Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes

Xinxin You, Chao Bian (), Qijie Zan, Xun Xu, Xin Liu, Jieming Chen, Jintu Wang, Ying Qiu, Wujiao Li, Xinhui Zhang, Ying Sun, Shixi Chen, Wanshu Hong, Yuxiang Li, Shifeng Cheng, Guangyi Fan, Chengcheng Shi, Jie Liang, Y. Tom Tang, Chengye Yang, Zhiqiang Ruan, Jie Bai, Chao Peng, Qian Mu, Jun Lu, Mingjun Fan, Shuang Yang, Zhiyong Huang, Xuanting Jiang, Xiaodong Fang, Guojie Zhang, Yong Zhang, Gianluca Polgar, Hui Yu, Jia Li, Zhongjian Liu, Guoqiang Zhang, Vydianathan Ravi, Steven L. Coon, Jian Wang, Huanming Yang, Byrappa Venkatesh, Jun Wang () and Qiong Shi ()
Additional contact information
Xinxin You: Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics
Chao Bian: Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics
Qijie Zan: Shenzhen Wild Animal Rescue Center
Xun Xu: BGI-Shenzhen
Xin Liu: BGI-Shenzhen
Jieming Chen: Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics
Jintu Wang: BGI-Shenzhen
Ying Qiu: Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics
Wujiao Li: Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics
Xinhui Zhang: Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics
Ying Sun: BGI-Shenzhen
Shixi Chen: College of Ocean and Earth Science, Xiamen University
Wanshu Hong: College of Ocean and Earth Science, Xiamen University
Yuxiang Li: BGI-Shenzhen
Shifeng Cheng: BGI-Shenzhen
Guangyi Fan: BGI-Shenzhen
Chengcheng Shi: BGI-Shenzhen
Jie Liang: BGI-Shenzhen
Y. Tom Tang: BGI-Shenzhen
Chengye Yang: BGI-Shenzhen
Zhiqiang Ruan: Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics
Jie Bai: Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics
Chao Peng: Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics
Qian Mu: BGI-Shenzhen
Jun Lu: BGI-Shenzhen
Mingjun Fan: Center for Fish Genomics, BGI-Wuhan
Shuang Yang: BGI-Shenzhen
Zhiyong Huang: BGI-Shenzhen
Xuanting Jiang: BGI-Shenzhen
Xiaodong Fang: BGI-Shenzhen
Guojie Zhang: BGI-Shenzhen
Yong Zhang: BGI-Shenzhen
Gianluca Polgar: Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Jln Tungku Link
Hui Yu: Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics
Jia Li: Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics
Zhongjian Liu: Shenzhen Key Laboratory for Orchid Conservation and Utilization of the Orchid Conservation and Research Center of Shenzhen
Guoqiang Zhang: Shenzhen Key Laboratory for Orchid Conservation and Utilization of the Orchid Conservation and Research Center of Shenzhen
Vydianathan Ravi: Institute of Molecular and Cell Biology, A*STAR, Biopolis
Steven L. Coon: Molecular Genomics Laboratory, National Institutes of Health
Jian Wang: BGI-Shenzhen
Huanming Yang: BGI-Shenzhen
Byrappa Venkatesh: Institute of Molecular and Cell Biology, A*STAR, Biopolis
Jun Wang: BGI-Shenzhen
Qiong Shi: Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics

Nature Communications, 2014, vol. 5, issue 1, 1-8

Abstract: Abstract Mudskippers are amphibious fishes that have developed morphological and physiological adaptations to match their unique lifestyles. Here we perform whole-genome sequencing of four representative mudskippers to elucidate the molecular mechanisms underlying these adaptations. We discover an expansion of innate immune system genes in the mudskippers that may provide defence against terrestrial pathogens. Several genes of the ammonia excretion pathway in the gills have experienced positive selection, suggesting their important roles in mudskippers’ tolerance to environmental ammonia. Some vision-related genes are differentially lost or mutated, illustrating genomic changes associated with aerial vision. Transcriptomic analyses of mudskippers exposed to air highlight regulatory pathways that are up- or down-regulated in response to hypoxia. The present study provides a valuable resource for understanding the molecular mechanisms underlying water-to-land transition of vertebrates.

Date: 2014
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DOI: 10.1038/ncomms6594

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