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Evaluating the potential of direct RNA nanopore sequencing : metatranscriptomics highlights possible seasonal differences in a marine pelagic crustacean zooplankton community

Ilias Semmouri (UGent) , Karel De Schamphelaere (UGent) , Jan Mees (UGent) , Colin Janssen (UGent) and Jana Asselman (UGent)
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Abstract
The implementation of cost-effective monitoring programs for zooplankton remains challenging due to the requirements of taxonomical expertise and the high costs of sampling and species identification. To reduce costs, molecular methods have been proposed as alternatives to morphology-based monitoring. Metatranscriptomics can contribute to promote both cost-effectiveness and accuracy of biological assessments of aquatic ecosystems. Here, we describe and evaluate the construction of a metatranscriptome dataset from a pelagic crustacean zooplankton community. We sampled zooplankton in one marine station, named LW02, in the North Sea, in both winter and summer, and generated transcripts using Oxford Nanopore Technology (ONT), a third-generation nanopore-based sequencing technology. ONT is, uniquely, capable of sequencing RNA directly, rather than depending on reverse transcription and PCR, and applicable to be used directly in the field. We found that metatranscriptomics is capable of species detection, including screening for the presence of endoparasites, hence competing with morphological identification. Taxonomic analysis based on ribosomal 18S transcripts identified calanoid copepods, particularly Temora longicornis and Acartia clausi, as the most abundant community members. Moreover, up to 40.4% and 50.5% of all sequences could be assigned to predicted genes in the winter and summer sample, respectively. The most abundant mRNA transcripts with known function coded for essential metabolic processes. GO term annotation revealed that genes involved in glycolytic and translation-related processes were most expressed in the community. Although small in scale, our study provides the basis for future efforts to characterize the metatranscriptome of marine zooplankton communities and its application in biomonitoring programs.
Keywords
Community transcriptomics, Metabarcoding, North sea, Copepods, Temora longicornis, MinIon, NORTH-SEA, PLANKTON COMMUNITIES, BIODIVERSITY, DNA, TRANSCRIPTION, ANNOTATION, BLAST2GO, POSITION, ECOLOGY, DEFENSE

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MLA
Semmouri, Ilias, et al. “Evaluating the Potential of Direct RNA Nanopore Sequencing : Metatranscriptomics Highlights Possible Seasonal Differences in a Marine Pelagic Crustacean Zooplankton Community.” MARINE ENVIRONMENTAL RESEARCH, vol. 153, 2020.
APA
Semmouri, I., De Schamphelaere, K., Mees, J., Janssen, C., & Asselman, J. (2020). Evaluating the potential of direct RNA nanopore sequencing : metatranscriptomics highlights possible seasonal differences in a marine pelagic crustacean zooplankton community. MARINE ENVIRONMENTAL RESEARCH, 153.
Chicago author-date
Semmouri, Ilias, Karel De Schamphelaere, Jan Mees, Colin Janssen, and Jana Asselman. 2020. “Evaluating the Potential of Direct RNA Nanopore Sequencing : Metatranscriptomics Highlights Possible Seasonal Differences in a Marine Pelagic Crustacean Zooplankton Community.” MARINE ENVIRONMENTAL RESEARCH 153.
Chicago author-date (all authors)
Semmouri, Ilias, Karel De Schamphelaere, Jan Mees, Colin Janssen, and Jana Asselman. 2020. “Evaluating the Potential of Direct RNA Nanopore Sequencing : Metatranscriptomics Highlights Possible Seasonal Differences in a Marine Pelagic Crustacean Zooplankton Community.” MARINE ENVIRONMENTAL RESEARCH 153.
Vancouver
1.
Semmouri I, De Schamphelaere K, Mees J, Janssen C, Asselman J. Evaluating the potential of direct RNA nanopore sequencing : metatranscriptomics highlights possible seasonal differences in a marine pelagic crustacean zooplankton community. MARINE ENVIRONMENTAL RESEARCH. 2020;153.
IEEE
[1]
I. Semmouri, K. De Schamphelaere, J. Mees, C. Janssen, and J. Asselman, “Evaluating the potential of direct RNA nanopore sequencing : metatranscriptomics highlights possible seasonal differences in a marine pelagic crustacean zooplankton community,” MARINE ENVIRONMENTAL RESEARCH, vol. 153, 2020.
@article{8634849,
  abstract     = {The implementation of cost-effective monitoring programs for zooplankton remains challenging due to the requirements of taxonomical expertise and the high costs of sampling and species identification. To reduce costs, molecular methods have been proposed as alternatives to morphology-based monitoring. Metatranscriptomics can contribute to promote both cost-effectiveness and accuracy of biological assessments of aquatic ecosystems. Here, we describe and evaluate the construction of a metatranscriptome dataset from a pelagic crustacean zooplankton community. We sampled zooplankton in one marine station, named LW02, in the North Sea, in both winter and summer, and generated transcripts using Oxford Nanopore Technology (ONT), a third-generation nanopore-based sequencing technology. ONT is, uniquely, capable of sequencing RNA directly, rather than depending on reverse transcription and PCR, and applicable to be used directly in the field. We found that metatranscriptomics is capable of species detection, including screening for the presence of endoparasites, hence competing with morphological identification. Taxonomic analysis based on ribosomal 18S transcripts identified calanoid copepods, particularly Temora longicornis and Acartia clausi, as the most abundant community members. Moreover, up to 40.4% and 50.5% of all sequences could be assigned to predicted genes in the winter and summer sample, respectively. The most abundant mRNA transcripts with known function coded for essential metabolic processes. GO term annotation revealed that genes involved in glycolytic and translation-related processes were most expressed in the community. Although small in scale, our study provides the basis for future efforts to characterize the metatranscriptome of marine zooplankton communities and its application in biomonitoring programs.},
  articleno    = {104836},
  author       = {Semmouri, Ilias and De Schamphelaere, Karel and Mees, Jan and Janssen, Colin and Asselman, Jana},
  issn         = {0141-1136},
  journal      = {MARINE ENVIRONMENTAL RESEARCH},
  keywords     = {Community transcriptomics,Metabarcoding,North sea,Copepods,Temora longicornis,MinIon,NORTH-SEA,PLANKTON COMMUNITIES,BIODIVERSITY,DNA,TRANSCRIPTION,ANNOTATION,BLAST2GO,POSITION,ECOLOGY,DEFENSE},
  language     = {eng},
  pages        = {11},
  title        = {Evaluating the potential of direct RNA nanopore sequencing : metatranscriptomics highlights possible seasonal differences in a marine pelagic crustacean zooplankton community},
  url          = {http://dx.doi.org/10.1016/j.marenvres.2019.104836},
  volume       = {153},
  year         = {2020},
}

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