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...

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Bibliographic Details
Published in:	Scientific data Vol. 10; no. 1; p. 330
Main Authors:	Libro, Pietro, Chiocchio, Andrea, De Rysky, Erika, Di Martino, Jessica, Bisconti, Roberta, Castrignanò, Tiziana, Canestrelli, Daniele
Format:	Journal Article
Language:	English
Published:	London Nature Publishing Group UK 27-05-2023 Nature Publishing Group Nature Portfolio
Subjects:	631/114/1314 631/158/2452 631/337/2019 Animals Annotations Biodiversity Data Descriptor Developmental biology Gene expression Gene Expression Profiling Gene mapping Genetic Association Studies High-Throughput Nucleotide Sequencing Homology Humanities and Social Sciences Larva - genetics Molecular Sequence Annotation multidisciplinary Proteomes Salamandra - genetics Salamandra salamandra Science Science (multidisciplinary) Transcriptome Transcriptomes
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Summary:	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.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 ObjectType-Undefined-3
ISSN:	2052-4463 2052-4463
DOI:	10.1038/s41597-023-02217-9