ArticleScientific data2023
De novo transcriptome assembly and annotation for gene discovery in Salamandra salamandra at the larval stage.
Article in Scientific data, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 10 citations in OpenAlex.
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- Commentary: a review of technical considerations for planning an RNA-Sequencing experiment.BMC genomics · 2025Review
- Bioinformatics perspectives on transcriptomics: A comprehensive review of bulk and single-cell RNA sequencing analyses.Quantitative biology (Beijing, China) · 2025Review
- Use of Field pathogenomics approach for Puccinia striiformis f. sp. tritici race identification and phylogenomic delineation in North India.World journal of microbiology & biotechnology · 2025Article
- HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets.BMC bioinformatics · 2025Article
- De novo transcriptome assembly of the Mediterranean sea-rock pool mosquitoes Aedes mariae and Aedes zammitii.Scientific data · 2025Article
- Behavioural underpinning of mito-nuclear discordances: insights from fire salamanders.Royal Society open science · 2024Article
- HPC-T-Annotator: an HPC tool for de novo transcriptome assembly annotation.BMC bioinformatics · 2024Article
- Integrated de novo transcriptome of Culex pipiens mosquito larvae as a resource for genetic control strategies.Scientific data · 2024Article
- De novo transcriptome assembly of an Antarctic nematode for the study of thermal adaptation in marine parasites.Scientific data · 2023Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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