Robert S. Cornman Laura S. Robertson 2014 We developed genetic resources for two North American frogs, <i>Lithobates clamitans</i> and <i>Pseudacris regilla</i>, widespread native amphibians that are potential indicator species of environmental health. For both species, mRNA from multiple tissues was sequenced using 454 technology. <i>De novo</i> assemblies with Mira3 resulted in 50 238 contigs (N50 = 687 bp) and 48 213 contigs (N50 = 686 bp) for <i>L. clamitans</i> and <i>P. regilla</i>, respectively, after clustering with CD-Hit-EST and purging contigs below 200 bp. We performed BLASTX similarity searches against the <i>Xenopus tropicalis</i> 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 resequencing across a broad taxonomic range, we performed an additional assembly of public short-read transcriptome data derived from two species of the genus <i>Rana</i> and identified reciprocal best TBLASTX matches among all assemblies. Although <i>P. regilla</i>, a hylid frog, is substantially more diverged from the ranid species, we identified 56 genes that were sufficiently conserved to allow nondegenerate 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. application/pdf 10.1111/1755-0998.12164 en Wiley Transcriptome resources for the frogs <i>Lithobates clamitans</i> and <i>Pseudacris regilla</i>, emphasizing antimicrobial peptides and conserved loci for phylogenetics article