Data from: Transcriptome resources for the frogs Lithobates clamitans and Pseudacris regilla, emphasizing antimicrobial peptides and conserved loci for phylogenetics

We developed genetic resources for two North American frogs, Lithobates clamitans and Pseudacris regilla, widespread native amphibians that are potential indicator species of environmental health. For both species, mRNA from multiple tissues was sequenced using 454 technology. De novo assemblies with Mira3 resulted in 50,238 contigs (N50 = 687 bp) and 48,213 contigs (N50 = 686 bp) for L. clamitans and P. regilla, respectively, after clustering with CD-Hit-EST and purging contigs below 200 bp. We performed BLASTX similarity searches against the Xenopus tropicalis proteome and, for predicted ORFs, HMMER similarity searches against the Pfam-A database. Because there is broad interest in amphibian immune factors, we manually annotated putative antimicrobial peptides. To identify conserved regions suitable for amplicon re-sequencing across a broad taxonomic range, we performed an additional assembly of public short-read transcriptome data derived from two species of the genus Rana and identified reciprocal best TBLASTX matches among all assemblies. Although P. regilla, a hylid frog, is substantially more diverged from the ranid species, we identified 56 genes that were sufficiently conserved to allow non-degenerate primer design with Primer3. In addition to providing a foundation for comparative genomics and quantitative gene expression analysis, our results enable quick development of nuclear sequence-based markers for phylogenetics or population genetics.

本研究针对两种北美本土两栖蛙类——美洲绿蛙（*Lithobates clamitans*）与太平洋树蛙（*Pseudacris regilla*）——开发了遗传资源；二者均为广泛分布的本土物种，亦是潜在的环境健康指示物种。针对这两个物种，我们利用454测序技术对多组织样本的mRNA进行了测序。使用Mira3软件进行从头组装后，再通过CD-Hit-EST进行聚类并剔除长度低于200 bp的重叠群（contig），最终美洲绿蛙得到50238条重叠群（N50=687 bp），太平洋树蛙得到48213条重叠群（N50=686 bp）。我们针对热带爪蟾（*Xenopus tropicalis*）蛋白质组开展了BLASTX相似性检索；针对预测得到的开放阅读框（ORF, Open Reading Frame），通过HMMER软件针对Pfam-A数据库进行了相似性检索。鉴于两栖动物免疫因子相关研究广受关注，我们对推定的抗菌肽进行了人工注释。为筛选适用于宽泛分类群的扩增子重测序保守区域，我们对公共数据库中来源于蛙属（*Rana*）两个物种的短读长转录组数据开展了额外组装，并在所有组装结果中鉴定出双向最佳TBLASTX匹配基因。尽管太平洋树蛙作为雨蛙科（Hylidae）物种，与蛙科（Ranidae）物种的演化分化程度较高，但我们仍鉴定出56个足够保守的基因，可通过Primer3软件设计非简并引物。本研究结果不仅为比较基因组学与基因定量表达分析提供了研究基础，同时也可快速开发用于系统发育学或群体遗传学研究的核基因序列标记。