Transcriptome Profiling of the Toadlet Brachycephalus garbeana (Amphibia: Anura: Brachycephalidae)

The genus Brachycephalus is a group of toads endemic to the Atlantic Forest of Brazil. Features such as the reduced body size, marked phenotypic variation and occurrence in allopatry suggest that the genus is an interesting model for evolutionary studies. Knowledge about phylogenetic relationships is still uncertain and to improve the resolution of the topologies already available for the genus, it is paramount to increase the number of loci used in phylogenetic reconstructions. In order to access thousands of species-specific gene sequences that could be used for primer or probe design, we characterized the first transcritptome for a Brachycephalus species. RNA-seq of B. garbeana generated over 13 gigabases of data. The reads were de novo assembled in 31,707 contigs (N50 of 1,322 bp) providing the first reference transcriptome for this group. A BLASTx against the nr database revealed homology for 18,211 sequences (57%) with most of the top-hits associated with Xenopus tropicalis and X. laevis proteins. More than 100,000 GO terms were assigned to 12,866 contigs and almost 50% of the terms belonged to the biological process ontology. The level 2 ontologies “catalytic activity”, “binding”, “metabolic process” and “cellular process” were the most represented. KEGG analyses identified 3,077 contigs involved in 126 different pathways and comprising over 600 enzymes. Sequences associated with nucleotide metabolism accounted alone for 11% of those with hit in the KEGG. The assembly and annotation of thousands of sequences for Brachycephalus are now providing useful information for the selection of genes suitable for phylogenetic studies.