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BMC Biol. 2016 Jan 4;14:1. doi: 10.1186/s12915-015-0223-4.

The Sinocyclocheilus cavefish genome provides insights into cave adaptation.

Yang J1, Chen X2, Bai J3,4,5, Fang D6,7, Qiu Y8,9,10, Jiang W11, Yuan H12, Bian C13,14, Lu J15,16, He S17,18, Pan X19, Zhang Y20,21, Wang X22, You X23,24, Wang Y25, Sun Y26,27, Mao D28, Liu Y29, Fan G30, Zhang H31, Chen X32, Zhang X33,34, Zheng L35, Wang J36, Cheng L37,38, Chen J39,40, Ruan Z41,42, Li J43,44,45, Yu H46,47,48, Peng C49,50, Ma X51,52, Xu J53,54, He Y55, Xu Z56, Xu P57, Wang J58,59, Yang H60,61, Wang J62,63, Whitten T64, Xu X65, Shi Q66,67,68,69.

Author information

1
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. yangjx@mail.kiz.ac.cn.
2
BGI-Shenzhen, Shenzhen, 518083, China. chenxiaoli@genomics.cn.
3
BGI-Shenzhen, Shenzhen, 518083, China. baijie@genomics.cn.
4
Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. baijie@genomics.cn.
5
Fauna & Flora International, Cambridge, CB1 2JD, UK. baijie@genomics.cn.
6
BGI-Shenzhen, Shenzhen, 518083, China. fangdongming@agis.org.cn.
7
Agricultural Genomes Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China. fangdongming@agis.org.cn.
8
BGI-Shenzhen, Shenzhen, 518083, China. qiuying@genomics.cn.
9
Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. qiuying@genomics.cn.
10
China National Genebank, Shenzhen, 518083, China. qiuying@genomics.cn.
11
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. jiangws@mail.kiz.ac.cn.
12
BGI-Shenzhen, Shenzhen, 518083, China. huiyuanChina@163.com.
13
BGI-Shenzhen, Shenzhen, 518083, China. bianchao@genomics.cn.
14
Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. bianchao@genomics.cn.
15
BGI-Shenzhen, Shenzhen, 518083, China. lujiang091009@163.com.
16
College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China. lujiang091009@163.com.
17
BGI-Shenzhen, Shenzhen, 518083, China. heshiyang@genomics.cn.
18
College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China. heshiyang@genomics.cn.
19
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. xiaofupan@163.com.
20
BGI-Shenzhen, Shenzhen, 518083, China. zyllei_1990@126.com.
21
School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China. zyllei_1990@126.com.
22
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. xueaiw@126.com.
23
BGI-Shenzhen, Shenzhen, 518083, China. youxinxin@genomics.cn.
24
Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. youxinxin@genomics.cn.
25
BGI-Shenzhen, Shenzhen, 518083, China. wangyongsi2012@163.com.
26
BGI-Shenzhen, Shenzhen, 518083, China. sunying@genomics.cn.
27
China National Genebank, Shenzhen, 518083, China. sunying@genomics.cn.
28
BGI-Shenzhen, Shenzhen, 518083, China. maodanqing@genomics.cn.
29
BGI-Shenzhen, Shenzhen, 518083, China. liuyong1530@163.com.
30
BGI-Shenzhen, Shenzhen, 518083, China. fanguangyi@genomics.cn.
31
BGI-Shenzhen, Shenzhen, 518083, China. zhanghe@genomics.cn.
32
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. chenxy@mail.kiz.ac.cn.
33
BGI-Shenzhen, Shenzhen, 518083, China. zhangxinhui@genomics.cn.
34
Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. zhangxinhui@genomics.cn.
35
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. casperlp@126.com.
36
BGI-Shenzhen, Shenzhen, 518083, China. wangjintu@genomics.cn.
37
China National Genebank, Shenzhen, 518083, China. chengle@genomics.cn.
38
BGI-Yunnan, Kunming, 650106, China. chengle@genomics.cn.
39
BGI-Shenzhen, Shenzhen, 518083, China. chenjieming@genomics.cn.
40
Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. chenjieming@genomics.cn.
41
BGI-Shenzhen, Shenzhen, 518083, China. ruanzhiqiang@genomics.cn.
42
Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. ruanzhiqiang@genomics.cn.
43
BGI-Shenzhen, Shenzhen, 518083, China. lijia1@genomics.cn.
44
Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. lijia1@genomics.cn.
45
College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China. lijia1@genomics.cn.
46
BGI-Shenzhen, Shenzhen, 518083, China. yuhui14@mails.ucas.ac.cn.
47
Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. yuhui14@mails.ucas.ac.cn.
48
College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China. yuhui14@mails.ucas.ac.cn.
49
BGI-Shenzhen, Shenzhen, 518083, China. pengchao@genomics.cn.
50
Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. pengchao@genomics.cn.
51
Shenzhen BGI Fisheries Sci & Tech Co. Ltd., Shenzhen, 518083, China. maxingyugood@163.com.
52
Zhenjiang BGI Fisheries Science & Technology Industrial Co. Ltd., Zhenjiang, 212000, China. maxingyugood@163.com.
53
Shenzhen BGI Fisheries Sci & Tech Co. Ltd., Shenzhen, 518083, China. xujunmin@genomics.cn.
54
Zhenjiang BGI Fisheries Science & Technology Industrial Co. Ltd., Zhenjiang, 212000, China. xujunmin@genomics.cn.
55
Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201204, China. heyou@sinap.ac.cn.
56
State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, 210029, China. njxzf@126.com.
57
Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China. xup@ffrc.cn.
58
BGI-Shenzhen, Shenzhen, 518083, China. wangjian@genomics.cn.
59
James D. Watson Institute of Genome Science, Hangzhou, 310008, China. wangjian@genomics.cn.
60
BGI-Shenzhen, Shenzhen, 518083, China. yanghm@genomics.cn.
61
James D. Watson Institute of Genome Science, Hangzhou, 310008, China. yanghm@genomics.cn.
62
BGI-Shenzhen, Shenzhen, 518083, China. wangj@genomics.cn.
63
Department of Biology, Ole Maaløes Vej 5, University of Copenhagen, DK-2200, Copenhagen, Denmark. wangj@genomics.cn.
64
Fauna & Flora International, Cambridge, CB1 2JD, UK. tony.whitten@fauna-flora.org.
65
BGI-Shenzhen, Shenzhen, 518083, China. xuxun@genomics.cn.
66
BGI-Shenzhen, Shenzhen, 518083, China. shiqiong@genomics.cn.
67
Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. shiqiong@genomics.cn.
68
Shenzhen BGI Fisheries Sci & Tech Co. Ltd., Shenzhen, 518083, China. shiqiong@genomics.cn.
69
Zhenjiang BGI Fisheries Science & Technology Industrial Co. Ltd., Zhenjiang, 212000, China. shiqiong@genomics.cn.

Abstract

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.

PMID:
26728391
PMCID:
PMC4698820
DOI:
10.1186/s12915-015-0223-4
[Indexed for MEDLINE]
Free PMC Article

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