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Open Access Highly Accessed Research article

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

Sara Lopez-Gomollon15, Matthew Beckers2, Tina Rathjen16, Simon Moxon27, Florian Maumus3, Irina Mohorianu1, Vincent Moulton2, Tamas Dalmay1* and Thomas Mock4*

Author Affiliations

1 School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK

2 School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, UK

3 UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles 78026, France

4 School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, UK

5 Current address: Estación Experimental Aula Dei, CSIC (Consejo Superior de Investigaciones Científicas), 50059 Zaragoza, Spain

6 Current address: Commonwealth Scientific and Industrial Research Organization Plant Industry, Canberra, Australian Capital Territory 2601, Australia

7 Current address: The Genome Analysis Centre, Norwich NR4 7UH, UK

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BMC Genomics 2014, 15:697  doi:10.1186/1471-2164-15-697

Published: 20 August 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.

Keywords:
Coccolithophores; Diatoms; Growth; Marine phytoplankton; MicroRNA; Non-coding RNAs; Small RNA; Stress; tRNA