Brain de novo transcriptome assembly of a toad species showing polymorphic anti-predatory behavior

Abstract

Understanding the genomic underpinnings of antipredatory behaviors is a hot topic in eco-evolutionary research. Yellow-bellied toad of the genus Bombina are textbook examples of the deimatic display, a time-structured behavior aimed at startling predators. Here, we generated the first de novo brain transcriptome of the Apennine yellow-bellied toad Bombina pachypus, a species showing inter-individual variation in the deimatic display. Through Rna-Seq experiments on a set of individuals showing distinct behavioral phenotypes, we generated 316,329,573 reads, which were assembled and annotated. The high-quality assembly was confirmed by assembly validators and by aligning the contigs against the de novo transcriptome with a mapping percentage higher than 91.0%. The homology annotation with DIAMOND (blastx) led to 77,391 contigs annotated on Nr, Swiss Prot and TrEMBL, whereas the domain and site protein prediction made with InterProScan led to 4747 GO-annotated and 1025 KEGG-annotated contigs. The B. pachypus transcriptome described here will be a valuable resource for further studies on the genomic underpinnings of behavioral variation in amphibians.

Fig. 1

The cleaned reads from all samples were assessed with FastQC and visualized with MultiQC. (a) Read count distribution for mean sequence quality. (b) Mean quality scores distribution. (c) Read length distribution. (d) Per Sequence GC Content.

Fig. 2

Workflow of the bioinformatic pipeline, from raw input data to annotated contigs, for the de novo transcriptome assembly of B. pachypus.

Fig. 3

Venn diagrams for the number of contigs annotated with DIAMOND (BLASTX (a) and BLASTP (b) functions) against the three databases: Nr, SwissProt, TREMBL.

Fig. 4

Most represented species and gene product hits. Top 10 best species (a) and protein (b) hits present in the reference database (Nr, BLASTX).

Fig. 5

Most represented species and gene product hits. Top 10 best species (a) and protein (b) hits present in the reference database (Nr, BLASTP).

Fig. 6

For each sample we have in blue the representation of total paired-reads, in orange the total paired-reads after the adapter removal and quality trimming and in azure we have the trimmed paired-reads mapped mapped-back against the B. pachypus assembled de novo transcriptome.