RNA sequencing indicates widespread conservation of circadian clocks in marine zooplankton

Abstract

Zooplankton are important eukaryotic constituents of marine ecosystems characterized by limited motility in the water. These metazoans predominantly occupy intermediate trophic levels and energetically link primary producers to higher trophic levels. Through processes including diel vertical migration (DVM) and production of sinking pellets they also contribute to the biological carbon pump which regulates atmospheric CO2 levels. Despite their prominent role in marine ecosystems, and perhaps, because of their staggering diversity, much remains to be discovered about zooplankton biology. In particular, the circadian clock, which is known to affect important processes such as DVM has been characterized only in a handful of zooplankton species. We present annotated de novo assembled transcriptomes from a diverse, representative cohort of 17 marine zooplankton representing six phyla and eight classes. These transcriptomes represent the first sequencing data for a number of these species. Subsequently, using translated proteomes derived from this data, we demonstrate in silico the presence of orthologs to most core circadian clock proteins from model metazoans in all sequenced species. Our findings, bolstered by sequence searches against publicly available data, indicate that the molecular machinery underpinning endogenous circadian clocks is widespread and potentially well conserved across marine zooplankton taxa.

Deciphering the mitochondrial genome ofOikopleura dioica(Chordata: Tunicata: Appendicularia)

“…A total of 65 poly-T/A sites were found in the assembled O. dioica mitochondrial genome. By mapping (1) the mitochondrial transcripts identified from the EST from Norway, and (2) the RNA contigs assembled from publicly available RNA reads from mainland Japan (Wang, et al 2015) and the North Sea (Raghavan, et al 2023) onto the DNA sequence assembled from the ONT reads, we were able to confirm the editing of 59 of these 65 poly-T/A sites to 6U-sites (see an example in Figure 2 and supplementary table S2, Supplementary Material online). For the remaining 6 sites, no direct RNA evidence for editing exists as we could not detect RNA reads or ESTs that mapped to the corresponding region.…”

“…Illumina RNA reads from O. dioica specimens from Japan and the North Sea were downloaded from the National Center for Biotechnology Information (NCBI) (accessions: SRR1693762, SRR1693765, SRR1693766, and SRR1693767) (Wang, et al 2015), and the European Nucleotide Archive (ENA) (accessions: SRR20015061) (Raghavan, et al 2023), respectively. The reads were then assembled with IDBA-UD v.1.1.3 (Zhu, et al 2010) using default parameters.…”

Plasticity and seasonality of the vertical migration behaviour of Antarctic krill using acoustic data from fishing vessels

“…On a side note, the synchronized ascent of krill swarms from depths greater than 300 m during the dark winter months arguably occurred with ambient light levels below their visual perception threshold [76]. This may indicate the involvement of endogenous clocks to synchronize vertical migration behaviour with the diel light cycle [22,59,[77][78][79], as otherwise it would remain unclear how swarms would be able to time their vertical movements without visual cues.…”

“…Diel and seasonal vertical migration are an integral part of zooplankton, and especially krill, ecology [15][16][17] and of great importance for biogeochemical cycles [18,19], species interactions, and spatial distribution through advection by depth-varying ocean currents [20]. Investigating vertical migration behaviour also yields information about the physiological functioning of the migrating organisms [21,22] and contributes to our overall understanding of the marine pelagic ecosystem. Observations over many years have shown that krill swarms can ascend and descend in the water column in synchrony with the daily light cycle [23][24][25].…”