title: Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes.
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.
authors.affiliation: 1] Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen 518083, China [2] BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Xinxin
authors.initials: X
authors.lastname: You
authors.affiliation: 1] Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen 518083, China [2] BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Bian
authors.affiliation: Shenzhen Wild Animal Rescue Center, Shenzhen 518040, China.
authors.forename: Qijie
authors.initials: Q
authors.lastname: Zan
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Xun
authors.initials: X
authors.lastname: Xu
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Liu
authors.affiliation: 1] Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen 518083, China [2] BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Jieming
authors.initials: J
authors.lastname: Chen
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Jintu
authors.initials: J
authors.lastname: Wang
authors.affiliation: 1] Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen 518083, China [2] BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Qiu
authors.affiliation: Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen 518083, China.
authors.forename: Wujiao
authors.initials: W
authors.lastname: Li
authors.affiliation: 1] Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen 518083, China [2] BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Xinhui
authors.initials: X
authors.lastname: Zhang
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Sun
authors.affiliation: College of Ocean and Earth Science, Xiamen University, Xiamen 361005, China.
authors.forename: Shixi
authors.initials: S
authors.lastname: Chen
authors.affiliation: College of Ocean and Earth Science, Xiamen University, Xiamen 361005, China.
authors.forename: Wanshu
authors.initials: W
authors.lastname: Hong
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Yuxiang
authors.initials: Y
authors.lastname: Li
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Shifeng
authors.initials: S
authors.lastname: Cheng
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Guangyi
authors.initials: G
authors.lastname: Fan
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Chengcheng
authors.initials: C
authors.lastname: Shi
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Liang
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Y
authors.initials: Y
authors.lastname: Tom Tang
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Chengye
authors.initials: C
authors.lastname: Yang
authors.affiliation: 1] Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen 518083, China [2] BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Zhiqiang
authors.initials: Z
authors.lastname: Ruan
authors.affiliation: 1] Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen 518083, China [2] BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Bai
authors.affiliation: 1] Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen 518083, China [2] BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Peng
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Qian
authors.initials: Q
authors.lastname: Mu
authors.affiliation: 1] BGI-Shenzhen, Shenzhen 518083, China [2] Shenzhen BGI Fisheries Sci &Tech Co. Ltd, Shenzhen 518083, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Lu
authors.affiliation: Center for Fish Genomics, BGI-Wuhan, Wuhan 430075, China.
authors.forename: Mingjun
authors.initials: M
authors.lastname: Fan
authors.affiliation: 1] BGI-Shenzhen, Shenzhen 518083, China [2] Center for Fish Genomics, BGI-Wuhan, Wuhan 430075, China.
authors.forename: Shuang
authors.initials: S
authors.lastname: Yang
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Huang
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Xuanting
authors.initials: X
authors.lastname: Jiang
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Fang
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Guojie
authors.initials: G
authors.lastname: Zhang
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Jln Tungku Link, BE1410 Brunei Darussalam.
authors.forename: Gianluca
authors.initials: G
authors.lastname: Polgar
authors.affiliation: 1] Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen 518083, China [2] BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Yu
authors.affiliation: 1] Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen 518083, China [2] BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Jia
authors.initials: J
authors.lastname: Li
authors.affiliation: Shenzhen Key Laboratory for Orchid Conservation and Utilization of the Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.
authors.forename: Zhongjian
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Shenzhen Key Laboratory for Orchid Conservation and Utilization of the Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.
authors.forename: Guoqiang
authors.initials: G
authors.lastname: Zhang
authors.affiliation: Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore.
authors.forename: Vydianathan
authors.initials: V
authors.lastname: Ravi
authors.affiliation: Molecular Genomics Laboratory, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Steven L
authors.initials: SL
authors.lastname: Coon
authors.affiliation: 1] BGI-Shenzhen, Shenzhen 518083, China [2] James D. Watson Institute of Genome Science, Hangzhou 310008, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.affiliation: 1] BGI-Shenzhen, Shenzhen 518083, China [2] James D. Watson Institute of Genome Science, Hangzhou 310008, China [3] Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.
authors.forename: Huanming
authors.initials: H
authors.lastname: Yang
authors.affiliation: Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore.
authors.forename: Byrappa
authors.initials: B
authors.lastname: Venkatesh
authors.affiliation: 1] BGI-Shenzhen, Shenzhen 518083, China [2] Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia [3] Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: 1] Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen 518083, China [2] BGI-Shenzhen, Shenzhen 518083, China [3] Shenzhen BGI Fisheries Sci &Tech Co. Ltd, Shenzhen 518083, China [4] Center for Fish Genomics, BGI-Wuhan, Wuhan 430075, China.
authors.forename: Qiong
authors.initials: Q
authors.lastname: Shi
mesh_terms: D000641:Ammonia / Q000378:metabolism; D000663:Amphibians / Q000235:genetics*; D000818:Animals; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D016678:Genome; D000860:Hypoxia / Q000235:genetics; D007113:Immunity, Innate / Q000235:genetics; D010473:Perciformes / Q000235:genetics*; D017422:Sequence Analysis, DNA; D014785:Vision, Ocular / Q000235:genetics
chemical_list: D000641:Ammonia