhang P3, Zhu WB7, Wen B8, Huang YJ7, Lin ZL8, Qiu BT3,9, Su XW7, Yang HM8,10, Zhang GJ3,4,9, Yan GM7, Zhou Q2,11.

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Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510089, China.
Life Sciences Institute, The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, Zhejiang University, Hangzhou 310058, China.
China National Genebank, BGI-Shenzhen, Shenzhen 518083, China.
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
School of Bioscience &Bioengineering, South China University of Technology, Guangzhou 510006, China.
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen K 1350, Denmark.
Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510089, China.
BGI-Shenzhen, Shenzhen 518083, China.
Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen DK-2100, Denmark.
James D. Watson Institute of Genome Sciences, Hangzhou 310058, China.
Department of Integrative Biology, University of California, Berkeley, Berkeley, California 94720, USA.


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.

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