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; Qiong Shi

doi:10.1038/ncomms6594

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 YangZhiqiang 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, Qiong Shi

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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.

Original language	English
Journal	Nature Communications
Volume	5
Issue number	5594
Number of pages	8
ISSN	2041-1723
DOIs	https://doi.org/10.1038/ncomms6594
Publication status	Published - Dec 2014

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Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishesFinal published version, 1.43 MB

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You, X, Bian, C, Zan, Q, Xu, X, Liu, X, Chen, J, Wang, J, Qiu, Y, Li, W, Zhang, X, Sun, Y, Chen, S, Hong, W, Li, Y, Cheng, S, Fan, G, Shi, C, Liang, J, Tom Tang, Y, Yang, C, Ruan, Z, Bai, J, Peng, C, Mu, Q, Lu, J, Fan, M, Yang, S, Huang, Z, Jiang, X, Fang, X, Zhang, G, Zhang, Y, Polgar, G, Yu, H, Li, J, Liu, Z, Zhang, G, Ravi, V, Coon, SL, Wang, J, Yang, H, Venkatesh, B, Wang, J & Shi, Q 2014, 'Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes', Nature Communications, vol. 5, no. 5594. https://doi.org/10.1038/ncomms6594

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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.",

author = "Xinxin You and Chao Bian and Qijie Zan and Xun Xu and Xin Liu and Jieming Chen and Jintu Wang and Ying Qiu and Wujiao Li and Xinhui Zhang and Ying Sun and Shixi Chen and Wanshu Hong and Yuxiang Li and Shifeng Cheng and Guangyi Fan and Chengcheng Shi and Jie Liang and {Tom Tang}, Y and Chengye Yang and Zhiqiang Ruan and Jie Bai and Chao Peng and Qian Mu and Jun Lu and Mingjun Fan and Shuang Yang and Zhiyong Huang and Xuanting Jiang and Xiaodong Fang and Guojie Zhang and Yong Zhang and Gianluca Polgar and Hui Yu and Jia Li and Zhongjian Liu and Guoqiang Zhang and Vydianathan Ravi and Coon, {Steven L} and Jian Wang and Huanming Yang and Byrappa Venkatesh and Jun Wang and Qiong Shi",

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doi = "10.1038/ncomms6594",

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journal = "Nature Communications",

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T1 - Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes

AU - You, Xinxin

AU - Bian, Chao

AU - Zan, Qijie

AU - Xu, Xun

AU - Liu, Xin

AU - Chen, Jieming

AU - Wang, Jintu

AU - Qiu, Ying

AU - Li, Wujiao

AU - Zhang, Xinhui

AU - Sun, Ying

AU - Chen, Shixi

AU - Hong, Wanshu

AU - Li, Yuxiang

AU - Cheng, Shifeng

AU - Fan, Guangyi

AU - Shi, Chengcheng

AU - Liang, Jie

AU - Tom Tang, Y

AU - Yang, Chengye

AU - Ruan, Zhiqiang

AU - Bai, Jie

AU - Peng, Chao

AU - Mu, Qian

AU - Lu, Jun

AU - Fan, Mingjun

AU - Yang, Shuang

AU - Huang, Zhiyong

AU - Jiang, Xuanting

AU - Fang, Xiaodong

AU - Zhang, Guojie

AU - Zhang, Yong

AU - Polgar, Gianluca

AU - Yu, Hui

AU - Li, Jia

AU - Liu, Zhongjian

AU - Zhang, Guoqiang

AU - Ravi, Vydianathan

AU - Coon, Steven L

AU - Wang, Jian

AU - Yang, Huanming

AU - Venkatesh, Byrappa

AU - Wang, Jun

AU - Shi, Qiong

PY - 2014/12

Y1 - 2014/12

N2 - 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.

AB - 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.

U2 - 10.1038/ncomms6594

DO - 10.1038/ncomms6594

M3 - Journal article

C2 - 25463417

SN - 2041-1723

VL - 5

JO - Nature Communications

JF - Nature Communications

IS - 5594

ER -

Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes

Abstract

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