Details

Autor(en) / Beteiligte

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

Titel

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

Ist Teil von

• Proceedings of the National Academy of Sciences - PNAS, 2015-03, Vol.112 (11), p.E1257-E1262

Ort / Verlag

United States: National Academy of Sciences

Erscheinungsjahr

2015

Quelle

Elektronische Zeitschriftenbibliothek (Open access)

Beschreibungen/Notizen

• 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. Significance We provide a de novo genome of the Tibetan frog, Nanorana parkeri , and conduct a series of comparisons with other vertebrates. Approximately one-half of the genome of Nanorana consists of transposable elements (TEs). The frequencies and distributional patterns of TEs differ considerably between Nanorana and Xenopus , the only other amphibian for which a genome has been sequenced. The genomes of these two frogs exhibit substantial homologous synteny blocks with rare interchromosomal and intrachromosomal rearrangements. We also identify 11 Mb of amphibian-specific conserved elements comprising 217 genes. These highly conserved genes provide a basis for comparative genomic analyses throughout frogs.