Annual transcriptome of a key zooplankton species, the copepod Calanus finmarchicus

Abstract

The copepod Calanus finmarchicus (Crustacea, Copepoda) is a key zooplanktonic species with a crucial position in the North Atlantic food web and significant contributor to ocean carbon flux. Like many other high latitude animals, it has evolved a programmed arrested development called diapause to cope with long periods of limited food supply, while growth and reproduction are timed to take advantage of seasonal peaks in primary production. However, anthropogenic warming is inducing changes in the expected timing of phytoplankton blooms, suggesting phenological mismatches with negative consequences for the N. Atlantic ecosystem. While diapause mechanisms are mainly studied in terrestrial arthropods, specifically on laboratory model species, such as the fruit fly Drosophila, the molecular investigations of annual rhythms in wild marine species remain fragmentary. Here we performed a rigorous year‐long monthly sampling campaign of C. finmarchicus in a Scottish Loch (UK; 56.45°N, 5.18°W) to generate an annual transcriptome. The mRNA of 36 samples (monthly triplicate of 25 individuals) have been deeply sequenced with an average depth of 137 ± 4 million reads (mean ± SE) per sample, aligned to the reference transcriptome, and filtered. We detail the quality assessment of the datasets and provide a high‐quality resource for the investigation of wild annual transcriptomic rhythms (35,357 components) in a key diapausing zooplanktonic species.

Revealing the profound influence of diapause on gene expression: Insights from the annual transcriptome of the copepod Calanus finmarchicus

“…Each copepod was orientated similarly for measurement, head to the left, on their right‐hand side. In all months, C. finmarchicus was the only Calanus species found (no C. helgolandicus ), supporting the assumption of extremely low risk of congener contamination (Payton, Noirot, et al., 2022). C. glacialis does not occur in this region.…”

“…The detailed procedure for generation of the transcriptomic dataset is available in Payton, Noirot, et al. (2022), and datasets are available in NCBI Sequence Read Archive (Payton et al., 2022a) and Figshare (Payton et al., 2022b). RNA sequencing was performed at the GeT‐PlaGe core facility, INRAE Toulouse, on normalized amounts of messenger RNA.…”

“…The 36 RNA sequencing libraries (three replicates per month) were prepared according to Illumina's protocols using the Illumina TruSeq Stranded mRNA sample prep kit to sequence mRNA on a NovaSeq S4 lane (Illumina) using a paired‐end read length of 2 × 150 pb with the Illumina NovaSeq Reagent Kits. The RNA sequencing libraries' read qualities were evaluated by checking the number of expected sequences, the GC percentage, the presence of adaptor, the overexpressed sequences, and putative contamination using FastQC (Payton, Noirot, et al., 2022). The quantification matrix was generated by alignment to the reference transcriptome (Lenz et al., 2014) using Salmon (Payton, Noirot, et al., 2022).…”

Equal bioavailability of omega‐3 PUFA from Calanus oil, fish oil and krill oil: A 12‐week randomized parallel study

“…Oils rich in omega‐3 polyunsaturated fatty acids (n3 PUFA) are mainly of marine origin such as cold‐water fish or krill. An alternative source of n3 PUFA is Calanus finmarchicus , a lipid‐rich copepod from the North Atlantic Ocean (Payton et al, 2022). The bonding form of n3 PUFA in CO is fundamentally different from conventional marine n3 oils.…”

Swimming Activity as an Indicator of Seasonal Diapause in the Copepod Calanus finmarchicus

“…Diapause is generally considered to be under endocrine control (e.g., Alldredge et al, 1984;Hirche, 1996;Baumgartner and Tarrant, 2017) and upstream expression of 'diapause associated' genes involved in antioxidative defense and lipid catabolism (Tarrant et al, 2008;Häfker et al, 2018a;Häfker et al, 2018b;Lenz et al, 2021;Payton et al, 2022). In addition, body size, lipid sac volume, and ambient temperature are all likely to affect metabolism at this time fueled by protein and lipid stores.…”