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

Sara Lopez-Gomollon; Matthew Beckers; Tina Rathjen; Simon Moxon; Florian Maumus; Irina Mohorianu; Vincent Moulton; Tamas Dalmay; Thomas Mock

doi:10.1186/1471-2164-15-697

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

Sara Lopez-Gomollon, Matthew Beckers, Tina Rathjen, Simon Moxon, Florian Maumus, Irina Mohorianu, Vincent Moulton, Tamas Dalmay, Thomas Mock

Research output: Contribution to journal › Article › peer-review

18 Citations (Scopus)

16 Downloads (Pure)

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.

Original language	English
Article number	697
Journal	BMC Genomics
Volume	15
Issue number	1
DOIs	https://doi.org/10.1186/1471-2164-15-697
Publication status	Published - 20 Aug 2014

Keywords

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

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1186/1471-2164-15-697Licence: CC BY

bmc-genomics
© 2014 Lopez-Gomollon et al.; licensee BioMed Central Ltd. 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.
Final published version, 3.61 MBLicence: CC BY

Tamas Dalmay
- T.Dalmayuea.acuk
- School of Biological Sciences - Professor of RNA Biology
- Plant Sciences - Member
Person: Research Group Member, Academic, Teaching & Research
Vincent Moulton
- v.moultonuea.acuk
- School of Computing Sciences - Professor in Computational Biology
- Norwich Epidemiology Centre - Member
- Computational Biology - Member
Person: Research Group Member, Academic, Teaching & Research
Simon Moxon
- S.Moxonuea.acuk
- School of Biological Sciences - Associate Professor in Bioinformatics
Person: Academic, Teaching & Research

Functional adaptation of diatoms to environmental conditions in sea ice of the Southern Ocean (UEA Lead)
Mock, T.
Natural Environment Research Council
1/12/10 → 30/11/13
Project: Research
Role of microRNAs in phenotypic plasticity to environmental change
Dalmay, T., Burke (Sheffield), T., Godfrey (Imperial), C., Johnston (St Andrews), I., Kinghorn (University of St Andrews), J. & Partridge (Uni. College London), L.
Natural Environment Research Council
1/12/04 → 28/02/09
Project: Research

Cite this

@article{1cb71094e2f6477d8f1ab0650a326238,

title = "Global discovery and characterization of small non-coding RNAs in marine microalgae",

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",

author = "Sara Lopez-Gomollon and Matthew Beckers and Tina Rathjen and Simon Moxon and Florian Maumus and Irina Mohorianu and Vincent Moulton and Tamas Dalmay and Thomas Mock",

note = "{\textcopyright} 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.",

year = "2014",

month = aug,

day = "20",

doi = "10.1186/1471-2164-15-697",

language = "English",

volume = "15",

journal = "BMC Genomics",

issn = "1471-2164",

publisher = "BioMed Central",

number = "1",

}

TY - JOUR

T1 - Global discovery and characterization of small non-coding RNAs in marine microalgae

AU - Lopez-Gomollon, Sara

AU - Beckers, Matthew

AU - Rathjen, Tina

AU - Moxon, Simon

AU - Maumus, Florian

AU - Mohorianu, Irina

AU - Moulton, Vincent

AU - Dalmay, Tamas

AU - Mock, Thomas

N1 - © 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.

PY - 2014/8/20

Y1 - 2014/8/20

N2 - 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.

AB - 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.

KW - Coccolithophores

KW - Diatoms

KW - Growth

KW - Marine phytoplankton

KW - MicroRNA

KW - Non-coding RNAs

KW - Small RNA

KW - Stress

KW - tRNA

U2 - 10.1186/1471-2164-15-697

DO - 10.1186/1471-2164-15-697

M3 - Article

VL - 15

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

IS - 1

M1 - 697

ER -

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

Abstract

Keywords

UN SDGs

Access to Document

Profiles

Tamas Dalmay

Vincent Moulton

Simon Moxon

Projects

Functional adaptation of diatoms to environmental conditions in sea ice of the Southern Ocean (UEA Lead)

Role of microRNAs in phenotypic plasticity to environmental change

Cite this