GSE107213
Bolitoglossa vallecula reference transcriptome
The order Caudata of amphibians has been important in the study of tissue regeneration. The most complete genetic available data from salamanders are from Ambystoma mexicanum (Ambystomidae) and Notophthalmus viridescens (Salamandridae). Transcriptome data obtained with Next-generation sequencing technology has become a useful tool to discover new candidate genes in non-model organisms without a genome of reference. This study highlights the need of performing RNA-sequencing in other salamander species to compare and identify important clusters of genes that could be modulating important biological process in amphibians. Here we describe a de novo reference transcriptome and its annotation of a non-model terrestrial salamander, Bolitoglossa vallecula (Caudata: Plethodontidae). For this purpose, we utilized genome protein databases from vertebrates, nucleotide sequences obtained for salamander species, and a de novo reference transcriptomes of Bolitoglossa ramosi to conduct a homology analysis. While the majority of the transcripts recovered homologs with Bolitoglossa ramosi, only a minority of the data (22%; n= 94,739) recovered homologs with other vertebrates. We also compared the transcriptome profile of skin tissue between these Bolitoglossa species. We found a group of antimicrobial peptides, such as cathelicidins, which have been not previously described in salamanders and could be important modulators of different biological process. All animals used in this work were collected under the Contract on Genetic Access for scientific research for non commercial profit (Contrato de acceso a recursos genéticos para la investigación científica sin interés commercial) to Resources number 118–2015. Overall design: To assembly the reference transcriptome, we sequenced individual samples which had pools of different adult animals we did pools of different animals to get limb tissue (two biological replicates, n = 2 animals), heart (one biological replicate, n = 1 animal), skin (one biological replicate, n = 1 animal). All animals used in this work were collected under the Contract on Genetic Access for scientific research for non commercial profit (Contrato de acceso a recursos genéticos para la investigación científica sin interés commercial) to Resources number 118–2015, which was delivered by the Ministerio del Medio Ambiente (Ministry of Environment) of Colombia to the Principal Investigator.