Journal Article

Whole-genome sequence of the Tibetan frogNanorana parkeriand the comparative evolution of tetrapod genomes

Chen, Hong-Man, Irwin, David, Xiong, Zi-Jun, Zhang, Bao-Lin, Yang, Min-Min, Zhang, Guo-Jie, Hillis, David M., Xiang, Xue-Yan, Feng, Shao-Hong, Zhou, Wei-Wei, Huang, Chao, Liu, Shi-Ping, Yang, Huan-Ming, Tu, Xiao-Long, Li, Fang, Wang, Jun, Zhou, Long, Wu, Dong-Dong, Sun, Yan-Bo, Wang, Lu, Che, Jing, Zhong, Li, Zhu, Chun-Ling, Zhang, Ya-Ping, Murphy, Robert W.

2015

Overview

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 ofXenopus 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 ofX. tropicalisand other vertebrates. This genome encodes more than 20,000 protein-coding genes, a number similar to that ofXenopus. Although the genome size ofNanoranais considerably larger than that ofXenopus(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. TheNanoranagenome offers an improved understanding of evolution of tetrapod genomes and also provides a genomic reference for other evolutionary studies.

• Publisher: National Academy of Sciences