Identification of MiRNA from Eggplant (Solanum melongena L.) by Small RNA Deep Sequencing and Their Response to Verticillium dahliae Infection
Identifieur interne : 001415 ( Ncbi/Merge ); précédent : 001414; suivant : 001416Identification of MiRNA from Eggplant (Solanum melongena L.) by Small RNA Deep Sequencing and Their Response to Verticillium dahliae Infection
Auteurs : Liu Yang ; Dengwei Jue ; Wang Li ; Ruijie Zhang ; Min Chen ; Qing YangSource :
- PLoS ONE [ 1932-6203 ] ; 2013.
Abstract
MiRNAs are a class of non-coding small RNAs that play important roles in the regulation of gene expression. Although plant miRNAs have been extensively studied in model systems, less is known in other plants with limited genome sequence data, including eggplant (
Url:
DOI: 10.1371/journal.pone.0072840
PubMed: 24015279
PubMed Central: 3754920
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PMC:3754920Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Identification of MiRNA from Eggplant (<italic>Solanum melongena</italic>
L.) by Small RNA Deep Sequencing and Their Response to <italic>Verticillium dahliae</italic>
Infection</title>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Identification of MiRNA from Eggplant (<italic>Solanum melongena</italic>
L.) by Small RNA Deep Sequencing and Their Response to <italic>Verticillium dahliae</italic>
Infection</title>
<author><name sortKey="Yang, Liu" sort="Yang, Liu" uniqKey="Yang L" first="Liu" last="Yang">Liu Yang</name>
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<author><name sortKey="Zhang, Ruijie" sort="Zhang, Ruijie" uniqKey="Zhang R" first="Ruijie" last="Zhang">Ruijie Zhang</name>
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<author><name sortKey="Chen, Min" sort="Chen, Min" uniqKey="Chen M" first="Min" last="Chen">Min Chen</name>
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<author><name sortKey="Yang, Qing" sort="Yang, Qing" uniqKey="Yang Q" first="Qing" last="Yang">Qing Yang</name>
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<front><div type="abstract" xml:lang="en"><p>MiRNAs are a class of non-coding small RNAs that play important roles in the regulation of gene expression. Although plant miRNAs have been extensively studied in model systems, less is known in other plants with limited genome sequence data, including eggplant (<italic>Solanum melongena</italic>
L.). To identify miRNAs in eggplant and their response to <italic>Verticillium dahliae</italic>
infection, a fungal pathogen for which clear understanding of infection mechanisms and effective cure methods are currently lacking, we deep-sequenced two small RNA (sRNA) libraries prepared from mock-infected and infected seedlings of eggplants. Specifically, 30,830,792 reads produced 7,716,328 unique miRNAs representing 99 known miRNA families that have been identified in other plant species. Two novel putative miRNAs were predicted with eggplant ESTs. The potential targets of the identified known and novel miRNAs were also predicted based on sequence homology search. It was observed that the length distribution of obtained sRNAs and the expression of 6 miRNA families were obviously different between the two libraries. These results provide a framework for further analysis of miRNAs and their role in regulating plant response to fungal infection and Verticillium wilt in particular.</p>
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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">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">24015279</article-id>
<article-id pub-id-type="pmc">3754920</article-id>
<article-id pub-id-type="publisher-id">PONE-D-13-00797</article-id>
<article-id pub-id-type="doi">10.1371/journal.pone.0072840</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
<subj-group subj-group-type="Discipline-v2"><subject>Agriculture</subject>
<subj-group><subject>Crops</subject>
<subj-group><subject>Crop Diseases</subject>
<subject>Vegetables</subject>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v2"><subject>Biology</subject>
<subj-group><subject>Computational Biology</subject>
<subj-group><subject>Genomics</subject>
<subj-group><subject>Genome Expression Analysis</subject>
<subject>Genome Sequencing</subject>
</subj-group>
</subj-group>
<subj-group><subject>Sequence Analysis</subject>
</subj-group>
</subj-group>
<subj-group><subject>Genomics</subject>
</subj-group>
<subj-group><subject>Plant Science</subject>
<subj-group><subject>Plant Genomics</subject>
<subject>Plant Pathology</subject>
</subj-group>
</subj-group>
</subj-group>
</article-categories>
<title-group><article-title>Identification of MiRNA from Eggplant (<italic>Solanum melongena</italic>
L.) by Small RNA Deep Sequencing and Their Response to <italic>Verticillium dahliae</italic>
Infection</article-title>
<alt-title alt-title-type="running-head">Deep Sequencing of Eggplant Small RNAs</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Yang</surname>
<given-names>Liu</given-names>
</name>
<xref ref-type="aff" rid="aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Jue</surname>
<given-names>Dengwei</given-names>
</name>
<xref ref-type="aff" rid="aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Li</surname>
<given-names>Wang</given-names>
</name>
<xref ref-type="aff" rid="aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Zhang</surname>
<given-names>Ruijie</given-names>
</name>
<xref ref-type="aff" rid="aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Chen</surname>
<given-names>Min</given-names>
</name>
<xref ref-type="aff" rid="aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Yang</surname>
<given-names>Qing</given-names>
</name>
<xref ref-type="aff" rid="aff1"></xref>
<xref ref-type="corresp" rid="cor1"><sup>*</sup>
</xref>
</contrib>
</contrib-group>
<aff id="aff1"><addr-line>College of Life Sciences, Nanjing Agricultural University, Nanjing, P.R. China</addr-line>
</aff>
<contrib-group><contrib contrib-type="editor"><name><surname>Vinatzer</surname>
<given-names>Boris Alexander</given-names>
</name>
<role>Editor</role>
<xref ref-type="aff" rid="edit1"></xref>
</contrib>
</contrib-group>
<aff id="edit1"><addr-line>Virginia Tech, United States of America</addr-line>
</aff>
<author-notes><corresp id="cor1">* E-mail: <email>qyang19@njau.edu.cn</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: LY QY. Performed the experiments: LY DJ WL RZ MC. Analyzed the data: LY DJ WL. Contributed reagents/materials/analysis tools: QY. Wrote the paper: LY QY.</p>
</fn>
</author-notes>
<pub-date pub-type="collection"><year>2013</year>
</pub-date>
<pub-date pub-type="epub"><day>27</day>
<month>8</month>
<year>2013</year>
</pub-date>
<volume>8</volume>
<issue>8</issue>
<elocation-id>e72840</elocation-id>
<history><date date-type="received"><day>31</day>
<month>12</month>
<year>2012</year>
</date>
<date date-type="accepted"><day>16</day>
<month>7</month>
<year>2013</year>
</date>
</history>
<permissions><copyright-year>2013</copyright-year>
<copyright-holder>Yang et al</copyright-holder>
<license><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p>
</license>
</permissions>
<abstract><p>MiRNAs are a class of non-coding small RNAs that play important roles in the regulation of gene expression. Although plant miRNAs have been extensively studied in model systems, less is known in other plants with limited genome sequence data, including eggplant (<italic>Solanum melongena</italic>
L.). To identify miRNAs in eggplant and their response to <italic>Verticillium dahliae</italic>
infection, a fungal pathogen for which clear understanding of infection mechanisms and effective cure methods are currently lacking, we deep-sequenced two small RNA (sRNA) libraries prepared from mock-infected and infected seedlings of eggplants. Specifically, 30,830,792 reads produced 7,716,328 unique miRNAs representing 99 known miRNA families that have been identified in other plant species. Two novel putative miRNAs were predicted with eggplant ESTs. The potential targets of the identified known and novel miRNAs were also predicted based on sequence homology search. It was observed that the length distribution of obtained sRNAs and the expression of 6 miRNA families were obviously different between the two libraries. These results provide a framework for further analysis of miRNAs and their role in regulating plant response to fungal infection and Verticillium wilt in particular.</p>
</abstract>
<funding-group><funding-statement>This study was supported financially by grants from the Jiangsu Agricultural Science and Technology Innovation Fund (NO. cx (11)1020), the National ‘863’ High-tech Program (NO. 2010AA10A108), the National Pear Industry Technology System (NO. CARS-29) and A Project Funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions: Modern horticultural science (PAPD). 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="10"></page-count>
</counts>
</article-meta>
</front>
</pmc>
<affiliations><list></list>
<tree><noCountry><name sortKey="Chen, Min" sort="Chen, Min" uniqKey="Chen M" first="Min" last="Chen">Min Chen</name>
<name sortKey="Jue, Dengwei" sort="Jue, Dengwei" uniqKey="Jue D" first="Dengwei" last="Jue">Dengwei Jue</name>
<name sortKey="Li, Wang" sort="Li, Wang" uniqKey="Li W" first="Wang" last="Li">Wang Li</name>
<name sortKey="Yang, Liu" sort="Yang, Liu" uniqKey="Yang L" first="Liu" last="Yang">Liu Yang</name>
<name sortKey="Yang, Qing" sort="Yang, Qing" uniqKey="Yang Q" first="Qing" last="Yang">Qing Yang</name>
<name sortKey="Zhang, Ruijie" sort="Zhang, Ruijie" uniqKey="Zhang R" first="Ruijie" last="Zhang">Ruijie Zhang</name>
</noCountry>
</tree>
</affiliations>
</record>
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