The Sinocyclocheilus cavefish genome provides insights into cave adaptation

CORC > 昆明动物研究所 > 昆明动物研究所 > 遗传资源与进化国家重点实验室 > 系统进化与生物地理学

	The Sinocyclocheilus cavefish genome provides insights into cave adaptation
	Yang JX[*]1; Chen XL 2; Bai J 2,3,4; Fang DM 2,6; Qiu Y 2,3,5; Jiang WS 1; Yuan H 2; Bian C 2,3; Lu J 2,7; He SY 2,7
刊名	BMC BIOLOGY
	2016
卷号	14 期号:1 页码:e1
关键词	Cavefish Genome Adaptation Evolution Qinghai-Tibetan Plateau Sinocyclocheilus
通讯作者	yangjx@mail.kiz.ac.cn
合作状况	其它
英文摘要	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.
收录类别	SCI
资助信息	We acknowledge financial support from the joint project by the Yunnan Provincial Science and Technology Department and Yunnan Provincial Environmental Protection Department (Ottelia & Golden-line barbel Project 2012CA014) and the grant for the Lake Dianchi Freshwater Biodiversity Restoration Project (World Bank: GEF TF051795) to Junxing Yang; the Shenzhen Key Lab of Marine Genomics (CXB201108250095A), the Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals (2013B090800017) and the China 863 Project (2012AA10A407-2) to Qiong Shi; and the Yunnan Special Program for BGI-Yunnan (2013DA008) and the Cultivation of Backup Young and Middle-aged Acad
语种	英语
内容类型	期刊论文
源URL	[http://159.226.149.26:8080/handle/152453/9520]
专题	昆明动物研究所_系统进化与生物地理学昆明动物研究所_遗传资源与进化国家重点实验室昆明动物研究所_东南亚野生动物多样性
作者单位	1.State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China. 2.2 BGI-Shenzhen, Shenzhen 518083, China 3.Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen 518083, China 4.Fauna & Flora International, Cambridge CB1 2JD, UK 5.China National Genebank, Shenzhen 518083, China 6.Agricultural Genomes Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China 7.College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China 8.School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China 9.BGI-Yunnan, Kunming 650106, China 10.Shenzhen BGI Fisheries Sci & Tech Co. Ltd., Shenzhen 518083, Chi
推荐引用方式 GB/T 7714	Yang JX[*],Chen XL,Bai J,et al. The Sinocyclocheilus cavefish genome provides insights into cave adaptation[J]. BMC BIOLOGY,2016,14(1):e1.
APA	Yang JX[].,Chen XL.,Bai J.,Fang DM.,Qiu Y.,...&Shi Q[].(2016).The Sinocyclocheilus cavefish genome provides insights into cave adaptation.BMC BIOLOGY,14(1),e1.
MLA	Yang JX[*],et al."The Sinocyclocheilus cavefish genome provides insights into cave adaptation".BMC BIOLOGY 14.1(2016):e1.