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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Spliced leader–based metatranscriptomic analyses lead to recognition of hidden genomic features in dinoflagellates</title><author><name sortKey="Lin, Senjie" sort="Lin, Senjie" uniqKey="Lin S" first="Senjie" last="Lin">Senjie Lin</name><affiliation><nlm:aff wicri:cut="; and" id="aff1">Department of Marine Sciences,<institution>University of Connecticut</institution>, Groton, CT 06340</nlm:aff></affiliation></author><author><name sortKey="Zhang, Huan" sort="Zhang, Huan" uniqKey="Zhang H" first="Huan" last="Zhang">Huan Zhang</name><affiliation><nlm:aff wicri:cut="; and" id="aff1">Department of Marine Sciences,<institution>University of Connecticut</institution>, Groton, CT 06340</nlm:aff></affiliation></author><author><name sortKey="Zhuang, Yunyun" sort="Zhuang, Yunyun" uniqKey="Zhuang Y" first="Yunyun" last="Zhuang">Yunyun Zhuang</name><affiliation><nlm:aff wicri:cut="; and" id="aff1">Department of Marine Sciences,<institution>University of Connecticut</institution>, Groton, CT 06340</nlm:aff></affiliation></author><author><name sortKey="Tran, Bao" sort="Tran, Bao" uniqKey="Tran B" first="Bao" last="Tran">Bao Tran</name><affiliation><nlm:aff id="aff2"><institution>J. Craig Venter Institute</institution>, Rockville, MD 20850</nlm:aff></affiliation></author><author><name sortKey="Gill, John" sort="Gill, John" uniqKey="Gill J" first="John" last="Gill">John Gill</name><affiliation><nlm:aff id="aff2"><institution>J. Craig Venter Institute</institution>, Rockville, MD 20850</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21041634</idno><idno type="pmc">2993343</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2993343</idno><idno type="RBID">PMC:2993343</idno><idno type="doi">10.1073/pnas.1007246107</idno><date when="2010">2010</date><idno type="wicri:Area/Pmc/Corpus">000390</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Spliced leader–based metatranscriptomic analyses lead to recognition of hidden genomic features in dinoflagellates</title><author><name sortKey="Lin, Senjie" sort="Lin, Senjie" uniqKey="Lin S" first="Senjie" last="Lin">Senjie Lin</name><affiliation><nlm:aff wicri:cut="; and" id="aff1">Department of Marine Sciences,<institution>University of Connecticut</institution>, Groton, CT 06340</nlm:aff></affiliation></author><author><name sortKey="Zhang, Huan" sort="Zhang, Huan" uniqKey="Zhang H" first="Huan" last="Zhang">Huan Zhang</name><affiliation><nlm:aff wicri:cut="; and" id="aff1">Department of Marine Sciences,<institution>University of Connecticut</institution>, Groton, CT 06340</nlm:aff></affiliation></author><author><name sortKey="Zhuang, Yunyun" sort="Zhuang, Yunyun" uniqKey="Zhuang Y" first="Yunyun" last="Zhuang">Yunyun Zhuang</name><affiliation><nlm:aff wicri:cut="; and" id="aff1">Department of Marine Sciences,<institution>University of Connecticut</institution>, Groton, CT 06340</nlm:aff></affiliation></author><author><name sortKey="Tran, Bao" sort="Tran, Bao" uniqKey="Tran B" first="Bao" last="Tran">Bao Tran</name><affiliation><nlm:aff id="aff2"><institution>J. Craig Venter Institute</institution>, Rockville, MD 20850</nlm:aff></affiliation></author><author><name sortKey="Gill, John" sort="Gill, John" uniqKey="Gill J" first="John" last="Gill">John Gill</name><affiliation><nlm:aff id="aff2"><institution>J. Craig Venter Institute</institution>, Rockville, MD 20850</nlm:aff></affiliation></author></analytic><series><title level="j">Proceedings of the National Academy of Sciences of the United States of America</title><idno type="ISSN">0027-8424</idno><idno type="eISSN">1091-6490</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Environmental transcriptomics (metatranscriptomics) for a specific lineage of eukaryotic microbes (e.g., Dinoflagellata) would be instrumental for unraveling the genetic mechanisms by which these microbes respond to the natural environment, but it has not been exploited because of technical difficulties. Using the recently discovered dinoflagellate mRNA-specific spliced leader as a selective primer, we constructed cDNA libraries (e-cDNAs) from one marine and two freshwater plankton assemblages. Small-scale sequencing of the e-cDNAs revealed functionally diverse transcriptomes proven to be of dinoflagellate origin. A set of dinoflagellate common genes and transcripts of dominant dinoflagellate species were identified. Further analyses of the dataset prompted us to delve into the existing, largely unannotated dinoflagellate EST datasets (DinoEST). Consequently, all four nucleosome core histones, two histone modification proteins, and a nucleosome assembly protein were detected, clearly indicating the presence of nucleosome-like machinery long thought not to exist in dinoflagellates. The isolation of rhodopsin from taxonomically and ecotypically diverse dinoflagellates and its structural similarity and phylogenetic affinity to xanthorhodopsin suggest a common genetic potential in dinoflagellates to use solar energy nonphotosynthetically. Furthermore, we found 55 cytoplasmic ribosomal proteins (RPs) from the e-cDNAs and 24 more from DinoEST, showing that the dinoflagellate phylum possesses all 79 eukaryotic RPs. Our results suggest that a sophisticated eukaryotic molecular machine operates in dinoflagellates that likely encodes many more unsuspected physiological capabilities and, meanwhile, demonstrate that unique spliced leaders are useful for profiling lineage-specific microbial transcriptomes in situ.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Proc Natl Acad Sci U S A</journal-id><journal-id journal-id-type="hwp">pnas</journal-id><journal-id journal-id-type="pmc">pnas</journal-id><journal-id journal-id-type="publisher-id">PNAS</journal-id><journal-title-group><journal-title>Proceedings of the National Academy of Sciences of the United States of America</journal-title></journal-title-group><issn pub-type="ppub">0027-8424</issn><issn pub-type="epub">1091-6490</issn><publisher><publisher-name>National Academy of Sciences</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">21041634</article-id><article-id pub-id-type="pmc">2993343</article-id><article-id pub-id-type="publisher-id">201007246</article-id><article-id pub-id-type="doi">10.1073/pnas.1007246107</article-id><article-categories><subj-group subj-group-type="heading"><subject>Biological Sciences</subject><subj-group><subject>Microbiology</subject></subj-group></subj-group><subj-group subj-group-type="heading"><subject>Physical Sciences</subject><subj-group><subject>Environmental Sciences</subject></subj-group></subj-group></article-categories><title-group><article-title>Spliced leader–based metatranscriptomic analyses lead to recognition of hidden genomic features in dinoflagellates</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Lin</surname><given-names>Senjie</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref><xref ref-type="corresp" rid="cor1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Huan</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zhuang</surname><given-names>Yunyun</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Tran</surname><given-names>Bao</given-names></name><xref ref-type="aff" rid="aff2"><sup>b</sup></xref></contrib><contrib contrib-type="author"><name><surname>Gill</surname><given-names>John</given-names></name><xref ref-type="aff" rid="aff2"><sup>b</sup></xref></contrib><aff id="aff1"><sup>a</sup>Department of Marine Sciences,<institution>University of Connecticut</institution>, Groton, CT 06340; and</aff><aff id="aff2"><sup>b</sup><institution>J. Craig Venter Institute</institution>, Rockville, MD 20850</aff></contrib-group><author-notes><corresp id="cor1"><sup>1</sup>To whom correspondence should be addressed. E-mail: <email>senjie.lin@uconn.edu</email>.</corresp><fn fn-type="edited-by"><p>Edited<xref ref-type="fn" rid="fn1">*</xref> by Woody Hastings, Harvard University, Cambridge, MA, and approved October 8, 2010 (received for review May 25, 2010)</p></fn><fn fn-type="con"><p>Author contributions: S.L. and H.Z. designed research; S.L., H.Z., B.T., and J.G. performed research; S.L., H.Z., and Y.Z. analyzed data; and S.L., H.Z., Y.Z., and J.G. wrote the paper.</p></fn></author-notes><pub-date pub-type="ppub"><day>16</day><month>11</month><year>2010</year></pub-date><pub-date pub-type="epub"><day>1</day><month>11</month><year>2010</year></pub-date><pub-date pub-type="pmc-release"><day>1</day><month>11</month><year>2010</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>107</volume><issue>46</issue><fpage>20033</fpage><lpage>20038</lpage><permissions><license license-type="open-access"><license-p>Freely available online through the PNAS open access option.</license-p></license></permissions><self-uri xlink:title="pdf" xlink:type="simple" xlink:href="pnas.201007246.pdf"></self-uri><abstract><p>Environmental transcriptomics (metatranscriptomics) for a specific lineage of eukaryotic microbes (e.g., Dinoflagellata) would be instrumental for unraveling the genetic mechanisms by which these microbes respond to the natural environment, but it has not been exploited because of technical difficulties. Using the recently discovered dinoflagellate mRNA-specific spliced leader as a selective primer, we constructed cDNA libraries (e-cDNAs) from one marine and two freshwater plankton assemblages. Small-scale sequencing of the e-cDNAs revealed functionally diverse transcriptomes proven to be of dinoflagellate origin. A set of dinoflagellate common genes and transcripts of dominant dinoflagellate species were identified. Further analyses of the dataset prompted us to delve into the existing, largely unannotated dinoflagellate EST datasets (DinoEST). Consequently, all four nucleosome core histones, two histone modification proteins, and a nucleosome assembly protein were detected, clearly indicating the presence of nucleosome-like machinery long thought not to exist in dinoflagellates. The isolation of rhodopsin from taxonomically and ecotypically diverse dinoflagellates and its structural similarity and phylogenetic affinity to xanthorhodopsin suggest a common genetic potential in dinoflagellates to use solar energy nonphotosynthetically. Furthermore, we found 55 cytoplasmic ribosomal proteins (RPs) from the e-cDNAs and 24 more from DinoEST, showing that the dinoflagellate phylum possesses all 79 eukaryotic RPs. Our results suggest that a sophisticated eukaryotic molecular machine operates in dinoflagellates that likely encodes many more unsuspected physiological capabilities and, meanwhile, demonstrate that unique spliced leaders are useful for profiling lineage-specific microbial transcriptomes in situ.</p></abstract><kwd-group><kwd>metatranscriptome</kwd><kwd>eukaryote</kwd><kwd>gene expression</kwd><kwd>alveolate</kwd></kwd-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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