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The de novo transcriptome of the freshwater copepod Cyclops abyssorum tatricus reveals high-elevation adaptation

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Abstract

Copepods, small aquatic crustaceans, are one of the most abundant zooplankton in the world. These animals play a critical ecological role in aquatic ecosystems such as oceans, streams, or, as in this study, alpine lakes. In these ecosystems, copepods have adapted to stressful and dynamic environments, a process which can be investigated via comparative transcriptomics. An assembled transcriptome is a pre-requisite to applying transcriptomic tools in physiological research, but there are few transcriptome assemblies available for copepods. To address this gap, we assembled a de novo transcriptome of Cyclops abyssorum tatricus by merging Pacific Bioscience long reads from copepods collected in two lakes at two different time points. The final assembly consisted of 52,521 contigs with a BUSCO score of 80.7%. We annotated a total of 26,255 (49.99%) protein sequences using the eggNOG database. Gene ontology analyses revealed that most gene annotations were involved in cellular processes and signaling (34.61%). Comparisons with two other copepod species showed that the transcriptome assembly of C. abyssorum tatricus is enriched for cold acclimation genes, consistent with its long-term adaptation to cold water environments. This de novo transcriptome will enable comparative transcriptomic studies in this species, allowing us to investigate physiological adaptations to alpine environments.

Data availability

All elements of this study are available to the general public via the NCBI BioProject PRJNA1377012 database (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1377012/). This unannotated transcriptome shotgun assembly project has been deposited at DDBJ/EMBL/GenBank under the accession number GLLG00000000. The version described in this paper is the first version, GLLG01000000, while the two raw PacBio datasets are accessible via the accession numbers SAMN53755002 (run number: SRR36346890 in .bam or SRR37062719 in .fastq) and SAMN53755001 (run number: SRR36346891 in .bam or SRR37062720 in .fastq). No custom code has been used in the creation of the dataset for this article.

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Acknowledgements

We would like to thank Paulina Kalita, Ethan Salino and Eric Weniger for their help in the field. We are grateful to Rujuta Vaidya and Abdul Ada for their support on the statistical analysis.

Funding

This research was funded by the Austrian Science Fund (FWF) [grant DOI https://doi.org/10.55776/P35886 to B.T].

Author information

Authors and Affiliations

  1. Department of Ecology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria

    Placide Ambre & Tartarotti Barbara

  2. Department of Biological Sciences, A309 Life Sciences Annex, Louisiana State University, Baton Rouge, LA, 70803, USA

    Kelly Morgan

Authors

  1. Placide Ambre
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  2. Kelly Morgan
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  3. Tartarotti Barbara
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Contributions

A.P. collected and identified specimens, extracted RNA, performed bioinformatic and statistical analyses and interpretation, curated the data for publication in the repository, and wrote the manuscript. M.K. provided statistical support and reviewed and edited the manuscript. B.T. designed and supervised the study, acquired the funding and made critical manuscript revisions. All authors approved of the final manuscript.

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Placide Ambre or Tartarotti Barbara.

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The authors declare no competing interests.

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Ambre, P., Morgan, K. & Barbara, T. The de novo transcriptome of the freshwater copepod Cyclops abyssorum tatricus reveals high-elevation adaptation.
Sci Rep (2026). https://doi.org/10.1038/s41598-026-46084-x

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  • DOI: https://doi.org/10.1038/s41598-026-46084-x

Keywords

  • Zooplankton
  • Long-read PacBio sequencing
  • Gene ontology
  • Alpine lakes

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