Data from: Microsatellite marker development by multiplex Ion Torrent PGM sequencing: a case study of the endangered Odorrana narina complex of frogs

The endangered Ryukyu tip-nosed frog Odorrana narina and its related species, Odorrana amamiensis, Odorrana supranarina, and Odorrana utsunomiyaorum, belong to the family Ranidae and are endemically distributed in Okinawa (O. narina), Amami and Tokunoshima (O. amamiensis), and Ishigaki and Iriomote (O. supranarina and O. utsunomiyaorum) Islands. Because of varying distribution patterns, this species complex is an intrinsic model for speciation and adaptation. For effective conservation and molecular ecological studies, further genetic information is needed. For rapid, cost-effective development of several microsatellite markers for these and 2 other species, we used next-generation sequencing technology of Ion Torrent PGM™. Distribution patterns of repeat motifs of microsatellite loci in these modern frog species (Neobatrachia) were similarly skewed. We isolated and characterized 20 new microsatellite loci of O. narina and validated cross-amplification in the three-related species. Seventeen, 16, and 13 loci were cross-amplified in O. amamiensis, O. supranarina, and O. utsunomiyaorum, respectively, reflecting close genetic relationships between them. Mean number of alleles and expected heterozygosity of newly isolated loci varied depending on the size of each inhabited island. Our findings suggested the suitability of Ion Torrent PGM™ for microsatellite marker development. The new markers developed for the O. narina complex will be applicable in conservation genetics and molecular ecological studies.

濒危的琉球尖吻蛙（Ryukyu tip-nosed frog，Odorrana narina）及其近缘物种Odorrana amamiensis、Odorrana supranarina与Odorrana utsunomiyaorum，均隶属于蛙科（Ranidae），其分布具有严格的地域性：冲绳岛特有O. narina，奄美大岛与德之岛特有O. amamiensis，石垣岛与西表岛特有O. supranarina和O. utsunomiyaorum。由于该物种复合体的分布格局存在显著差异，其成为物种形成与适应性演化研究的理想天然模型。为推进高效的保护生物学与分子生态学研究，亟需补充更多遗传信息。为快速且经济高效地为上述物种及另外2个物种开发多款微卫星（microsatellite）分子标记，我们采用了Ion Torrent PGM™下一代测序技术。本次研究涉及的现代蛙类（新蛙亚目Neobatrachia）中，微卫星位点的重复基序分布模式同样呈现偏态分布。我们成功分离并鉴定了O. narina的20个全新微卫星位点，并验证了其在3个近缘物种中的跨物种扩增效果：O. amamiensis、O. supranarina和O. utsunomiyaorum中分别有17、16和13个位点可实现跨物种扩增，这反映出它们之间紧密的遗传亲缘关系。新分离位点的平均等位基因数与期望杂合度，会因各物种所栖息岛屿的面积不同而存在差异。本研究结果证实，Ion Torrent PGM™平台适用于微卫星分子标记的开发。本次为O. narina物种复合体开发的全新分子标记，可应用于保护遗传学与分子生态学相关研究。