De novo assembly of Aureococcus anophagefferens transcriptomes reveals diverse responses to the low nutrient and low light conditions present during blooms
Identifieur interne : 000246 ( Pmc/Checkpoint ); précédent : 000245; suivant : 000247De novo assembly of Aureococcus anophagefferens transcriptomes reveals diverse responses to the low nutrient and low light conditions present during blooms
Auteurs : Kyle R. Frischkorn [États-Unis] ; Matthew J. Harke [États-Unis] ; Christopher J. Gobler [États-Unis] ; Sonya T. Dyhrman [États-Unis]Source :
- Frontiers in Microbiology [ 1664-302X ] ; 2014.
Abstract
Transcriptome profiling was performed on the harmful algal bloom-forming pelagophyte
Url:
DOI: 10.3389/fmicb.2014.00375
PubMed: 25104951
PubMed Central: 4109616
Affiliations:
Links toward previous steps (curation, corpus...)
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PMC:4109616Le document en format XML
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assembly of <italic>Aureococcus anophagefferens</italic>
transcriptomes reveals diverse responses to the low nutrient and low light conditions present during blooms</title>
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<author><name sortKey="Dyhrman, Sonya T" sort="Dyhrman, Sonya T" uniqKey="Dyhrman S" first="Sonya T." last="Dyhrman">Sonya T. Dyhrman</name>
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<idno type="doi">10.3389/fmicb.2014.00375</idno>
<date when="2014">2014</date>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main"><italic>De novo</italic>
assembly of <italic>Aureococcus anophagefferens</italic>
transcriptomes reveals diverse responses to the low nutrient and low light conditions present during blooms</title>
<author><name sortKey="Frischkorn, Kyle R" sort="Frischkorn, Kyle R" uniqKey="Frischkorn K" first="Kyle R." last="Frischkorn">Kyle R. Frischkorn</name>
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<country>Palisades, NY, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea></wicri:regionArea>
<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
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<author><name sortKey="Harke, Matthew J" sort="Harke, Matthew J" uniqKey="Harke M" first="Matthew J." last="Harke">Matthew J. Harke</name>
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<country>Southampton, NY, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea></wicri:regionArea>
<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
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<author><name sortKey="Gobler, Christopher J" sort="Gobler, Christopher J" uniqKey="Gobler C" first="Christopher J." last="Gobler">Christopher J. Gobler</name>
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<country>Southampton, NY, USA</country>
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<country xml:lang="fr">États-Unis</country>
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<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
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<author><name sortKey="Dyhrman, Sonya T" sort="Dyhrman, Sonya T" uniqKey="Dyhrman S" first="Sonya T." last="Dyhrman">Sonya T. Dyhrman</name>
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<country>Palisades, NY, USA</country>
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<country xml:lang="fr">États-Unis</country>
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<series><title level="j">Frontiers in Microbiology</title>
<idno type="eISSN">1664-302X</idno>
<imprint><date when="2014">2014</date>
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<front><div type="abstract" xml:lang="en"><p>Transcriptome profiling was performed on the harmful algal bloom-forming pelagophyte <italic>Aureococcus anophagefferens</italic>
strain CCMP 1850 to assess responses to common stressors for dense phytoplankton blooms: low inorganic nitrogen concentrations, low inorganic phosphorus concentrations, low light levels, and a replete control. The <italic>de novo</italic>
assemblies of pooled reads from all treatments reconstructed ~54,000 transcripts using Trinity, and ~31,000 transcripts using ABySS. Comparison to the strain CCMP 1984 genome showed that the majority of the gene models were present in both <italic>de novo</italic>
assemblies and that roughly 95% of contigs from both assemblies mapped to the genome, with Trinity capturing slightly more genome content. Sequence reads were mapped back to the <italic>de novo</italic>
assemblies as well as the gene models and differential expression was analyzed using a Bayesian approach called Analysis of Sequence Counts (ASC). On average, 93% of significantly upregulated transcripts recovered by genome mapping were present in the significantly upregulated pool from both <italic>de novo</italic>
assembly methods. Transcripts related to the transport and metabolism of nitrogen were upregulated in the low nitrogen treatment, transcripts encoding enzymes that hydrolyze organic phosphorus or relieve arsenic toxicity were upregulated in the low phosphorus treatment, and transcripts for enzymes that catabolize organic compounds, restructure lipid membranes, or are involved in sulfolipid biosynthesis were upregulated in the low light treatment. A comparison of this transcriptome to the nutrient regulated transcriptional response of CCMP 1984 identified conserved responses between these two strains. These analyses reveal the transcriptional underpinnings of physiological shifts that could contribute to the ecological success of this species <italic>in situ</italic>
: organic matter processing, metal detoxification, lipid restructuring, and photosynthetic apparatus turnover.</p>
</div>
</front>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Front Microbiol</journal-id>
<journal-id journal-id-type="iso-abbrev">Front Microbiol</journal-id>
<journal-id journal-id-type="publisher-id">Front. Microbiol.</journal-id>
<journal-title-group><journal-title>Frontiers in Microbiology</journal-title>
</journal-title-group>
<issn pub-type="epub">1664-302X</issn>
<publisher><publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">25104951</article-id>
<article-id pub-id-type="pmc">4109616</article-id>
<article-id pub-id-type="doi">10.3389/fmicb.2014.00375</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Microbiology</subject>
<subj-group><subject>Original Research Article</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group><article-title><italic>De novo</italic>
assembly of <italic>Aureococcus anophagefferens</italic>
transcriptomes reveals diverse responses to the low nutrient and low light conditions present during blooms</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Frischkorn</surname>
<given-names>Kyle R.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
<uri xlink:type="simple" xlink:href="http://community.frontiersin.org/people/u/137194"></uri>
</contrib>
<contrib contrib-type="author"><name><surname>Harke</surname>
<given-names>Matthew J.</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
<uri xlink:type="simple" xlink:href="http://community.frontiersin.org/people/u/171892"></uri>
</contrib>
<contrib contrib-type="author"><name><surname>Gobler</surname>
<given-names>Christopher J.</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Dyhrman</surname>
<given-names>Sonya T.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn001"><sup>*</sup>
</xref>
<uri xlink:type="simple" xlink:href="http://community.frontiersin.org/people/u/15987"></uri>
</contrib>
</contrib-group>
<aff id="aff1"><sup>1</sup>
<institution>Department of Earth and Environmental Sciences and the Lamont-Doherty Earth Observatory, Columbia University</institution>
<country>Palisades, NY, USA</country>
</aff>
<aff id="aff2"><sup>2</sup>
<institution>School of Marine and Atmospheric Sciences, Stony Brook University</institution>
<country>Southampton, NY, USA</country>
</aff>
<author-notes><fn fn-type="edited-by"><p>Edited by: Anton F. Post, MBL, USA</p>
</fn>
<fn fn-type="edited-by"><p>Reviewed by: Tom O. Delmont, Marine Biological Laboratory, USA; Lisa Campbell, Texas A&M Univeresity, USA; Chris Dupont, J. Craig Venter Institute, USA</p>
</fn>
<corresp id="fn001">*Correspondence: Sonya T. Dyhrman, Department of Earth and Environmental Sciences and Lamont-Doherty Earth Observatory, Columbia University, 61 Route 9W, Palisades, NY 10964, USA e-mail: <email xlink:type="simple">sdyhrman@ldeo.columbia.edu</email>
</corresp>
<fn fn-type="other" id="fn002"><p>This article was submitted to Aquatic Microbiology, a section of the journal Frontiers in Microbiology.</p>
</fn>
</author-notes>
<pub-date pub-type="epub"><day>24</day>
<month>7</month>
<year>2014</year>
</pub-date>
<pub-date pub-type="collection"><year>2014</year>
</pub-date>
<volume>5</volume>
<elocation-id>375</elocation-id>
<history><date date-type="received"><day>04</day>
<month>3</month>
<year>2014</year>
</date>
<date date-type="accepted"><day>03</day>
<month>7</month>
<year>2014</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2014 Frischkorn, Harke, Gobler and Dyhrman.</copyright-statement>
<copyright-year>2014</copyright-year>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/3.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</license-p>
</license>
</permissions>
<abstract><p>Transcriptome profiling was performed on the harmful algal bloom-forming pelagophyte <italic>Aureococcus anophagefferens</italic>
strain CCMP 1850 to assess responses to common stressors for dense phytoplankton blooms: low inorganic nitrogen concentrations, low inorganic phosphorus concentrations, low light levels, and a replete control. The <italic>de novo</italic>
assemblies of pooled reads from all treatments reconstructed ~54,000 transcripts using Trinity, and ~31,000 transcripts using ABySS. Comparison to the strain CCMP 1984 genome showed that the majority of the gene models were present in both <italic>de novo</italic>
assemblies and that roughly 95% of contigs from both assemblies mapped to the genome, with Trinity capturing slightly more genome content. Sequence reads were mapped back to the <italic>de novo</italic>
assemblies as well as the gene models and differential expression was analyzed using a Bayesian approach called Analysis of Sequence Counts (ASC). On average, 93% of significantly upregulated transcripts recovered by genome mapping were present in the significantly upregulated pool from both <italic>de novo</italic>
assembly methods. Transcripts related to the transport and metabolism of nitrogen were upregulated in the low nitrogen treatment, transcripts encoding enzymes that hydrolyze organic phosphorus or relieve arsenic toxicity were upregulated in the low phosphorus treatment, and transcripts for enzymes that catabolize organic compounds, restructure lipid membranes, or are involved in sulfolipid biosynthesis were upregulated in the low light treatment. A comparison of this transcriptome to the nutrient regulated transcriptional response of CCMP 1984 identified conserved responses between these two strains. These analyses reveal the transcriptional underpinnings of physiological shifts that could contribute to the ecological success of this species <italic>in situ</italic>
: organic matter processing, metal detoxification, lipid restructuring, and photosynthetic apparatus turnover.</p>
</abstract>
<kwd-group><kwd><italic>Aureococcus anophagefferens</italic>
</kwd>
<kwd>phytoplankton</kwd>
<kwd>harmful algal bloom</kwd>
<kwd>eco-physiology</kwd>
<kwd>transcriptome</kwd>
<kwd><italic>de novo</italic>
assembly</kwd>
<kwd>gene expression</kwd>
</kwd-group>
<counts><fig-count count="7"></fig-count>
<table-count count="7"></table-count>
<equation-count count="0"></equation-count>
<ref-count count="93"></ref-count>
<page-count count="16"></page-count>
<word-count count="13653"></word-count>
</counts>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>États-Unis</li>
</country>
</list>
<tree><country name="États-Unis"><noRegion><name sortKey="Frischkorn, Kyle R" sort="Frischkorn, Kyle R" uniqKey="Frischkorn K" first="Kyle R." last="Frischkorn">Kyle R. Frischkorn</name>
</noRegion>
<name sortKey="Dyhrman, Sonya T" sort="Dyhrman, Sonya T" uniqKey="Dyhrman S" first="Sonya T." last="Dyhrman">Sonya T. Dyhrman</name>
<name sortKey="Gobler, Christopher J" sort="Gobler, Christopher J" uniqKey="Gobler C" first="Christopher J." last="Gobler">Christopher J. Gobler</name>
<name sortKey="Harke, Matthew J" sort="Harke, Matthew J" uniqKey="Harke M" first="Matthew J." last="Harke">Matthew J. Harke</name>
</country>
</tree>
</affiliations>
</record>
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