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<p><i>Acartia tonsa</i> 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 <i>A. tonsa</i> 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 <i>de novo</i> transcriptome of <i>A. tonsa</i> 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 <i>A. tonsa</i> and, specifically, its response to currently used pesticides.</p>

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De novo transcriptome assembly of Acartia tonsa adults using Nanopore long-read sequencing

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年7月1日

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  • Florencia Mohamed,
  • Marco Picone,
  • Greta Battaggia,
  • Ilenia Urso,
  • Elisa Camatti,
  • Alessandro Vezzi,
  • Gabriele Sales

摘要

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.