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 identi...

本研究针对两种北美蛙类——绿蛙（Lithobates clamitans）与太平洋树蛙（Pseudacris regilla）开发了遗传资源；二者均为分布广泛的本土两栖动物，亦是潜在的环境健康指示物种。针对这两个物种，我们采用454测序技术对多组织来源的mRNA进行了测序。使用Mira3完成从头组装后，再通过CD-Hit-EST进行聚类并剔除长度低于200 bp的重叠群（contig），最终绿蛙得到50238条重叠群，其N50长度为687 bp；太平洋树蛙得到48213条重叠群，其N50长度为686 bp。我们针对热带爪蟾（Xenopus tropicalis）蛋白质组开展了BLASTX相似性比对分析；对于预测得到的开放阅读框（ORF），则通过HMMER对Pfam-A数据库进行了相似性搜索。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手动注释。为鉴定适用于广泛分类类群的扩增子重测序的保守区域，我们对来自蛙属（Rana）两个物种的公共短读长转录组数据开展了额外组装，并得到了……