机构：[1]State Key Laboratory of Genetic Resources and Evolution, Kunming Instituteof Zoology, Chinese Academy of Sciences, Kunming 650223, China[2]BGI-Shenzhen, Shenzhen 518083, China[3]Shenzhen Key Lab of MarineGenomics, State Key Laboratory of Agricultural Genomics, Shenzhen 518083,China[4]Fauna & Flora International, Cambridge CB1 2JD, UK[5]China NationalGenebank, Shenzhen 518083, China[6]Agricultural Genomes Institute atShenzhen, 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 ofElectronic Science and Technology of China, Chengdu 610054, China[9]BGI-Yunnan, Kunming 650106, China[10]Shenzhen BGI Fisheries Sci & TechCo. Ltd., Shenzhen 518083, China[11]Zhenjiang BGI Fisheries Science &Technology Industrial Co. Ltd., Zhenjiang 212000, China[12]ShanghaiSynchrotron Radiation Facility, Shanghai Institute of Applied Physics, ChineseAcademy of Sciences, Shanghai 201204, China[13]State Key Laboratory ofReproductive Medicine, Department of Prenatal Diagnosis, Nanjing Maternityand Child Health Care Hospital, Nanjing Medical University, Nanjing 210029,China[14]Freshwater Fisheries Research Center, Chinese Academy of FisherySciences, Wuxi 214081, China[15]James D. Watson Institute of GenomeScience, Hangzhou 310008, China[16]Department of Biology, Ole Maaløes Vej5, University of Copenhagen, DK-2200 Copenhagen, Denmark.
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.
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.
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.
基金：
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 Academic Technology Leaders in Yunnan Province
(2014HB053) to Le Cheng.
语种：
外文
PubmedID：
中科院(CAS)分区：
出版当年[2016]版：
大类|1 区生物
小类|1 区生物学
最新[2023]版：
大类|1 区生物学
小类|1 区生物学
第一作者：
第一作者机构：[1]State Key Laboratory of Genetic Resources and Evolution, Kunming Instituteof Zoology, Chinese Academy of Sciences, Kunming 650223, China
共同第一作者：
通讯作者：
通讯机构：[2]BGI-Shenzhen, Shenzhen 518083, China[3]Shenzhen Key Lab of MarineGenomics, State Key Laboratory of Agricultural Genomics, Shenzhen 518083,China[10]Shenzhen BGI Fisheries Sci & TechCo. Ltd., Shenzhen 518083, China[11]Zhenjiang BGI Fisheries Science &Technology Industrial Co. Ltd., Zhenjiang 212000, China
生物