2023
DOI: 10.1093/nargab/lqad007
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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 … Show more

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Cited by 4 publications
(5 citation statements)
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“…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.…”
Section: Resultsmentioning
confidence: 99%
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“…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.…”
Section: Resultsmentioning
confidence: 99%
“…A total of 65 poly-A/T 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-A/T sites to 6Usites (see an example in Figure 2 and supplementary table S2, Supplementary Material online). Of note, we performed a barcoding analysis that supports the hypothesis that our DNA sample, the EST data, and the North Sea RNA reads originated from the same species, while the RNA reads from mainland Japan likely originated from a different species (see Materials and Methods, Masunaga et al 2022;Plessy et al 2024).…”
Section: Evidence Of Rrna Editingmentioning
confidence: 94%
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“…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.…”
Section: Diel Patternsmentioning
confidence: 99%
“…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].…”
Section: Introductionmentioning
confidence: 99%