Article open access publication

Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes

Proceedings of the National Academy of Sciences of the United States of America, Proceedings of the National Academy of Sciences, ISSN 0027-8424

Volume 112, 11, 2015

DOI:10.1073/pnas.1501764112, Dimensions: pub.1026574330, PMC: PMC4371989, PMID: 25733869,

Authors

Xiong, Zi-Jun (2) (3) (4)
Xiang, Xue-Yan (2) (3) (4) (5)
Liu, Shi-Ping (2) (3) (4) (6)
Tu, Xiao-Long (1) (7)
Zhong, Li (8)
Wang, Lin (8)
Zhang, Bao-Lin (1) (8)
Li, Fang (3) (4)
Zhou, Long (3) (4)
Feng, Shao-Hong (3) (4)
Huang, Chao (3) (4) (6)
Zhang, Guo-Jie (3) (4) (9)
Irwin, David (1) (10) (11)
Yang, Huan-Ming (4) (14) (15)
Che, Jing (1)
Wang, Jun (4) (9) (15) (16) (17)
Zhang, Ya-Ping (1) (8)

Affiliations

Organisations

  1. (1) Kunming Institute of Zoology, grid.419010.d
  2. (2) Shenzhen Key Laboratory of Transomics Biotechnologies,
  3. (3) China National GeneBank and
  4. (4) Beijing Genomics Institute, grid.21155.32
  5. (5) Sichuan University, grid.13291.38
  6. (6) South China University of Technology, grid.79703.3a
  7. (7) Chinese Academy of Sciences, grid.9227.e
  8. (8) Yunnan University, grid.440773.3
  9. (9) University of Copenhagen, grid.5254.6, KU
  10. (10) Department of Laboratory Medicine and Pathobiology and
  11. (11) University of Toronto, grid.17063.33
  12. (12) The University of Texas at Austin, grid.89336.37
  13. (13) Royal Ontario Museum, grid.421647.2
  14. (14) James D. Watson Institute of Genome Science, Hangzhou 310008, China;
  15. (15) King Abdulaziz University, grid.412125.1
  16. (16) Macau University of Science and Technology, Taipa, Macau 999078, China; and
  17. (17) University of Hong Kong, grid.194645.b

Description

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.

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University of Copenhagen

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2015: Unused

Research area: Science & Technology

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2015: Level 2

Research area: Science & Technology

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Times Cited: 105

Field Citation Ratio (FCR): 14.14

Relative Citation ratio (RCR): 5.49

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