数字农科院2.0

The Sinocyclocheilus cavefish genome provides insights into cave adaptation

文献类型: 外文期刊

作者: Yang, Junxing;Jiang, Wansheng;Pan, Xiaofu;Wang, Xiaoai;Chen, Xiaoyong;Zheng, Lanping;Chen, Xiaoli;Bai, Jie;Fang, Dongming;Qiu, Ying;Yuan, Hui;Bian, Chao;Lu, Jiang;He, Shiyang;Zhang, Yaolei;You, Xinxin;Wang, Yongsi;Sun, Ying;Mao, Danqing;Liu, Yong;Fan, Guangyi;Zhang, He;Zhang, Xinhui;Wang, Jintu;Chen, Jieming;Ruan, Zhiqiang;Li, Jia;Yu, Hui;Peng, Chao;Wang, Jian;Yang, Huanming;Wang, Jun;Xu, Xun;Bai, Jie;Qiu, Ying;Bian, Chao;You, Xinxin;Zhang, Xinhui;Chen, Jieming;Ruan, Zhiqiang;Li, Jia;Yu, Hui;Peng, Chao;Bai, Jie;Whitten, Tony;Qiu, Ying;Sun, Ying;Cheng, Le;Fang, Dongming;Lu, Jiang;He, Shiyang;Li, Jia;Yu, Hui;Zhang, Yaolei;Cheng, Le;Ma, Xingyu;Xu, Junmin;Shi, Qiong;Ma, Xingyu;Xu, Junmin;Shi, Qiong;He, You;Xu, Zhengfeng;Xu, Pao;Wang, Jian;Yang, Huanming;Wang, Jun

作者机构:

关键词: Cavefish;Genome;Adaptation;Evolution;Qinghai-Tibetan Plateau;Sinocyclocheilus

期刊名称: BMC BIOLOGY

ISSN: 1741-7007

年卷期: 2016 年 14 卷

页码:

收录情况: SCI

摘要: Background: An emerging cavefish model, the cyprinid genus Sinocyclocheilus, is endemic to the massive southwestern karst area adjacent to the Qinghai-Tibetan Plateau of China. In order to understand whether orogeny influenced the evolution of these species, and how genomes change under isolation, especially in subterranean habitats, we performed whole-genome sequencing and comparative analyses of three species in this genus, S. grahami, S. rhinocerous and S. anshuiensis. These species are surface-dwelling, semi-cave-dwelling and cave-restricted, respectively. Results: The assembled genome sizes of S. grahami, S. rhinocerous and S. anshuiensis are 1.75 Gb, 1.73 Gb and 1.68 Gb, respectively. Divergence time and population history analyses of these species reveal that their speciation and population dynamics are correlated with the different stages of uplifting of the Qinghai-Tibetan Plateau. We carried out comparative analyses of these genomes and found that many genetic changes, such as gene loss (e.g. opsin genes), pseudogenes (e.g. crystallin genes), mutations (e.g. melanogenesis-related genes), deletions (e.g. scale-related genes) and down-regulation (e.g. circadian rhythm pathway genes), are possibly associated with the regressive features (such as eye degeneration, albinism, rudimentary scales and lack of circadian rhythms), and that some gene expansion (e.g. taste-related transcription factor gene) may point to the constructive features (such as enhanced taste buds) which evolved in these cave fishes. Conclusion: As the first report on cavefish genomes among distinct species in Sinocyclocheilus, our work provides not only insights into genetic mechanisms of cave adaptation, but also represents a fundamental resource for a better understanding of cavefish biology.

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[1]Additional file 7: Figure S29â S32. of The Sinocyclocheilus cavefish genome provides insights into cave adaptation. Lanping Zheng,Zhang, He,Junmin Xu,Jintu Wang,Junxing Yang,He, You,Xu, Xun,Liu, Yong,Li, Jia,Yongsi Wang,Xiaoyong Chen,Huanming Yang,Xiaoai Wang,Xiaoli Chen,Danqing Mao,Wang, Jun,Wansheng Jiang,Zhengfeng Xu,Bian, Chao,Yuan, Hui,Yu, Hui,Lu, Jiang,Xingyu Ma,Jieming Chen,Xinhui Zhang,Xinxin You,Peng, Chao,Zhiqiang Ruan,Bai, Jie,Shi, Qiong,Qiu, Ying,Shiyang He,Whitten, Tony,Guangyi Fan,Xiaofu Pan,Cheng, Le,Pao Xu,Yaolei Zhang,Wang, Jian,Sun, Ying,Dongming Fang

[2]The Sinocyclocheilus cavefish genome provides insights into cave adaptation. Jieming Chen,Dongming Fang,Danqing Mao,Shiyang He,Guangyi Fan,Li, Jia,Cheng, Le,Yaolei Zhang,Zhiqiang Ruan,Yu, Hui,Pao Xu,Xingyu Ma,Yongsi Wang,Bian, Chao,Shi, Qiong,Zhang, He,Whitten, Tony,Wansheng Jiang,Xinhui Zhang,Xu, Xun,Xiaoyong Chen,Xiaofu Pan,Junxing Yang,Sun, Ying,Xiaoli Chen,Qiu, Ying,Wang, Jun,Jintu Wang,Lu, Jiang,Huanming Yang,Lanping Zheng,Xinxin You,Wang, Jian,Junmin Xu,Yuan, Hui,Bai, Jie,Zhengfeng Xu,He, You,Peng, Chao,Liu, Yong,Xiaoai Wang

[3]Additional file 9: of The Sinocyclocheilus cavefish genome provides insights into cave adaptation. Shi, Qiong,Dongming Fang,Zhang, He,Whitten, Tony,Yu, Hui,Cheng, Le,Wang, Jian,Zhiqiang Ruan,Xiaoai Wang,Zhengfeng Xu,Sun, Ying,Xiaofu Pan,Junmin Xu,Pao Xu,Danqing Mao,Peng, Chao,Jintu Wang,Xiaoyong Chen,Xu, Xun,Guangyi Fan,He, You,Lu, Jiang,Wang, Jun,Jieming Chen,Liu, Yong,Lanping Zheng,Qiu, Ying,Yongsi Wang,Yaolei Zhang,Huanming Yang,Bian, Chao,Shiyang He,Xiaoli Chen,Xingyu Ma,Li, Jia,Yuan, Hui,Bai, Jie,Xinhui Zhang,Junxing Yang,Xinxin You,Wansheng Jiang

[4]Additional file 10: Table S30. of The Sinocyclocheilus cavefish genome provides insights into cave adaptation. Wang, Jun,Huanming Yang,Shiyang He,Yuan, Hui,Sun, Ying,Yaolei Zhang,Bian, Chao,Guangyi Fan,Jieming Chen,Lanping Zheng,Xinhui Zhang,Wang, Jian,Xiaofu Pan,Junmin Xu,Liu, Yong,Zhang, He,Wansheng Jiang,Yongsi Wang,Junxing Yang,Yu, Hui,Jintu Wang,Xiaoyong Chen,Shi, Qiong,Xiaoli Chen,Xu, Xun,Danqing Mao,Li, Jia,Xiaoai Wang,Xingyu Ma,Cheng, Le,Qiu, Ying,Zhengfeng Xu,He, You,Whitten, Tony,Peng, Chao,Dongming Fang,Lu, Jiang,Xinxin You,Bai, Jie,Zhiqiang Ruan,Pao Xu

[5]Additional file 1: Figure S1. of The Sinocyclocheilus cavefish genome provides insights into cave adaptation. Shi, Qiong,Junxing Yang,Li, Jia,Xu, Xun,Jintu Wang,Guangyi Fan,Cheng, Le,Sun, Ying,Junmin Xu,Wansheng Jiang,Peng, Chao,Whitten, Tony,Xinhui Zhang,Xiaoli Chen,Bian, Chao,Xiaoyong Chen,Lanping Zheng,Zhengfeng Xu,Shiyang He,Xiaofu Pan,Yongsi Wang,He, You,Xiaoai Wang,Liu, Yong,Lu, Jiang,Zhiqiang Ruan,Yuan, Hui,Yu, Hui,Wang, Jian,Zhang, He,Pao Xu,Bai, Jie,Dongming Fang,Danqing Mao,Huanming Yang,Yaolei Zhang,Xingyu Ma,Xinxin You,Wang, Jun,Jieming Chen,Qiu, Ying

[6]Additional file 8: Table S29. of The Sinocyclocheilus cavefish genome provides insights into cave adaptation. Shiyang He,Xiaoli Chen,Danqing Mao,Yuan, Hui,Xingyu Ma,Jieming Chen,Wansheng Jiang,Xu, Xun,Wang, Jian,Xiaofu Pan,Junxing Yang,Zhang, He,Guangyi Fan,Cheng, Le,Whitten, Tony,Yongsi Wang,Peng, Chao,Liu, Yong,Lanping Zheng,Junmin Xu,Zhengfeng Xu,Qiu, Ying,Xinhui Zhang,Sun, Ying,Xiaoyong Chen,Li, Jia,Bai, Jie,Yu, Hui,Xinxin You,Yaolei Zhang,Xiaoai Wang,Dongming Fang,He, You,Pao Xu,Bian, Chao,Shi, Qiong,Zhiqiang Ruan,Wang, Jun,Huanming Yang,Lu, Jiang,Jintu Wang

[7]Additional file 4: Figure S8â S14. of The Sinocyclocheilus cavefish genome provides insights into cave adaptation. Xu, Xun,Guangyi Fan,Bai, Jie,Wang, Jun,Dongming Fang,Wang, Jian,Jintu Wang,Lanping Zheng,Xiaoyong Chen,Junmin Xu,Xinhui Zhang,Cheng, Le,Shiyang He,Bian, Chao,Xiaoli Chen,Zhiqiang Ruan,Xiaofu Pan,Jieming Chen,Xiaoai Wang,Huanming Yang,Lu, Jiang,Whitten, Tony,Junxing Yang,He, You,Liu, Yong,Sun, Ying,Pao Xu,Yongsi Wang,Danqing Mao,Li, Jia,Yuan, Hui,Zhang, He,Yu, Hui,Shi, Qiong,Zhengfeng Xu,Wansheng Jiang,Xinxin You,Yaolei Zhang,Qiu, Ying,Peng, Chao,Xingyu Ma

[8]Additional file 2: Table S1–S28. of The Sinocyclocheilus cavefish genome provides insights into cave adaptation. Bian, Chao,Qiu, Ying,Yongsi Wang,Cheng, Le,Huanming Yang,Zhiqiang Ruan,Wang, Jian,Shi, Qiong,Wansheng Jiang,Xinxin You,Yaolei Zhang,Shiyang He,Lanping Zheng,Sun, Ying,Xiaoli Chen,Jintu Wang,Whitten, Tony,Xu, Xun,Xingyu Ma,Junmin Xu,He, You,Lu, Jiang,Li, Jia,Xiaofu Pan,Yu, Hui,Dongming Fang,Zhang, He,Xiaoyong Chen,Yuan, Hui,Wang, Jun,Junxing Yang,Jieming Chen,Zhengfeng Xu,Xiaoai Wang,Danqing Mao,Xinhui Zhang,Peng, Chao,Bai, Jie,Guangyi Fan,Pao Xu,Liu, Yong

[9]Additional file 5: Figure S15â S17. of The Sinocyclocheilus cavefish genome provides insights into cave adaptation. Pao Xu,Li, Jia,Xinxin You,Xiaofu Pan,Zhiqiang Ruan,Peng, Chao,Whitten, Tony,Bai, Jie,Xingyu Ma,Huanming Yang,Jieming Chen,Xiaoli Chen,Wang, Jun,Qiu, Ying,Liu, Yong,Shi, Qiong,Jintu Wang,Junxing Yang,Junmin Xu,Bian, Chao,Xu, Xun,Yu, Hui,Xiaoai Wang,He, You,Yongsi Wang,Sun, Ying,Zhang, He,Shiyang He,Yaolei Zhang,Xinhui Zhang,Wansheng Jiang,Lu, Jiang,Danqing Mao,Guangyi Fan,Dongming Fang,Cheng, Le,Wang, Jian,Xiaoyong Chen,Zhengfeng Xu,Yuan, Hui,Lanping Zheng

[10]Additional file 3: Figures S2â S7. of The Sinocyclocheilus cavefish genome provides insights into cave adaptation. Shiyang He,Junmin Xu,Junxing Yang,Dongming Fang,Lanping Zheng,He, You,Xiaoai Wang,Bai, Jie,Zhengfeng Xu,Yaolei Zhang,Xinhui Zhang,Wang, Jian,Xinxin You,Cheng, Le,Xiaoli Chen,Danqing Mao,Guangyi Fan,Pao Xu,Huanming Yang,Jintu Wang,Li, Jia,Liu, Yong,Sun, Ying,Whitten, Tony,Lu, Jiang,Xiaofu Pan,Xiaoyong Chen,Jieming Chen,Yuan, Hui,Zhang, He,Yongsi Wang,Peng, Chao,Yu, Hui,Shi, Qiong,Qiu, Ying,Xingyu Ma,Bian, Chao,Xu, Xun,Zhiqiang Ruan,Wang, Jun,Wansheng Jiang

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