Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes.
The development of efficient sequencing techniques has resulted in large numbers of genomes being available for evolutionary studies. However, only one genome is available for all amphibians, that of Xenopus tropicalis, which is distantly related from the majority of frogs. More than 96% of frogs belong to the Neobatrachia, and no genome exists for this group. This dearth of amphibian genomes greatly restricts genomic studies of amphibians and, more generally, our understanding of tetrapod genome evolution. To fill this gap, we provide the de novo genome of a Tibetan Plateau frog, Nanorana parkeri, and compare it to that of X. tropicalis and other vertebrates. This genome encodes more than 20,000 protein-coding genes, a number similar to that of Xenopus. Although the genome size of Nanorana is considerably larger than that of Xenopus (2.3 vs. 1.5 Gb), most of the difference is due to the respective number of transposable elements in the two genomes. The two frogs exhibit considerable conserved whole-genome synteny despite having diverged approximately 266 Ma, indicating a slow rate of DNA structural evolution in anurans. Multigenome synteny blocks further show that amphibians have fewer interchromosomal rearrangements than mammals but have a comparable rate of intrachromosomal rearrangements. Our analysis also identifies 11 Mb of anuran-specific highly conserved elements that will be useful for comparative genomic analyses of frogs. The Nanorana genome offers an improved understanding of evolution of tetrapod genomes and also provides a genomic reference for other evolutionary studies.
State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
Yan-Bo
YB
Sun
China National GeneBank and Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China;
Zi-Jun
ZJ
Xiong
China National GeneBank and Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, Sichuan University, Chengdu 610064, China;
Xue-Yan
XY
Xiang
China National GeneBank and Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China; School of Bioscience and Biotechnology, South China University of Technology, Guangzhou 510641, China;
Shi-Ping
SP
Liu
State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
Wei-Wei
WW
Zhou
State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Science, Chinese Academy of Sciences, Kunming 650204, China;
Xiao-Long
XL
Tu
Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming 650091, China;
Li
L
Zhong
Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming 650091, China;
Lu
L
Wang
State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
Dong-Dong
DD
Wu
State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming 650091, China;
Bao-Lin
BL
Zhang
State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
Chun-Ling
CL
Zhu
State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
Min-Min
MM
Yang
State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
Hong-Man
HM
Chen
China National GeneBank and BGI-Shenzhen, Shenzhen 518083, China;
Fang
F
Li
China National GeneBank and BGI-Shenzhen, Shenzhen 518083, China;
Long
L
Zhou
China National GeneBank and BGI-Shenzhen, Shenzhen 518083, China;
Shao-Hong
SH
Feng
China National GeneBank and BGI-Shenzhen, Shenzhen 518083, China; School of Bioscience and Biotechnology, South China University of Technology, Guangzhou 510641, China;
Chao
C
Huang
China National GeneBank and BGI-Shenzhen, Shenzhen 518083, China; Centre for Social Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark;
Guo-Jie
GJ
Zhang
State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Department of Laboratory Medicine and Pathobiology and Banting and Best Diabetes Centre, University of Toronto, Toronto, ON, M5S 1A8, Canada;
David
D
Irwin
Department of Integrative Biology and Center for Computational Biology and Bioinformatics, University of Texas at Austin, Austin, TX 78712; dhillis@austin.utexas.edu chej@mail.kiz.ac.cn wangjun30@gmail.com zhangyp@mail.kiz.ac.cn.
David M
DM
Hillis
State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, M5S 2C6, Canada;
Robert W
RW
Murphy
BGI-Shenzhen, Shenzhen 518083, China; Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia; James D. Watson Institute of Genome Science, Hangzhou 310008, China;
Huan-Ming
HM
Yang
State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; dhillis@austin.utexas.edu chej@mail.kiz.ac.cn wangjun30@gmail.com zhangyp@mail.kiz.ac.cn.
Jing
J
Che
BGI-Shenzhen, Shenzhen 518083, China; Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark; Macau University of Science and Technology, Taipa, Macau 999078, China; and Department of Medicine, University of Hong Kong, Hong Kong dhillis@austin.utexas.edu chej@mail.kiz.ac.cn wangjun30@gmail.com zhangyp@mail.kiz.ac.cn.
Jun
J
Wang
State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming 650091, China; dhillis@austin.utexas.edu chej@mail.kiz.ac.cn wangjun30@gmail.com zhangyp@mail.kiz.ac.cn.
Ya-Ping
YP
Zhang
D000818:Animals; D001001:Anura / Q000235:genetics*; D001483:Base Sequence; D002645:Chickens / Q000235:genetics; D002875:Chromosomes / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics; D019143:Evolution, Molecular; D005260:Female; D016678:Genome / Q000235:genetics*; D006801:Humans; D005810:Multigene Family; D026801:Synteny / Q000235:genetics; D018609:Tibet
D004251:DNA Transposable Elements
chromosome rearrangement; de novo genome; highly conserved element; transposable elements