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

Lopez-Gomollon, Sara, Beckers, Matthew, Rathjen, Tina, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Maumus, Florian, Mohorianu, Irina, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Mock, Thomas ORCID: https://orcid.org/0000-0001-9604-0362 (2014) Global discovery and characterization of small non-coding RNAs in marine microalgae. BMC Genomics, 15 (1). ISSN 1471-2164

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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.

Item Type:	Article
Additional Information:	© 2014 Lopez-Gomollon et al This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Uncontrolled Keywords:	coccolithophores,diatoms,growth,marine phytoplankton,microrna,non-coding rnas,small rna,stress,trna,sdg 14 - life below water ,/dk/atira/pure/sustainabledevelopmentgoals/life_below_water
Faculty \ School:	Faculty of Science > School of Biological Sciences Faculty of Science > School of Computing Sciences Faculty of Science > School of Environmental Sciences
UEA Research Groups:	Faculty of Science > Research Groups > Computational Biology > Computational biology of RNA (former - to 2018) Faculty of Science > Research Groups > Computational Biology > Phylogenetics (former - to 2018) Faculty of Science > Research Groups > Computational Biology Faculty of Science > Research Groups > Norwich Epidemiology Centre Faculty of Medicine and Health Sciences > Research Groups > Norwich Epidemiology Centre Faculty of Science > Research Groups > Plant Sciences Faculty of Science > Research Centres > Centre for Ecology, Evolution and Conservation Faculty of Science > Research Groups > Environmental Biology Faculty of Science > Research Groups > Resources, Sustainability and Governance (former - to 2018) Faculty of Science > Research Groups > Marine and Atmospheric Sciences (former - to 2017) Faculty of Science > Research Groups > Centre for Ocean and Atmospheric Sciences
Depositing User:	Pure Connector
Date Deposited:	12 Sep 2014 12:22
Last Modified:	21 Mar 2024 15:31
URI:	https://ueaeprints.uea.ac.uk/id/eprint/50088
DOI:	10.1186/1471-2164-15-697

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