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....
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-05-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-023-02217-9 |
| _version_ | 1797818229517713408 |
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| author | Pietro Libro Andrea Chiocchio Erika De Rysky Jessica Di Martino Roberta Bisconti Tiziana Castrignanò Daniele Canestrelli |
| author_facet | Pietro Libro Andrea Chiocchio Erika De Rysky Jessica Di Martino Roberta Bisconti Tiziana Castrignanò Daniele Canestrelli |
| author_sort | Pietro Libro |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-13T09:05:04Z |
| format | Article |
| id | doaj.art-aec672a8236647d9b9e7d6824754cfb1 |
| institution | Directory Open Access Journal |
| issn | 2052-4463 |
| language | English |
| last_indexed | 2024-03-13T09:05:04Z |
| publishDate | 2023-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj.art-aec672a8236647d9b9e7d6824754cfb12023-05-28T11:08:11ZengNature PortfolioScientific Data2052-44632023-05-011011910.1038/s41597-023-02217-9De novo transcriptome assembly and annotation for gene discovery in Salamandra salamandra at the larval stagePietro Libro0Andrea Chiocchio1Erika De Rysky2Jessica Di Martino3Roberta Bisconti4Tiziana Castrignanò5Daniele Canestrelli6Università degli Studi della Tuscia, Dipartimento di Scienze ecologiche e Biologiche, Largo dell’Università sncUniversità degli Studi della Tuscia, Dipartimento di Scienze ecologiche e Biologiche, Largo dell’Università sncUniversità degli Studi della Tuscia, Dipartimento di Scienze ecologiche e Biologiche, Largo dell’Università sncUniversità degli Studi della Tuscia, Dipartimento di Scienze ecologiche e Biologiche, Largo dell’Università sncUniversità degli Studi della Tuscia, Dipartimento di Scienze ecologiche e Biologiche, Largo dell’Università sncUniversità degli Studi della Tuscia, Dipartimento di Scienze ecologiche e Biologiche, Largo dell’Università sncUniversità degli Studi della Tuscia, Dipartimento di Scienze ecologiche e Biologiche, Largo dell’Università sncAbstract 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.https://doi.org/10.1038/s41597-023-02217-9 |
| spellingShingle | Pietro Libro Andrea Chiocchio Erika De Rysky Jessica Di Martino Roberta Bisconti Tiziana Castrignanò Daniele Canestrelli De novo transcriptome assembly and annotation for gene discovery in Salamandra salamandra at the larval stage Scientific Data |
| title | De novo transcriptome assembly and annotation for gene discovery in Salamandra salamandra at the larval stage |
| title_full | De novo transcriptome assembly and annotation for gene discovery in Salamandra salamandra at the larval stage |
| title_fullStr | De novo transcriptome assembly and annotation for gene discovery in Salamandra salamandra at the larval stage |
| title_full_unstemmed | De novo transcriptome assembly and annotation for gene discovery in Salamandra salamandra at the larval stage |
| title_short | De novo transcriptome assembly and annotation for gene discovery in Salamandra salamandra at the larval stage |
| title_sort | de novo transcriptome assembly and annotation for gene discovery in salamandra salamandra at the larval stage |
| url | https://doi.org/10.1038/s41597-023-02217-9 |
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