title: Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper.
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.
authors.affiliation: Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510089, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Yin
authors.affiliation: 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.
authors.forename: Zong-Ji
authors.initials: ZJ
authors.lastname: Wang
authors.affiliation: 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.|Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen K 1350, Denmark.
authors.forename: Qi-Ye
authors.initials: QY
authors.lastname: Li
authors.affiliation: China National Genebank, BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Jin-Ming
authors.initials: JM
authors.lastname: Lian
authors.affiliation: China National Genebank, BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510089, China.
authors.forename: Bing-Zheng
authors.initials: BZ
authors.lastname: Lu
authors.affiliation: China National Genebank, BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Li-Jun
authors.initials: LJ
authors.lastname: Jin
authors.affiliation: Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510089, China.
authors.forename: Peng-Xin
authors.initials: PX
authors.lastname: Qiu
authors.affiliation: China National Genebank, BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Pei
authors.initials: P
authors.lastname: Zhang
authors.affiliation: Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510089, China.
authors.forename: Wen-Bo
authors.initials: WB
authors.lastname: Zhu
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Wen
authors.affiliation: Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510089, China.
authors.forename: Yi-Jun
authors.initials: YJ
authors.lastname: Huang
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Zhi-Long
authors.initials: ZL
authors.lastname: Lin
authors.affiliation: China National Genebank, BGI-Shenzhen, Shenzhen 518083, China.|Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen DK-2100, Denmark.
authors.forename: Bi-Tao
authors.identifier: 0000-0003-4588-7680
authors.initials: BT
authors.lastname: Qiu
authors.affiliation: Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510089, China.
authors.forename: Xing-Wen
authors.initials: XW
authors.lastname: Su
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.|James D. Watson Institute of Genome Sciences, Hangzhou 310058, China.
authors.forename: Huan-Ming
authors.initials: HM
authors.lastname: Yang
authors.affiliation: 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.|Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen DK-2100, Denmark.
authors.forename: Guo-Jie
authors.initials: GJ
authors.lastname: Zhang
authors.affiliation: Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510089, China.
authors.forename: Guang-Mei
authors.initials: GM
authors.lastname: Yan
authors.affiliation: Life Sciences Institute, The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, Zhejiang University, Hangzhou 310058, China.|Department of Integrative Biology, University of California, Berkeley, Berkeley, California 94720, USA.
authors.forename: Qi
authors.initials: Q
authors.lastname: Zhou
mesh_terms: D000818:Animals; D005075:Biological Evolution; D019070:Cell Lineage; D004251:DNA Transposable Elements; D019143:Evolution, Molecular; D005260:Female; D005552:Forelimb; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D016678:Genome; D006614:Hindlimb; D008116:Lizards / Q000235:genetics; D008297:Male; D010802:Phylogeny; D011995:Recombination, Genetic; D012730:Sex Chromosomes; D012911:Snakes / Q000033:anatomy & histology* / Q000235:genetics*; D059467:Transcriptome
chemical_list: D004251:DNA Transposable Elements