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Global discovery and characterization of small non-coding RNAs in marine microalgae

AuthorsLópez-Gomollón, Sara CSIC ORCID; Beckers, Matthew; Rathjen, Tina; Moxon, Simon; Maumus, Florian; Mohorianu, Irina; Moulton, Vincent; Dalmay, Tamas; Mock, Thomas
Marine phytoplankton
Non- coding RNAs
Small RNA
Issue Date20-Aug-2014
PublisherBioMed Central
CitationBMC Genomics 15: 697 (2014)
Abstract[Background] Marine phytoplankton are responsible for 50% of the CO2 that is fixed annually worldwide and contribute massively to other biogeochemical cycles in the oceans. Diatoms and coccolithophores play a significant role as the base of the marine food web and they sequester carbon due to their ability to form blooms and to biomineralise. To discover the presence and regulation of short non-coding RNAs (sRNAs) in these two important phytoplankton groups, we sequenced short RNA transcriptomes of two diatom species (Thalassiosira pseudonana, Fragilariopsis cylindrus) and validated them by Northern blots along with the coccolithophore Emiliania huxleyi.
[Results] Despite an exhaustive search, we did not find canonical miRNAs in diatoms. The most prominent classes of sRNAs in diatoms were repeat-associated sRNAs and tRNA-derived sRNAs. The latter were also present in E. huxleyi. tRNA-derived sRNAs in diatoms were induced under important environmental stress conditions (iron and silicate limitation, oxidative stress, alkaline pH), and they were very abundant especially in the polar diatom F. cylindrus (20.7% of all sRNAs) even under optimal growth conditions.
[Conclusions] This study provides first experimental evidence for the existence of short non-coding RNAs in marine microalgae. Our data suggest that canonical miRNAs are absent from diatoms. However, the group of tRNA-derived sRNAs seems to be very prominent in diatoms and coccolithophores and maybe used for acclimation to environmental conditions.
Description13 p., 5 figs, 6 additional files. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.
Additional file 1 (Format: PDF): Supplementary figures (S1 to S6). Additional file 2 (Format: CSV): Predicted miRNA annotations. Additional file 3 (Format: XLSX): Feature count table. Additional file 4 (Format: CSV): Probe sequences. Additional file 5 (Format: CSV): tRNAscan predicted tRNAs. Additional file 6 (Format: CSV): tRNA summary.
Publisher version (URL)http://dx.doi.org/10.1016/j.envexpbot.2014.06.016
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