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Genome-Wide Analysis of Alternative Splicing Landscapes Modulated during Plant-Virus Interactions in Brachypodium distachyon

Identifieur interne : 000099 ( Pmc/Checkpoint ); précédent : 000098; suivant : 000100

Genome-Wide Analysis of Alternative Splicing Landscapes Modulated during Plant-Virus Interactions in Brachypodium distachyon

Auteurs : Kranthi K. Mandadi ; Karen-Beth G. Scholthof

Source :

The Plant Cell [ 1040-4651 ] ; 2015.

RBID : PMC:4330581

Abstract

Virus infection altered alternative splicing in >100 Brachypodium distachyon defense-related genes, with little effect on the genome-wide ratios of different splicing types.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4330581

DOI: 10.1105/tpc.114.133991
PubMed: 25634987
PubMed Central: 4330581

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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genome-Wide Analysis of Alternative Splicing Landscapes Modulated during Plant-Virus Interactions in <italic>Brachypodium distachyon</italic>
</title>
<author><name sortKey="Mandadi, Kranthi K" sort="Mandadi, Kranthi K" uniqKey="Mandadi K" first="Kranthi K." last="Mandadi">Kranthi K. Mandadi</name>
</author>
<author><name sortKey="Scholthof, Karen Beth G" sort="Scholthof, Karen Beth G" uniqKey="Scholthof K" first="Karen-Beth G." last="Scholthof">Karen-Beth G. Scholthof</name>
</author>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Genome-Wide Analysis of Alternative Splicing Landscapes Modulated during Plant-Virus Interactions in <italic>Brachypodium distachyon</italic>
</title>
<author><name sortKey="Mandadi, Kranthi K" sort="Mandadi, Kranthi K" uniqKey="Mandadi K" first="Kranthi K." last="Mandadi">Kranthi K. Mandadi</name>
</author>
<author><name sortKey="Scholthof, Karen Beth G" sort="Scholthof, Karen Beth G" uniqKey="Scholthof K" first="Karen-Beth G." last="Scholthof">Karen-Beth G. Scholthof</name>
</author>
</analytic>
<series><title level="j">The Plant Cell</title>
<idno type="ISSN">1040-4651</idno>
<idno type="eISSN">1532-298X</idno>
<imprint><date when="2015">2015</date>
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<front><div type="abstract" xml:lang="en"><p>Virus infection altered alternative splicing in >100 <italic>Brachypodium distachyon</italic>
 defense-related genes, with little effect on the genome-wide ratios of different splicing types.</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">Plant Cell</journal-id>
<journal-id journal-id-type="iso-abbrev">Plant Cell</journal-id>
<journal-id journal-id-type="hwp">plantcell</journal-id>
<journal-id journal-id-type="publisher-id">aspb</journal-id>
<journal-title-group><journal-title>The Plant Cell</journal-title>
</journal-title-group>
<issn pub-type="ppub">1040-4651</issn>
<issn pub-type="epub">1532-298X</issn>
<publisher><publisher-name>American Society of Plant Biologists</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">25634987</article-id>
<article-id pub-id-type="pmc">4330581</article-id>
<article-id pub-id-type="publisher-id">133991</article-id>
<article-id pub-id-type="doi">10.1105/tpc.114.133991</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Large-Scale Biology Articles</subject>
</subj-group>
</article-categories>
<title-group><article-title>Genome-Wide Analysis of Alternative Splicing Landscapes Modulated during Plant-Virus Interactions in <italic>Brachypodium distachyon</italic>
</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0003-2986-4016</contrib-id>
<name><surname>Mandadi</surname>
<given-names>Kranthi K.</given-names>
</name>
<xref ref-type="author-notes" rid="afn2"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Scholthof</surname>
<given-names>Karen-Beth G.</given-names>
</name>
<xref ref-type="corresp" rid="cor1"><sup>2</sup>
</xref>
</contrib>
<aff id="aff1">Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843</aff>
</contrib-group>
<author-notes><fn><p><ext-link ext-link-type="uri" xlink:href="http://www.plantcell.org/cgi/doi/10.1105/tpc.114.133991">www.plantcell.org/cgi/doi/10.1105/tpc.114.133991</ext-link>
</p>
</fn>
<corresp id="cor1"><label>2</label>
Address correspondence to <email>kbgs@tamu.edu</email>
.</corresp>
<fn id="afn1"><p>The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (<ext-link ext-link-type="uri" xlink:href="http://www.plantcell.org">www.plantcell.org</ext-link>
) is: Karen-Beth G. Scholthof (<email>kbgs@tamu.edu</email>
).</p>
</fn>
<fn id="afn2" fn-type="present-address"><label>1</label>
<p>Current address: Department of Plant Pathology and Microbiology, Texas A&M AgriLife Research & Extension, 2415 E. Highway 83, Weslaco, TX 78596.</p>
</fn>
</author-notes>
<pmc-comment>Fake ppub date generated by PMC from publisher pub-date/@pub-type='epub-ppub' </pmc-comment>
      <pub-date pub-type="ppub"><month>1</month>
<year>2015</year>
</pub-date>
<pub-date pub-type="epub"><day>29</day>
<month>1</month>
<year>2015</year>
</pub-date>
<volume>27</volume>
<issue>1</issue>
<fpage>71</fpage>
<lpage>85</lpage>
<history><date date-type="received"><day>04</day>
<month>11</month>
<year>2014</year>
</date>
<date date-type="rev-recd"><day>19</day>
<month>12</month>
<year>2014</year>
</date>
<date date-type="accepted"><day>09</day>
<month>1</month>
<year>2015</year>
</date>
</history>
<permissions><copyright-statement>© 2015 American Society of Plant Biologists. All rights reserved.</copyright-statement>
<copyright-year>2015</copyright-year>
</permissions>
<self-uri xlink:role="icon" xlink:href="PC_133991_ic1.gif"></self-uri>
<abstract abstract-type="precis"><p>Virus infection altered alternative splicing in >100 <italic>Brachypodium distachyon</italic>
 defense-related genes, with little effect on the genome-wide ratios of different splicing types.</p>
</abstract>
<abstract><p>In eukaryotes, alternative splicing (<xref ref-type="def" rid="def1">AS</xref>
) promotes transcriptome and proteome diversity. The extent of genome-wide <xref ref-type="def" rid="def1">AS</xref>
 changes occurring during a plant-microbe interaction is largely unknown. Here, using high-throughput, paired-end RNA sequencing, we generated an isoform-level spliceome map of <italic>Brachypodium distachyon</italic>
 infected with <italic>Panicum mosaic virus</italic>
 and its satellite virus. Overall, we detected ∼44,443 transcripts in <italic>B. distachyon</italic>
, ∼30% more than those annotated in the reference genome. Expression of ∼28,900 transcripts was ≥2 fragments per kilobase of transcript per million mapped fragments, and ∼42% of multi-exonic genes were alternatively spliced. Comparative analysis of <xref ref-type="def" rid="def1">AS</xref>
 patterns in <italic>B. distachyon</italic>
, rice (<italic>Oryza sativa</italic>
), maize (<italic>Zea mays</italic>
), sorghum (<italic>Sorghum bicolor</italic>
), <italic>Arabidopsis thaliana</italic>
, potato (<italic>Solanum tuberosum</italic>
), <italic>Medicago truncatula</italic>
, and poplar (<italic>Populus trichocarpa</italic>
) revealed conserved ratios of the <xref ref-type="def" rid="def1">AS</xref>
 types between monocots and dicots. Virus infection quantitatively altered <xref ref-type="def" rid="def1">AS</xref>
 events in Brachypodium with little effect on the <xref ref-type="def" rid="def1">AS</xref>
 ratios. We discovered <xref ref-type="def" rid="def1">AS</xref>
 events for >100 immune-related genes encoding receptor-like kinases, NB-LRR resistance proteins, transcription factors, RNA silencing, and splicing-associated proteins. Cloning and molecular characterization of <italic>SCL33</italic>
, a serine/arginine-rich splicing factor, identified multiple novel intron-retaining splice variants that are developmentally regulated and modulated during virus infection. <italic>B. distachyon SCL33</italic>
 splicing patterns are also strikingly conserved compared with a distant Arabidopsis <italic>SCL33</italic>
 ortholog. This analysis provides new insights into <xref ref-type="def" rid="def1">AS</xref>
 landscapes conserved among monocots and dicots and uncovered <xref ref-type="def" rid="def1">AS</xref>
 events in plant defense-related genes.</p>
</abstract>
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<custom-meta-group><custom-meta><meta-name> DJS Export </meta-name>
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<notes><glossary><title>Glossary</title>
<def-list><def-item><term id="term1">AS</term>
<def id="def1"><p>alternative splicing</p>
</def>
</def-item>
<def-item><term id="term2">SPMV</term>
<def id="def2"><p><italic>Panicum mosaic virus</italic>
 satellite virus</p>
</def>
</def-item>
<def-item><term id="term3">PMV</term>
<def id="def3"><p><italic>Panicum mosaic virus</italic>
</p>
</def>
</def-item>
<def-item><term id="term4">RNA-seq</term>
<def id="def4"><p>RNA sequencing</p>
</def>
</def-item>
<def-item><term id="term5">dpi</term>
<def id="def5"><p>days postinoculation</p>
</def>
</def-item>
<def-item><term id="term6">FPKM</term>
<def id="def6"><p>fragments per kilobase of transcript per million mapped fragments</p>
</def>
</def-item>
<def-item><term id="term7">IR</term>
<def id="def7"><p>intron retention</p>
</def>
</def-item>
<def-item><term id="term8">ES</term>
<def id="def8"><p>exon skipping</p>
</def>
</def-item>
<def-item><term id="term9">AA</term>
<def id="def9"><p>alternate acceptor</p>
</def>
</def-item>
<def-item><term id="term10">AD</term>
<def id="def10"><p>alternate donor</p>
</def>
</def-item>
<def-item><term id="term11">FDR</term>
<def id="def11"><p>false discovery rate</p>
</def>
</def-item>
<def-item><term id="term12">GO</term>
<def id="def12"><p>Gene Ontology</p>
</def>
</def-item>
<def-item><term id="term13">NB-LRR</term>
<def id="def13"><p>nucleotide-binding site leucine-rich repeat</p>
</def>
</def-item>
</def-list>
</glossary>
</notes>
</front>
</pmc>
<affiliations><list></list>
<tree><noCountry><name sortKey="Mandadi, Kranthi K" sort="Mandadi, Kranthi K" uniqKey="Mandadi K" first="Kranthi K." last="Mandadi">Kranthi K. Mandadi</name>
<name sortKey="Scholthof, Karen Beth G" sort="Scholthof, Karen Beth G" uniqKey="Scholthof K" first="Karen-Beth G." last="Scholthof">Karen-Beth G. Scholthof</name>
</noCountry>
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</affiliations>
</record>

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Genome-Wide Analysis of Alternative Splicing Landscapes Modulated during Plant-Virus Interactions in Brachypodium distachyon

Genome-Wide Analysis of Alternative Splicing Landscapes Modulated during Plant-Virus Interactions in Brachypodium distachyon

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Abstract

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