De novo transcriptome assembly and annotation for gene discovery in Salamandra salamandra at the larval stage

Abstract

Dispersal is a key process in ecology and evolutionary biology, as it shapes biodiversity patterns over space and time. Attitude to disperse is unevenly distributed among individuals within populations, and that individual personality can have pivotal roles in the shaping of this attitude. Here, we assembled and annotated the first de novo transcriptome of the head tissues of Salamandra salamandra from individuals, representative of distinct behavioral profiles. We obtained 1,153,432,918 reads, which were successfully assembled and annotated. The high-quality of the assembly was confirmed by three assembly validators. The alignment of contigs against the de novo transcriptome led to a mapping percentage higher than 94%. The homology annotation with DIAMOND led to 153,048 (blastx) and 95,942 (blastp) shared contigs, annotated on NR, Swiss-Prot and TrEMBL. The domain and site protein prediction led to 9850 GO-annotated contigs. This de novo transcriptome represents reliable reference for comparative gene expression studies between alternative behavioral types, for comparative gene expression studies within Salamandra, and for whole transcriptome and proteome studies in amphibians.

Fig. 1

Workflow of the bioinformatic pipeline, from raw data to annotated scripts, for the de novo transcriptome assembly of S. salamandra. Each step was progressively numbered.

Fig. 2

BUSCO assessment results.

Fig. 3

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 Salamandra salamandra assembled de novo transcriptome.

Fig. 4

Venn diagrams for the number of contigs annotated with DIAMOND (blastx and blastp functions) against the three databases: NCBI nr, Swiss-Prot, TREMBL.