Transcriptome comparison and gene coexpression network analysis provide a systems view of citrus response to ‘Candidatus Liberibacter asiaticus’ infection
Identifieur interne : 000C85 ( Main/Merge ); précédent : 000C84; suivant : 000C86Transcriptome comparison and gene coexpression network analysis provide a systems view of citrus response to ‘Candidatus Liberibacter asiaticus’ infection
Auteurs : Zhi-Liang Zheng [République populaire de Chine] ; Yihong Zhao [États-Unis]Source :
- BMC Genomics [ 1471-2164 ] ; 2013.
English descriptors
- KwdEn :
- Biological Transport (genetics), Citrus sinensis (cytology), Citrus sinensis (genetics), Citrus sinensis (metabolism), Citrus sinensis (microbiology), Gene Expression Profiling, Gene Regulatory Networks, Genes, Plant (genetics), Plant Diseases (immunology), Plant Diseases (microbiology), Plant Growth Regulators (metabolism), Rhizobiaceae (physiology), Signal Transduction (genetics), Time Factors, Up-Regulation, Zinc (metabolism).
- MESH :
- chemical , metabolism : Plant Growth Regulators, Zinc.
- cytology : Citrus sinensis.
- genetics : Biological Transport, Citrus sinensis, Genes, Plant, Signal Transduction.
- immunology : Plant Diseases.
- metabolism : Citrus sinensis.
- microbiology : Citrus sinensis, Plant Diseases.
- physiology : Rhizobiaceae.
- Gene Expression Profiling, Gene Regulatory Networks, Time Factors, Up-Regulation.
Abstract
Huanglongbing (HLB) is arguably the most destructive disease for the citrus industry. HLB is caused by infection of the bacterium,
As a first step towards a mechanistic view of citrus in response to the HLB bacterial infection, we performed a comparative transcriptome analysis and found that a total of 21 Probesets are commonly up-regulated by the HLB bacterial infection. In addition, a number of genes are likely regulated specifically at early, late or very late stages of the infection. Furthermore, using Pearson correlation coefficient-based gene coexpression analysis, we constructed a citrus HLB response network consisting of 3,507 Probesets and 56,287 interactions. Genes involved in carbohydrate and nitrogen metabolic processes, transport, defense, signaling and hormone response were overrepresented in the HLB response network and the subnetworks for these processes were constructed. Analysis of the defense and hormone response subnetworks indicates that hormone response is interconnected with defense response. In addition, mapping the commonly up-regulated HLB responsive genes into the HLB response network resulted in a core subnetwork where transport plays a key role in the citrus response to the HLB bacterial infection. Moreover, analysis of a phloem protein subnetwork indicates a role for this protein and zinc transporters or zinc-binding proteins in the citrus HLB defense response.
Through integrating transcriptome comparison and gene coexpression network analysis, we have provided for the first time a systems view of citrus in response to the
Url:
DOI: 10.1186/1471-2164-14-27
PubMed: 23324561
PubMed Central: 3577516
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PMC:3577516Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Transcriptome comparison and gene coexpression network analysis provide a systems view of citrus response to ‘<italic>Candidatus</italic> Liberibacter asiaticus’ infection</title><author><name sortKey="Zheng, Zhi Liang" sort="Zheng, Zhi Liang" uniqKey="Zheng Z" first="Zhi-Liang" last="Zheng">Zhi-Liang Zheng</name><affiliation wicri:level="1"><nlm:aff id="I1">Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, Citrus Research Institute & College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400712, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, Citrus Research Institute & College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400712</wicri:regionArea><wicri:noRegion>400712</wicri:noRegion></affiliation></author><author><name sortKey="Zhao, Yihong" sort="Zhao, Yihong" uniqKey="Zhao Y" first="Yihong" last="Zhao">Yihong Zhao</name><affiliation wicri:level="4"><nlm:aff id="I2">Department of Psychiatry, Columbia University, New York, NY, 10032, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Psychiatry, Columbia University, New York, NY, 10032</wicri:regionArea><orgName type="university">Université Columbia</orgName><placeName><settlement type="city">New York</settlement><region type="state">État de New York</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">23324561</idno><idno type="pmc">3577516</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3577516</idno><idno type="RBID">PMC:3577516</idno><idno type="doi">10.1186/1471-2164-14-27</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">000B18</idno><idno type="wicri:Area/Pmc/Curation">000B17</idno><idno type="wicri:Area/Pmc/Checkpoint">000955</idno><idno type="wicri:source">PubMed</idno><idno type="wicri:Area/PubMed/Corpus">000500</idno><idno type="wicri:Area/PubMed/Curation">000500</idno><idno type="wicri:Area/PubMed/Checkpoint">000500</idno><idno type="wicri:Area/Ncbi/Merge">001194</idno><idno type="wicri:Area/Ncbi/Curation">001194</idno><idno type="wicri:Area/Ncbi/Checkpoint">001194</idno><idno type="wicri:Area/Main/Merge">000C85</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Transcriptome comparison and gene coexpression network analysis provide a systems view of citrus response to ‘<italic>Candidatus</italic> Liberibacter asiaticus’ infection</title><author><name sortKey="Zheng, Zhi Liang" sort="Zheng, Zhi Liang" uniqKey="Zheng Z" first="Zhi-Liang" last="Zheng">Zhi-Liang Zheng</name><affiliation wicri:level="1"><nlm:aff id="I1">Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, Citrus Research Institute & College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400712, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, Citrus Research Institute & College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400712</wicri:regionArea><wicri:noRegion>400712</wicri:noRegion></affiliation></author><author><name sortKey="Zhao, Yihong" sort="Zhao, Yihong" uniqKey="Zhao Y" first="Yihong" last="Zhao">Yihong Zhao</name><affiliation wicri:level="4"><nlm:aff id="I2">Department of Psychiatry, Columbia University, New York, NY, 10032, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Psychiatry, Columbia University, New York, NY, 10032</wicri:regionArea><orgName type="university">Université Columbia</orgName><placeName><settlement type="city">New York</settlement><region type="state">État de New York</region></placeName></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Biological Transport (genetics)</term><term>Citrus sinensis (cytology)</term><term>Citrus sinensis (genetics)</term><term>Citrus sinensis (metabolism)</term><term>Citrus sinensis (microbiology)</term><term>Gene Expression Profiling</term><term>Gene Regulatory Networks</term><term>Genes, Plant (genetics)</term><term>Plant Diseases (immunology)</term><term>Plant Diseases (microbiology)</term><term>Plant Growth Regulators (metabolism)</term><term>Rhizobiaceae (physiology)</term><term>Signal Transduction (genetics)</term><term>Time Factors</term><term>Up-Regulation</term><term>Zinc (metabolism)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Plant Growth Regulators</term><term>Zinc</term></keywords><keywords scheme="MESH" qualifier="cytology" xml:lang="en"><term>Citrus sinensis</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Biological Transport</term><term>Citrus sinensis</term><term>Genes, Plant</term><term>Signal Transduction</term></keywords><keywords scheme="MESH" qualifier="immunology" xml:lang="en"><term>Plant Diseases</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Citrus sinensis</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Citrus sinensis</term><term>Plant Diseases</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Rhizobiaceae</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Expression Profiling</term><term>Gene Regulatory Networks</term><term>Time Factors</term><term>Up-Regulation</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Huanglongbing (HLB) is arguably the most destructive disease for the citrus industry. HLB is caused by infection of the bacterium, <italic>Candidatus</italic> Liberibacter spp. Several citrus GeneChip studies have revealed thousands of genes that are up- or down-regulated by infection with <italic>Ca.</italic> Liberibacter asiaticus. However, whether and how these host genes act to protect against HLB remains poorly understood.</p></sec><sec><title>Results</title><p>As a first step towards a mechanistic view of citrus in response to the HLB bacterial infection, we performed a comparative transcriptome analysis and found that a total of 21 Probesets are commonly up-regulated by the HLB bacterial infection. In addition, a number of genes are likely regulated specifically at early, late or very late stages of the infection. Furthermore, using Pearson correlation coefficient-based gene coexpression analysis, we constructed a citrus HLB response network consisting of 3,507 Probesets and 56,287 interactions. Genes involved in carbohydrate and nitrogen metabolic processes, transport, defense, signaling and hormone response were overrepresented in the HLB response network and the subnetworks for these processes were constructed. Analysis of the defense and hormone response subnetworks indicates that hormone response is interconnected with defense response. In addition, mapping the commonly up-regulated HLB responsive genes into the HLB response network resulted in a core subnetwork where transport plays a key role in the citrus response to the HLB bacterial infection. Moreover, analysis of a phloem protein subnetwork indicates a role for this protein and zinc transporters or zinc-binding proteins in the citrus HLB defense response.</p></sec><sec><title>Conclusion</title><p>Through integrating transcriptome comparison and gene coexpression network analysis, we have provided for the first time a systems view of citrus in response to the <italic>Ca.</italic> Liberibacter spp. infection causing HLB.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Zhao, Xy" uniqKey="Zhao X">XY Zhao</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="De Graca, Jv" uniqKey="De Graca J">JV de Graça</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, N" uniqKey="Wang N">N Wang</name></author><author><name sortKey="Li, W" uniqKey="Li W">W Li</name></author><author><name sortKey="Irey, M" uniqKey="Irey M">M Irey</name></author><author><name 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