Comprehensive meta-analysis, co-expression, and miRNA nested network analysis identifies gene candidates in citrus against Huanglongbing disease
Identifieur interne : 000560 ( Pmc/Checkpoint ); précédent : 000559; suivant : 000561Comprehensive meta-analysis, co-expression, and miRNA nested network analysis identifies gene candidates in citrus against Huanglongbing disease
Auteurs : Nidhi Rawat [États-Unis] ; Sandhya P. Kiran [Inde] ; Dongliang Du [États-Unis] ; Fred G. Gmitter [États-Unis] ; Zhanao Deng [États-Unis]Source :
- BMC Plant Biology [ 1471-2229 ] ; 2015.
Abstract
Huanglongbing (HLB), the most devastating disease of citrus, is associated with infection by
Twenty-two publically available transcriptome studies on citrus–HLB interactions, comprising 18 susceptible (S) datasets and four resistant (R) datasets, were investigated using Limma and RankProd methods of meta-analysis. A combined list of 7,412 differentially expressed probe sets was generated using a Teradata in-house Structured Query Language (SQL) script. We identified the 65 most common probe sets modulated in HLB disease among different tissues from the S and R datasets. Gene ontology analysis of these probe sets suggested that carbohydrate metabolism, nutrient transport, and biotic stress were the core pathways that were modulated in citrus by
Most of the potential candidate hub probe sets were co-expressed with gibberellin pathway (GA)-related probe sets, implying the role of GA signalling in HLB resistance. Our findings contribute to the integration of existing citrus–HLB transcriptome data that will help to elucidate the holistic picture of the citrus–HLB interaction. The citrus probe sets identified in this analysis signify a robust set of HLB-responsive candidates that are useful for further validation.
The online version of this article (doi:10.1186/s12870-015-0568-4) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12870-015-0568-4
PubMed: 26215595
PubMed Central: 4517500
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Comprehensive meta-analysis, co-expression, and miRNA nested network analysis identifies gene candidates in citrus against Huanglongbing disease</title><author><name sortKey="Rawat, Nidhi" sort="Rawat, Nidhi" uniqKey="Rawat N" first="Nidhi" last="Rawat">Nidhi Rawat</name><affiliation wicri:level="2"><nlm:aff id="Aff1">University of Florida, Institute of Food and Agricultural Sciences, Gulf Coast Research and Education Center, Wimauma, FL 33598 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>University of Florida, Institute of Food and Agricultural Sciences, Gulf Coast Research and Education Center, Wimauma</wicri:cityArea></affiliation></author><author><name sortKey="Kiran, Sandhya P" sort="Kiran, Sandhya P" uniqKey="Kiran S" first="Sandhya P." last="Kiran">Sandhya P. Kiran</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Ocimum BioSolutions, Banjara Hills Road No. 1, VI Floor Reliance Classic, Hyderabad, 500039 India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Ocimum BioSolutions, Banjara Hills Road No. 1, VI Floor Reliance Classic, Hyderabad</wicri:regionArea><wicri:noRegion>Hyderabad</wicri:noRegion></affiliation></author><author><name sortKey="Du, Dongliang" sort="Du, Dongliang" uniqKey="Du D" first="Dongliang" last="Du">Dongliang Du</name><affiliation wicri:level="2"><nlm:aff id="Aff3">University of Florida, Institute of Food and Agricultural Sciences, Citrus Research and Education Center, Lake Alfred, FL 33850 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>University of Florida, Institute of Food and Agricultural Sciences, Citrus Research and Education Center, Lake Alfred</wicri:cityArea></affiliation></author><author><name sortKey="Gmitter, Fred G" sort="Gmitter, Fred G" uniqKey="Gmitter F" first="Fred G." last="Gmitter">Fred G. Gmitter</name><affiliation wicri:level="2"><nlm:aff id="Aff3">University of Florida, Institute of Food and Agricultural Sciences, Citrus Research and Education Center, Lake Alfred, FL 33850 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>University of Florida, Institute of Food and Agricultural Sciences, Citrus Research and Education Center, Lake Alfred</wicri:cityArea></affiliation></author><author><name sortKey="Deng, Zhanao" sort="Deng, Zhanao" uniqKey="Deng Z" first="Zhanao" last="Deng">Zhanao Deng</name><affiliation wicri:level="2"><nlm:aff id="Aff1">University of Florida, Institute of Food and Agricultural Sciences, Gulf Coast Research and Education Center, Wimauma, FL 33598 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>University of Florida, Institute of Food and Agricultural Sciences, Gulf Coast Research and Education Center, Wimauma</wicri:cityArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26215595</idno><idno type="pmc">4517500</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517500</idno><idno type="RBID">PMC:4517500</idno><idno type="doi">10.1186/s12870-015-0568-4</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000631</idno><idno type="wicri:Area/Pmc/Curation">000630</idno><idno type="wicri:Area/Pmc/Checkpoint">000560</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Comprehensive meta-analysis, co-expression, and miRNA nested network analysis identifies gene candidates in citrus against Huanglongbing disease</title><author><name sortKey="Rawat, Nidhi" sort="Rawat, Nidhi" uniqKey="Rawat N" first="Nidhi" last="Rawat">Nidhi Rawat</name><affiliation wicri:level="2"><nlm:aff id="Aff1">University of Florida, Institute of Food and Agricultural Sciences, Gulf Coast Research and Education Center, Wimauma, FL 33598 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>University of Florida, Institute of Food and Agricultural Sciences, Gulf Coast Research and Education Center, Wimauma</wicri:cityArea></affiliation></author><author><name sortKey="Kiran, Sandhya P" sort="Kiran, Sandhya P" uniqKey="Kiran S" first="Sandhya P." last="Kiran">Sandhya P. Kiran</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Ocimum BioSolutions, Banjara Hills Road No. 1, VI Floor Reliance Classic, Hyderabad, 500039 India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Ocimum BioSolutions, Banjara Hills Road No. 1, VI Floor Reliance Classic, Hyderabad</wicri:regionArea><wicri:noRegion>Hyderabad</wicri:noRegion></affiliation></author><author><name sortKey="Du, Dongliang" sort="Du, Dongliang" uniqKey="Du D" first="Dongliang" last="Du">Dongliang Du</name><affiliation wicri:level="2"><nlm:aff id="Aff3">University of Florida, Institute of Food and Agricultural Sciences, Citrus Research and Education Center, Lake Alfred, FL 33850 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>University of Florida, Institute of Food and Agricultural Sciences, Citrus Research and Education Center, Lake Alfred</wicri:cityArea></affiliation></author><author><name sortKey="Gmitter, Fred G" sort="Gmitter, Fred G" uniqKey="Gmitter F" first="Fred G." last="Gmitter">Fred G. Gmitter</name><affiliation wicri:level="2"><nlm:aff id="Aff3">University of Florida, Institute of Food and Agricultural Sciences, Citrus Research and Education Center, Lake Alfred, FL 33850 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>University of Florida, Institute of Food and Agricultural Sciences, Citrus Research and Education Center, Lake Alfred</wicri:cityArea></affiliation></author><author><name sortKey="Deng, Zhanao" sort="Deng, Zhanao" uniqKey="Deng Z" first="Zhanao" last="Deng">Zhanao Deng</name><affiliation wicri:level="2"><nlm:aff id="Aff1">University of Florida, Institute of Food and Agricultural Sciences, Gulf Coast Research and Education Center, Wimauma, FL 33598 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>University of Florida, Institute of Food and Agricultural Sciences, Gulf Coast Research and Education Center, Wimauma</wicri:cityArea></affiliation></author></analytic><series><title level="j">BMC Plant Biology</title><idno type="eISSN">1471-2229</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Huanglongbing (HLB), the most devastating disease of citrus, is associated with infection by <italic>Candidatus</italic> Liberibacter asiaticus (<italic>Ca</italic>Las) and is vectored by the Asian citrus psyllid (ACP). Recently, the molecular basis of citrus–HLB interactions has been examined using transcriptome analyses, and these analyses have identified many probe sets and pathways modulated by <italic>Ca</italic>Las infection among different citrus cultivars. However, lack of consistency among reported findings indicates that an integrative approach is needed. This study was designed to identify the candidate probe sets in citrus–HLB interactions using meta-analysis and gene co-expression network modelling.</p></sec><sec><title>Results</title><p>Twenty-two publically available transcriptome studies on citrus–HLB interactions, comprising 18 susceptible (S) datasets and four resistant (R) datasets, were investigated using Limma and RankProd methods of meta-analysis. A combined list of 7,412 differentially expressed probe sets was generated using a Teradata in-house Structured Query Language (SQL) script. We identified the 65 most common probe sets modulated in HLB disease among different tissues from the S and R datasets. Gene ontology analysis of these probe sets suggested that carbohydrate metabolism, nutrient transport, and biotic stress were the core pathways that were modulated in citrus by <italic>Ca</italic>Las infection and HLB development. We also identified R-specific probe sets, which encoded leucine-rich repeat proteins, chitinase, constitutive disease resistance (CDR), miraculins, and lectins. Weighted gene co-expression network analysis (WGCNA) was conducted on 3,499 probe sets, and 21 modules with major hub probe sets were identified. Further, a miRNA nested network was created to examine gene regulation of the 3,499 target probe sets. Results suggest that csi-miR167 and csi-miR396 could affect ion transporters and defence response pathways, respectively.</p></sec><sec><title>Conclusion</title><p>Most of the potential candidate hub probe sets were co-expressed with gibberellin pathway (GA)-related probe sets, implying the role of GA signalling in HLB resistance. Our findings contribute to the integration of existing citrus–HLB transcriptome data that will help to elucidate the holistic picture of the citrus–HLB interaction. The citrus probe sets identified in this analysis signify a robust set of HLB-responsive candidates that are useful for further validation.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12870-015-0568-4) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Albrecht, U" uniqKey="Albrecht U">U Albrecht</name></author><author><name sortKey="Bowman, Kd" uniqKey="Bowman K">KD Bowman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Albrecht, U" uniqKey="Albrecht U">U Albrecht</name></author><author><name sortKey="Bowman, Kd" uniqKey="Bowman K">KD Bowman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Aritua, V" uniqKey="Aritua V">V Aritua</name></author><author><name sortKey="Achor, D" uniqKey="Achor D">D 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<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Plant Biol</journal-id><journal-id journal-id-type="iso-abbrev">BMC Plant Biol</journal-id><journal-title-group><journal-title>BMC Plant Biology</journal-title></journal-title-group><issn pub-type="epub">1471-2229</issn><publisher><publisher-name>BioMed Central</publisher-name><publisher-loc>London</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">26215595</article-id><article-id pub-id-type="pmc">4517500</article-id><article-id pub-id-type="publisher-id">568</article-id><article-id pub-id-type="doi">10.1186/s12870-015-0568-4</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>Comprehensive meta-analysis, co-expression, and miRNA nested network analysis identifies gene candidates in citrus against Huanglongbing disease</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Rawat</surname><given-names>Nidhi</given-names></name><address><email>nrawat@ufl.edu</email></address><xref ref-type="aff" rid="Aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Kiran</surname><given-names>Sandhya P.</given-names></name><address><email>p_sandhyakiran@yahoo.com</email></address><xref ref-type="aff" rid="Aff2"></xref></contrib><contrib contrib-type="author"><name><surname>Du</surname><given-names>Dongliang</given-names></name><address><email>dldu@ufl.edu</email></address><xref ref-type="aff" rid="Aff3"></xref></contrib><contrib contrib-type="author"><name><surname>Gmitter</surname><given-names>Fred G.</given-names><suffix>Jr</suffix></name><address><email>fgmitter@ufl.edu</email></address><xref ref-type="aff" rid="Aff3"></xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Deng</surname><given-names>Zhanao</given-names></name><address><email>zdeng@ufl.edu</email></address><xref ref-type="aff" rid="Aff1"></xref></contrib><aff id="Aff1"><label></label>University of Florida, Institute of Food and Agricultural Sciences, Gulf Coast Research and Education Center, Wimauma, FL 33598 USA</aff><aff id="Aff2"><label></label>Ocimum BioSolutions, Banjara Hills Road No. 1, VI Floor Reliance Classic, Hyderabad, 500039 India</aff><aff id="Aff3"><label></label>University of Florida, Institute of Food and Agricultural Sciences, Citrus Research and Education Center, Lake Alfred, FL 33850 USA</aff></contrib-group><pub-date pub-type="epub"><day>28</day><month>7</month><year>2015</year></pub-date><pub-date pub-type="pmc-release"><day>28</day><month>7</month><year>2015</year></pub-date><pub-date pub-type="collection"><year>2015</year></pub-date><volume>15</volume><elocation-id>184</elocation-id><history><date date-type="received"><day>9</day><month>4</month><year>2015</year></date><date date-type="accepted"><day>7</day><month>7</month><year>2015</year></date></history><permissions><copyright-statement>© Rawat et al. 2015</copyright-statement><license license-type="open-access"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0">http://creativecommons.org/licenses/by/4.0</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>) applies to the data made available in this article, unless otherwise stated.</license-p></license></permissions><abstract id="Abs1"><sec><title>Background</title><p>Huanglongbing (HLB), the most devastating disease of citrus, is associated with infection by <italic>Candidatus</italic> Liberibacter asiaticus (<italic>Ca</italic>Las) and is vectored by the Asian citrus psyllid (ACP). Recently, the molecular basis of citrus–HLB interactions has been examined using transcriptome analyses, and these analyses have identified many probe sets and pathways modulated by <italic>Ca</italic>Las infection among different citrus cultivars. However, lack of consistency among reported findings indicates that an integrative approach is needed. This study was designed to identify the candidate probe sets in citrus–HLB interactions using meta-analysis and gene co-expression network modelling.</p></sec><sec><title>Results</title><p>Twenty-two publically available transcriptome studies on citrus–HLB interactions, comprising 18 susceptible (S) datasets and four resistant (R) datasets, were investigated using Limma and RankProd methods of meta-analysis. A combined list of 7,412 differentially expressed probe sets was generated using a Teradata in-house Structured Query Language (SQL) script. We identified the 65 most common probe sets modulated in HLB disease among different tissues from the S and R datasets. Gene ontology analysis of these probe sets suggested that carbohydrate metabolism, nutrient transport, and biotic stress were the core pathways that were modulated in citrus by <italic>Ca</italic>Las infection and HLB development. We also identified R-specific probe sets, which encoded leucine-rich repeat proteins, chitinase, constitutive disease resistance (CDR), miraculins, and lectins. Weighted gene co-expression network analysis (WGCNA) was conducted on 3,499 probe sets, and 21 modules with major hub probe sets were identified. Further, a miRNA nested network was created to examine gene regulation of the 3,499 target probe sets. Results suggest that csi-miR167 and csi-miR396 could affect ion transporters and defence response pathways, respectively.</p></sec><sec><title>Conclusion</title><p>Most of the potential candidate hub probe sets were co-expressed with gibberellin pathway (GA)-related probe sets, implying the role of GA signalling in HLB resistance. Our findings contribute to the integration of existing citrus–HLB transcriptome data that will help to elucidate the holistic picture of the citrus–HLB interaction. The citrus probe sets identified in this analysis signify a robust set of HLB-responsive candidates that are useful for further validation.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12870-015-0568-4) contains supplementary material, which is available to authorized users.</p></sec></abstract><kwd-group xml:lang="en"><title>Keywords</title><kwd>Citrus</kwd><kwd>Gene co-expression analysis</kwd><kwd>Gene ontology</kwd><kwd>Huanglongbing</kwd><kwd>HLB resistance</kwd><kwd>Meta-analysis</kwd><kwd>miRNA network analysis</kwd><kwd>Common and R-specific probe sets</kwd></kwd-group><custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name><meta-value>© The Author(s) 2015</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc><affiliations><list><country><li>Inde</li><li>États-Unis</li></country><region><li>Floride</li></region></list><tree><country name="États-Unis"><region name="Floride"><name sortKey="Rawat, Nidhi" sort="Rawat, Nidhi" uniqKey="Rawat N" first="Nidhi" last="Rawat">Nidhi Rawat</name></region><name sortKey="Deng, Zhanao" sort="Deng, Zhanao" uniqKey="Deng Z" first="Zhanao" last="Deng">Zhanao Deng</name><name sortKey="Du, Dongliang" sort="Du, Dongliang" uniqKey="Du D" first="Dongliang" last="Du">Dongliang Du</name><name sortKey="Gmitter, Fred G" sort="Gmitter, Fred G" uniqKey="Gmitter F" first="Fred G." last="Gmitter">Fred G. Gmitter</name></country><country name="Inde"><noRegion><name sortKey="Kiran, Sandhya P" sort="Kiran, Sandhya P" uniqKey="Kiran S" first="Sandhya P." last="Kiran">Sandhya P. Kiran</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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