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

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.

Automated summary

Dispersal is a crucial process in ecology and evolutionary biology, which shapes biodiversity patterns. Individual attitudes to disperse vary within populations and individual personality plays a key role in shaping these attitudes. In this study, we generated and annotated the first de novo transcriptome of head tissues from Salamandra salamandra individuals with distinct behavioral profiles. The resulting transcriptome provides a reliable reference for comparative gene expression studies and whole transcriptome and proteome studies in amphibians.