Hartline, D.K., M.C. Cieslak, A.M. Castelfranco, B. Lieberman, V. Roncalli & P.H. Lenz. (2023). De novo transcriptomes of six calanoid copepods (Crustacea): a resource for the discovery of novel genes. Scientific Data. 10(1):1-14. APR 2023.

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10.1038/s41597-023-02130-1 [view]

Hartline, D.K., M.C. Cieslak, A.M. Castelfranco, B. Lieberman, V. Roncalli & P.H. Lenz

2023

10(1):1-14. APR 2023

Publication

Available for editors   [request]

This study presents eight new high-quality de novo transcriptomes from six co-occurring species of calanoid copepods, the first published for Neocalanus plumchrus, N. cristatus, Eucalanus bungii and Metridia pacifica and additional ones for N. flemingeri and Calanus marshallae. They are ecologically-important members of sub-arctic North Pacific marine zooplankton communities. 'Omics data for this diverse and numerous taxonomic group are sparse and difficult to obtain. Total RNA from single individuals was used to construct gene libraries that were sequenced on an Illumina Next-Seq platform. Quality filtered reads were assembled with Trinity software and validated using multiple criteria. The study's primary purpose is to provide a resource for gene expression studies. The integrated database can be used for quantitative inter- and intra-species comparisons of gene expression patterns across biological processes. An example of an additional use is provided for discovering novel and evolutionarily-significant proteins within the Calanoida. A workflow was designed to find and characterize unannotated transcripts with homologies across de novo assemblies that have also been shown to be eco-responsive.

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