De Novo Transcriptomes of a Mixotrophic and a Heterotrophic Ciliate from Marine Plankton
Identifieur interne : 000543 ( Ncbi/Merge ); précédent : 000542; suivant : 000544De Novo Transcriptomes of a Mixotrophic and a Heterotrophic Ciliate from Marine Plankton
Auteurs : Luciana F. Santoferrara [États-Unis] ; Stephanie Guida [États-Unis] ; Huan Zhang [États-Unis] ; George B. Mcmanus [États-Unis]Source :
- PLoS ONE [ 1932-6203 ] ; 2014.
Abstract
Studying non-model organisms is crucial in the context of the current development of genomics and transcriptomics for both physiological experimentation and environmental characterization. We investigated the transcriptomes of two marine planktonic ciliates, the mixotrophic oligotrich
Url:
DOI: 10.1371/journal.pone.0101418
PubMed: 24983246
PubMed Central: 4077812
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en"><italic>De Novo</italic> Transcriptomes of a Mixotrophic and a Heterotrophic Ciliate from Marine Plankton</title><author><name sortKey="Santoferrara, Luciana F" sort="Santoferrara, Luciana F" uniqKey="Santoferrara L" first="Luciana F." last="Santoferrara">Luciana F. Santoferrara</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Marine Sciences, University of Connecticut, Groton, Connecticut</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author><author><name sortKey="Guida, Stephanie" sort="Guida, Stephanie" uniqKey="Guida S" first="Stephanie" last="Guida">Stephanie Guida</name><affiliation wicri:level="2"><nlm:aff id="aff2"><addr-line>The National Center for Genome Resources, Santa Fe, New Mexico, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>The National Center for Genome Resources, Santa Fe, New Mexico</wicri:regionArea><placeName><region type="state">Nouveau-Mexique</region></placeName></affiliation></author><author><name sortKey="Zhang, Huan" sort="Zhang, Huan" uniqKey="Zhang H" first="Huan" last="Zhang">Huan Zhang</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Marine Sciences, University of Connecticut, Groton, Connecticut</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author><author><name sortKey="Mcmanus, George B" sort="Mcmanus, George B" uniqKey="Mcmanus G" first="George B." last="Mcmanus">George B. Mcmanus</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Marine Sciences, University of Connecticut, Groton, Connecticut</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24983246</idno><idno type="pmc">4077812</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4077812</idno><idno type="RBID">PMC:4077812</idno><idno type="doi">10.1371/journal.pone.0101418</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000084</idno><idno type="wicri:Area/Pmc/Curation">000084</idno><idno type="wicri:Area/Pmc/Checkpoint">000247</idno><idno type="wicri:Area/Ncbi/Merge">000543</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main"><italic>De Novo</italic> Transcriptomes of a Mixotrophic and a Heterotrophic Ciliate from Marine Plankton</title><author><name sortKey="Santoferrara, Luciana F" sort="Santoferrara, Luciana F" uniqKey="Santoferrara L" first="Luciana F." last="Santoferrara">Luciana F. Santoferrara</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Marine Sciences, University of Connecticut, Groton, Connecticut</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author><author><name sortKey="Guida, Stephanie" sort="Guida, Stephanie" uniqKey="Guida S" first="Stephanie" last="Guida">Stephanie Guida</name><affiliation wicri:level="2"><nlm:aff id="aff2"><addr-line>The National Center for Genome Resources, Santa Fe, New Mexico, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>The National Center for Genome Resources, Santa Fe, New Mexico</wicri:regionArea><placeName><region type="state">Nouveau-Mexique</region></placeName></affiliation></author><author><name sortKey="Zhang, Huan" sort="Zhang, Huan" uniqKey="Zhang H" first="Huan" last="Zhang">Huan Zhang</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Marine Sciences, University of Connecticut, Groton, Connecticut</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author><author><name sortKey="Mcmanus, George B" sort="Mcmanus, George B" uniqKey="Mcmanus G" first="George B." last="Mcmanus">George B. Mcmanus</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Marine Sciences, University of Connecticut, Groton, Connecticut</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Studying non-model organisms is crucial in the context of the current development of genomics and transcriptomics for both physiological experimentation and environmental characterization. We investigated the transcriptomes of two marine planktonic ciliates, the mixotrophic oligotrich <italic>Strombidium rassoulzadegani</italic> and the heterotrophic choreotrich <italic>Strombidinopsis</italic> sp., and their respective algal food using Illumina RNAseq. Our aim was to characterize the transcriptomes of these contrasting ciliates and to identify genes potentially involved in mixotrophy. We detected approximately 10,000 and 7,600 amino acid sequences for <italic>S. rassoulzadegani</italic> and <italic>Strombidinopsis</italic> sp., respectively. About half of these transcripts had significant BLASTP hits (E-value <10<sup>−6</sup>) against previously-characterized sequences, mostly from the model ciliate <italic>Oxytricha trifallax</italic>. Transcriptomes from both the mixotroph and the heterotroph species provided similar annotations for GO terms and KEGG pathways. Most of the identified genes were related to housekeeping activity and pathways such as the metabolism of carbohydrates, lipids, amino acids, nucleotides, and vitamins. Although <italic>S. rassoulzadegani</italic> can keep and use chloroplasts from its prey, we did not find genes clearly linked to chloroplast maintenance and functioning in the transcriptome of this ciliate. While chloroplasts are known sources of reactive oxygen species (ROS), we found the same complement of antioxidant pathways in both ciliates, except for one enzyme possibly linked to ascorbic acid recycling found exclusively in the mixotroph. Contrary to our expectations, we did not find qualitative differences in genes potentially related to mixotrophy. However, these transcriptomes will help to establish a basis for the evaluation of differential gene expression in oligotrichs and choreotrichs and experimental investigation of the costs and benefits of mixotrophy.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Agatha, S" uniqKey="Agatha S">S Agatha</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sherr, E" uniqKey="Sherr E">E Sherr</name></author><author><name sortKey="Sherr, B" uniqKey="Sherr B">B Sherr</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Strom, Sl" uniqKey="Strom S">SL Strom</name></author><author><name sortKey="Macri, El" uniqKey="Macri E">EL Macri</name></author><author><name sortKey="Olson, Mb" uniqKey="Olson M">MB Olson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Santoferrara, L" uniqKey="Santoferrara L">L 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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">24983246</article-id><article-id pub-id-type="pmc">4077812</article-id><article-id pub-id-type="publisher-id">PONE-D-14-19473</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0101418</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Biology and Life Sciences</subject><subj-group><subject>Cell Biology</subject></subj-group><subj-group><subject>Ecology</subject><subj-group><subject>Marine Ecology</subject><subject>Microbial Ecology</subject></subj-group></subj-group><subj-group><subject>Genetics</subject><subj-group><subject>Genomics</subject><subj-group><subject>Genome Analysis</subject><subj-group><subject>Transcriptome Analysis</subject><subj-group><subject>Next-Generation Sequencing</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group><subject>Microbiology</subject><subj-group><subject>Protozoology</subject></subj-group></subj-group><subj-group><subject>Molecular Biology</subject><subj-group><subject>Molecular Biology Techniques</subject><subj-group><subject>Sequencing Techniques</subject><subj-group><subject>High Throughput Sequencing</subject></subj-group></subj-group></subj-group></subj-group><subj-group><subject>Organisms</subject><subj-group><subject>Plants</subject><subj-group><subject>Algae</subject></subj-group></subj-group><subj-group><subject>Protozoans</subject><subj-group><subject>Ciliate Protozoans</subject></subj-group></subj-group></subj-group></subj-group></article-categories><title-group><article-title><italic>De Novo</italic> Transcriptomes of a Mixotrophic and a Heterotrophic Ciliate from Marine Plankton</article-title><alt-title alt-title-type="running-head">Transcriptomes of Mixotrophic and Heterotrophic Ciliates</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Santoferrara</surname><given-names>Luciana F.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>Guida</surname><given-names>Stephanie</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Huan</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>McManus</surname><given-names>George B.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib></contrib-group><aff id="aff1"><label>1</label><addr-line>Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America</addr-line></aff><aff id="aff2"><label>2</label><addr-line>The National Center for Genome Resources, Santa Fe, New Mexico, United States of America</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Waller</surname><given-names>Ross Frederick</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>University of Cambridge, United Kingdom</addr-line></aff><author-notes><corresp id="cor1">* E-mail: <email>luciana.santoferrara@uconn.edu</email></corresp><fn fn-type="conflict"><p><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p></fn><fn fn-type="con"><p>Conceived and designed the experiments: GBM HZ. Performed the experiments: GBM HZ. Analyzed the data: LFS SG. Contributed reagents/materials/analysis tools: GBM HZ. Contributed to the writing of the manuscript: LFS SG HZ GBM.</p></fn></author-notes><pub-date pub-type="collection"><year>2014</year></pub-date><pub-date pub-type="epub"><day>1</day><month>7</month><year>2014</year></pub-date><volume>9</volume><issue>7</issue><elocation-id>e101418</elocation-id><history><date date-type="received"><day>5</day><month>5</month><year>2014</year></date><date date-type="accepted"><day>6</day><month>6</month><year>2014</year></date></history><permissions><copyright-year>2014</copyright-year><copyright-holder>Santoferrara et al</copyright-holder><license><license-p>This is an open-access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p></license></permissions><abstract><p>Studying non-model organisms is crucial in the context of the current development of genomics and transcriptomics for both physiological experimentation and environmental characterization. We investigated the transcriptomes of two marine planktonic ciliates, the mixotrophic oligotrich <italic>Strombidium rassoulzadegani</italic> and the heterotrophic choreotrich <italic>Strombidinopsis</italic> sp., and their respective algal food using Illumina RNAseq. Our aim was to characterize the transcriptomes of these contrasting ciliates and to identify genes potentially involved in mixotrophy. We detected approximately 10,000 and 7,600 amino acid sequences for <italic>S. rassoulzadegani</italic> and <italic>Strombidinopsis</italic> sp., respectively. About half of these transcripts had significant BLASTP hits (E-value <10<sup>−6</sup>) against previously-characterized sequences, mostly from the model ciliate <italic>Oxytricha trifallax</italic>. Transcriptomes from both the mixotroph and the heterotroph species provided similar annotations for GO terms and KEGG pathways. Most of the identified genes were related to housekeeping activity and pathways such as the metabolism of carbohydrates, lipids, amino acids, nucleotides, and vitamins. Although <italic>S. rassoulzadegani</italic> can keep and use chloroplasts from its prey, we did not find genes clearly linked to chloroplast maintenance and functioning in the transcriptome of this ciliate. While chloroplasts are known sources of reactive oxygen species (ROS), we found the same complement of antioxidant pathways in both ciliates, except for one enzyme possibly linked to ascorbic acid recycling found exclusively in the mixotroph. Contrary to our expectations, we did not find qualitative differences in genes potentially related to mixotrophy. However, these transcriptomes will help to establish a basis for the evaluation of differential gene expression in oligotrichs and choreotrichs and experimental investigation of the costs and benefits of mixotrophy.</p></abstract><funding-group><funding-statement>This research was funded by the Gordon and Betty Moore Foundation through Grant GBMF2637 to NCGR and by the US National Science Foundation through Grant OCE1130033 to GBM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement></funding-group><counts><page-count count="9"></page-count></counts><custom-meta-group><custom-meta id="data-availability"><meta-name>Data Availability</meta-name><meta-value>The authors confirm that all data underlying the findings are fully available without restriction. All relevant data are within the paper and its Supporting Information files.</meta-value></custom-meta></custom-meta-group></article-meta><notes><title>Data Availability</title><p>The authors confirm that all data underlying the findings are fully available without restriction. All relevant data are within the paper and its Supporting Information files.</p></notes></front></pmc><affiliations><list><country><li>États-Unis</li></country><region><li>Connecticut</li><li>Nouveau-Mexique</li></region></list><tree><country name="États-Unis"><region name="Connecticut"><name sortKey="Santoferrara, Luciana F" sort="Santoferrara, Luciana F" uniqKey="Santoferrara L" first="Luciana F." last="Santoferrara">Luciana F. Santoferrara</name></region><name sortKey="Guida, Stephanie" sort="Guida, Stephanie" uniqKey="Guida S" first="Stephanie" last="Guida">Stephanie Guida</name><name sortKey="Mcmanus, George B" sort="Mcmanus, George B" uniqKey="Mcmanus G" first="George B." last="Mcmanus">George B. Mcmanus</name><name sortKey="Zhang, Huan" sort="Zhang, Huan" uniqKey="Zhang H" first="Huan" last="Zhang">Huan Zhang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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