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| Main Authors: | , , , , , , |
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| Format: | Artículo científico |
| Language: | en |
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Scientific data
2025
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| Online Access: | https://pubmed.ncbi.nlm.nih.gov/40593801/ |
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| _version_ | 1868266184087961601 |
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| author | Mohamed, Florencia Picone, Marco Battaggia, Greta Urso, Ilenia Camatti, Elisa Vezzi, Alessandro Sales, Gabriele |
| author_facet | Mohamed, Florencia Picone, Marco Battaggia, Greta Urso, Ilenia Camatti, Elisa Vezzi, Alessandro Sales, Gabriele Mohamed, Florencia Picone, Marco Battaggia, Greta Urso, Ilenia Camatti, Elisa Vezzi, Alessandro Sales, Gabriele |
| collection | PubMed - marine biology |
| contents | De novo transcriptome assembly of Acartia tonsa adults using Nanopore long-read sequencing. Mohamed, Florencia Picone, Marco Battaggia, Greta Urso, Ilenia Camatti, Elisa Vezzi, Alessandro Sales, Gabriele Transcriptome Animals Copepoda Nanopore Sequencing Neonicotinoids Molecular Sequence Annotation Acartia tonsa is a calanoid copepod with a cosmopolitan distribution. Its ecological relevance makes it a useful bioindicator organism for assessing the toxicity of various compounds. However, transcriptomic assemblies of A. tonsa using long-read technologies have not yet been described. The use of long-read sequencing technologies in transcriptomics allows the study of alternative splicing, structural variations and alternative polyadenylation sites. In this study, we present a de novo transcriptome of A. tonsa adult copepods exposed to different neonicotinoids obtained from Nanopore sequences. This transcriptome (261,560 total transcripts, with 31,291 representative sequences) exhibits 88.3% completeness and an N50 of 2,580 bases, showing better results than previous assemblies of the same organism. We also performed a full annotation by sequence homology (NR database), domain identification (InterProScan) and functional classification (Gene Ontology); 54.3% of representative transcripts were annotated in at least one database. Our transcriptome represents a solid baseline for further transcriptomic studies on A. tonsa and, specifically, its response to currently used pesticides. |
| format | Artículo científico |
| id | pubmed_40593801 |
| institution | PubMed |
| language | en |
| publishDate | 2025 |
| publisher | Scientific data |
| record_format | pubmed |
| spellingShingle | De novo transcriptome assembly of Acartia tonsa adults using Nanopore long-read sequencing. Mohamed, Florencia Picone, Marco Battaggia, Greta Urso, Ilenia Camatti, Elisa Vezzi, Alessandro Sales, Gabriele Transcriptome Animals Copepoda Nanopore Sequencing Neonicotinoids Molecular Sequence Annotation De novo transcriptome assembly of Acartia tonsa adults using Nanopore long-read sequencing. Mohamed, Florencia Picone, Marco Battaggia, Greta Urso, Ilenia Camatti, Elisa Vezzi, Alessandro Sales, Gabriele Transcriptome Animals Copepoda Nanopore Sequencing Neonicotinoids Molecular Sequence Annotation Acartia tonsa is a calanoid copepod with a cosmopolitan distribution. Its ecological relevance makes it a useful bioindicator organism for assessing the toxicity of various compounds. However, transcriptomic assemblies of A. tonsa using long-read technologies have not yet been described. The use of long-read sequencing technologies in transcriptomics allows the study of alternative splicing, structural variations and alternative polyadenylation sites. In this study, we present a de novo transcriptome of A. tonsa adult copepods exposed to different neonicotinoids obtained from Nanopore sequences. This transcriptome (261,560 total transcripts, with 31,291 representative sequences) exhibits 88.3% completeness and an N50 of 2,580 bases, showing better results than previous assemblies of the same organism. We also performed a full annotation by sequence homology (NR database), domain identification (InterProScan) and functional classification (Gene Ontology); 54.3% of representative transcripts were annotated in at least one database. Our transcriptome represents a solid baseline for further transcriptomic studies on A. tonsa and, specifically, its response to currently used pesticides. |
| title | De novo transcriptome assembly of Acartia tonsa adults using Nanopore long-read sequencing. |
| topic | Transcriptome Animals Copepoda Nanopore Sequencing Neonicotinoids Molecular Sequence Annotation |
| url | https://pubmed.ncbi.nlm.nih.gov/40593801/ |