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
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;
China National GeneBank and Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China;
Proc Natl Acad Sci U S A. 2015 Mar 17;112(11):E1257-62. doi: 10.1073/pnas.1501764112. Epub 2015 Mar 2.
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.
高效测序技术的发展使得大量基因组可用于进化研究。然而，所有两栖动物只有一个基因组可供使用，即热带爪蟾的基因组，它与大多数蛙类的亲缘关系较远。超过96%的蛙类属于新蛙亚目，而该类群尚无基因组。两栖动物基因组的这种匮乏极大地限制了对两栖动物的基因组研究，更广泛地说，限制了我们对四足动物基因组进化的理解。为填补这一空白，我们提供了青藏高原蛙高山倭蛙的从头基因组，并将其与热带爪蟾及其他脊椎动物的基因组进行比较。该基因组编码超过20,000个蛋白质编码基因，数量与爪蟾的相似。尽管高山倭蛙的基因组大小比爪蟾的大得多（2.3Gb对1.5Gb），但大部分差异是由于两个基因组中转座元件的数量不同。尽管这两种蛙已经分化了约2.66亿年，但它们仍表现出相当程度的全基因组共线性，这表明无尾两栖类的DNA结构进化速度较慢。多基因组共线性模块进一步表明，两栖动物的染色体间重排比哺乳动物少，但染色体内重排速率相当。我们的分析还鉴定出11Mb的无尾两栖类特异性高度保守元件，这将有助于蛙类的比较基因组分析。高山倭蛙基因组有助于更好地理解四足动物基因组的进化，也为其他进化研究提供了基因组参考。
