Global discovery and characterization of small non-coding RNAs in marine microalgae
Identifieur interne : 003897 ( Main/Exploration ); précédent : 003896; suivant : 003898Global discovery and characterization of small non-coding RNAs in marine microalgae
Auteurs : Sara Lopez-Gomollon [Espagne] ; Matthew Beckers ; Tina Rathjen [Australie] ; Simon Moxon ; Florian Maumus [France] ; Irina Mohorianu ; Vincent Moulton ; Tamas Dalmay ; Thomas MockSource :
- BMC Genomics [ 1471-2164 ] ; 2014.
Abstract
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 (
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
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.
The online version of this article (doi:10.1186/1471-2164-15-697) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/1471-2164-15-697
PubMed: 25142467
PubMed Central: 4156623
Affiliations:
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Territory</wicri:regionArea><wicri:noRegion>Australian Capital Territory</wicri:noRegion></affiliation></author><author><name sortKey="Moxon, Simon" sort="Moxon, Simon" uniqKey="Moxon S" first="Simon" last="Moxon">Simon Moxon</name><affiliation><nlm:aff id="Aff6">School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ UK</nlm:aff><wicri:noCountry code="subfield">NR4 7TJ UK</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff11">The Genome Analysis Centre, Norwich, NR4 7UH UK</nlm:aff><wicri:noCountry code="subfield">NR4 7UH UK</wicri:noCountry></affiliation></author><author><name sortKey="Maumus, Florian" sort="Maumus, Florian" uniqKey="Maumus F" first="Florian" last="Maumus">Florian Maumus</name><affiliation wicri:level="3"><nlm:aff id="Aff7">UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles, 78026 France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>UR1164 URGI-Research Unit in 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sort="Dalmay, Tamas" uniqKey="Dalmay T" first="Tamas" last="Dalmay">Tamas Dalmay</name><affiliation><nlm:aff id="Aff5">School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ UK</nlm:aff><wicri:noCountry code="subfield">NR4 7TJ UK</wicri:noCountry></affiliation></author><author><name sortKey="Mock, Thomas" sort="Mock, Thomas" uniqKey="Mock T" first="Thomas" last="Mock">Thomas Mock</name><affiliation><nlm:aff id="Aff8">School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ UK</nlm:aff><wicri:noCountry code="subfield">NR4 7TJ UK</wicri:noCountry></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25142467</idno><idno type="pmc">4156623</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4156623</idno><idno type="RBID">PMC:4156623</idno><idno type="doi">10.1186/1471-2164-15-697</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000A73</idno><idno 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Lopez-Gomollon</name><affiliation><nlm:aff id="Aff5">School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ UK</nlm:aff><wicri:noCountry code="subfield">NR4 7TJ UK</wicri:noCountry></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff9">Estación Experimental Aula Dei, CSIC (Consejo Superior de Investigaciones Científicas), 50059 Zaragoza, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Estación Experimental Aula Dei, CSIC (Consejo Superior de Investigaciones Científicas), 50059 Zaragoza</wicri:regionArea><wicri:noRegion>50059 Zaragoza</wicri:noRegion></affiliation></author><author><name sortKey="Beckers, Matthew" sort="Beckers, Matthew" uniqKey="Beckers M" first="Matthew" last="Beckers">Matthew Beckers</name><affiliation><nlm:aff id="Aff6">School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ UK</nlm:aff><wicri:noCountry code="subfield">NR4 7TJ UK</wicri:noCountry></affiliation></author><author><name sortKey="Rathjen, Tina" sort="Rathjen, Tina" uniqKey="Rathjen T" first="Tina" last="Rathjen">Tina Rathjen</name><affiliation><nlm:aff id="Aff5">School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ UK</nlm:aff><wicri:noCountry code="subfield">NR4 7TJ UK</wicri:noCountry></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff10">Commonwealth Scientific and Industrial Research Organization Plant Industry, Canberra, Australian Capital Territory, 2601 Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Commonwealth Scientific and Industrial Research Organization Plant Industry, Canberra, Australian Capital Territory</wicri:regionArea><wicri:noRegion>Australian Capital Territory</wicri:noRegion></affiliation></author><author><name sortKey="Moxon, Simon" sort="Moxon, Simon" uniqKey="Moxon S" first="Simon" last="Moxon">Simon Moxon</name><affiliation><nlm:aff id="Aff6">School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ UK</nlm:aff><wicri:noCountry code="subfield">NR4 7TJ UK</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff11">The Genome Analysis Centre, Norwich, NR4 7UH UK</nlm:aff><wicri:noCountry code="subfield">NR4 7UH UK</wicri:noCountry></affiliation></author><author><name sortKey="Maumus, Florian" sort="Maumus, Florian" uniqKey="Maumus F" first="Florian" last="Maumus">Florian Maumus</name><affiliation wicri:level="3"><nlm:aff id="Aff7">UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles, 78026 France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles</wicri:regionArea><placeName><region type="region">Île-de-France</region><region type="old region">Île-de-France</region><settlement type="city">Versailles</settlement></placeName></affiliation></author><author><name sortKey="Mohorianu, Irina" sort="Mohorianu, Irina" uniqKey="Mohorianu I" first="Irina" last="Mohorianu">Irina Mohorianu</name><affiliation><nlm:aff id="Aff5">School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ UK</nlm:aff><wicri:noCountry code="subfield">NR4 7TJ UK</wicri:noCountry></affiliation></author><author><name sortKey="Moulton, Vincent" sort="Moulton, Vincent" uniqKey="Moulton V" first="Vincent" last="Moulton">Vincent Moulton</name><affiliation><nlm:aff id="Aff6">School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ UK</nlm:aff><wicri:noCountry code="subfield">NR4 7TJ UK</wicri:noCountry></affiliation></author><author><name sortKey="Dalmay, Tamas" sort="Dalmay, Tamas" uniqKey="Dalmay T" first="Tamas" last="Dalmay">Tamas Dalmay</name><affiliation><nlm:aff id="Aff5">School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ UK</nlm:aff><wicri:noCountry code="subfield">NR4 7TJ UK</wicri:noCountry></affiliation></author><author><name sortKey="Mock, Thomas" sort="Mock, Thomas" uniqKey="Mock T" first="Thomas" last="Mock">Thomas Mock</name><affiliation><nlm:aff id="Aff8">School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ UK</nlm:aff><wicri:noCountry code="subfield">NR4 7TJ UK</wicri:noCountry></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Marine phytoplankton are responsible for 50% of the CO<sub>2</sub> 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 (<italic>Thalassiosira pseudonana</italic>, <italic>Fragilariopsis cylindrus</italic>) and validated them by Northern blots along with the coccolithophore <italic>Emiliania huxleyi</italic>.</p></sec><sec><title>Results</title><p>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 <italic>E. huxleyi</italic>. 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 <italic>F. cylindrus</italic> (20.7% of all sRNAs) even under optimal growth conditions.</p></sec><sec><title>Conclusions</title><p>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.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/1471-2164-15-697) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Field, Cb" uniqKey="Field C">CB Field</name></author><author><name sortKey="Behrenfeld, Mj" uniqKey="Behrenfeld M">MJ Behrenfeld</name></author><author><name sortKey="Randerson, Jt" uniqKey="Randerson J">JT Randerson</name></author><author><name sortKey="Falkowski, Pg" uniqKey="Falkowski P">PG Falkowski</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Furnas, Mj" uniqKey="Furnas M">MJ Furnas</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Smetacek, 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Rognes</name></author><author><name sortKey="Ussery, Dw" uniqKey="Ussery D">DW Ussery</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Burge, Sw" uniqKey="Burge S">SW Burge</name></author><author><name sortKey="Daub, J" uniqKey="Daub J">J Daub</name></author><author><name sortKey="Eberhardt, R" uniqKey="Eberhardt R">R Eberhardt</name></author><author><name sortKey="Tate, J" uniqKey="Tate J">J Tate</name></author><author><name sortKey="Barquist, L" uniqKey="Barquist L">L Barquist</name></author><author><name sortKey="Nawrocki, Ep" uniqKey="Nawrocki E">EP Nawrocki</name></author><author><name sortKey="Eddy, Sr" uniqKey="Eddy S">SR Eddy</name></author><author><name sortKey="Gardner, Pp" uniqKey="Gardner P">PP Gardner</name></author><author><name sortKey="Bateman, A" uniqKey="Bateman A">A Bateman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Altschul, Sf" uniqKey="Altschul S">SF Altschul</name></author><author><name sortKey="Gish, W" uniqKey="Gish W">W Gish</name></author><author><name sortKey="Miller, W" uniqKey="Miller W">W Miller</name></author><author><name sortKey="Myers, Ew" uniqKey="Myers E">EW Myers</name></author><author><name sortKey="Lipman, Dj" uniqKey="Lipman D">DJ Lipman</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Australie</li><li>Espagne</li><li>France</li></country><region><li>Île-de-France</li></region><settlement><li>Versailles</li></settlement></list><tree><noCountry><name sortKey="Beckers, Matthew" sort="Beckers, Matthew" uniqKey="Beckers M" first="Matthew" last="Beckers">Matthew Beckers</name><name sortKey="Dalmay, Tamas" sort="Dalmay, Tamas" uniqKey="Dalmay T" first="Tamas" last="Dalmay">Tamas Dalmay</name><name sortKey="Mock, Thomas" sort="Mock, Thomas" uniqKey="Mock T" first="Thomas" last="Mock">Thomas Mock</name><name sortKey="Mohorianu, Irina" sort="Mohorianu, Irina" uniqKey="Mohorianu I" first="Irina" last="Mohorianu">Irina Mohorianu</name><name sortKey="Moulton, Vincent" sort="Moulton, Vincent" uniqKey="Moulton V" first="Vincent" last="Moulton">Vincent Moulton</name><name sortKey="Moxon, Simon" sort="Moxon, Simon" uniqKey="Moxon S" first="Simon" last="Moxon">Simon Moxon</name></noCountry><country name="Espagne"><noRegion><name sortKey="Lopez Gomollon, Sara" sort="Lopez Gomollon, Sara" uniqKey="Lopez Gomollon S" first="Sara" last="Lopez-Gomollon">Sara Lopez-Gomollon</name></noRegion></country><country name="Australie"><noRegion><name sortKey="Rathjen, Tina" sort="Rathjen, Tina" uniqKey="Rathjen T" first="Tina" last="Rathjen">Tina Rathjen</name></noRegion></country><country name="France"><region name="Île-de-France"><name sortKey="Maumus, Florian" sort="Maumus, Florian" uniqKey="Maumus F" first="Florian" last="Maumus">Florian Maumus</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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|wiki= Wicri/Asie
|area= AustralieFrV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= PMC:4156623
|texte= Global discovery and characterization of small non-coding RNAs in marine microalgae
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:25142467" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a AustralieFrV1
| This area was generated with Dilib version V0.6.33. |  |