Transcriptome analysis of sweet orange trees infected with ‘Candidatus Liberibacter asiaticus’ and two strains of Citrus Tristeza Virus
Identifieur interne : 000017 ( Main/Exploration ); précédent : 000016; suivant : 000018Transcriptome analysis of sweet orange trees infected with ‘Candidatus Liberibacter asiaticus’ and two strains of Citrus Tristeza Virus
Auteurs : Shimin Fu [République populaire de Chine, États-Unis] ; Jonathan Shao [États-Unis] ; Changyong Zhou [République populaire de Chine] ; John S. Hartung [États-Unis]Source :
- BMC Genomics [ 1471-2164 ] ; 2016.
Abstract
Huanglongbing (HLB) and tristeza, are diseases of citrus caused by a member of the α-proteobacteria, ‘
Transcriptome profiles obtained through RNA-seq revealed 611, 404 and 285 differentially expressed transcripts (DETs) after infection with CaLas-B232, CTV-B6 and CTV-B2. These DETs were components of a wide range of pathways involved in circadian rhythm, cell wall modification and cell organization, as well as transcription factors, transport, hormone response and secondary metabolism, signaling and stress response. The number of transcripts that responded to both CTV-B6 and CaLas-B232 was much larger than the number of transcripts that responded to both strains of CTV or to both CTV-B2 and CaLas-B232. A total of 38 genes were assayed by RT-qPCR and the correlation coefficients between Gfold and RT-qPCR were 0.82, 0.69, 0.81 for sweet orange plants infected with CTV-B2, CTV-B6 and CaLas-B232, respectively.
The number and composition of DETs reflected the complexity of symptoms caused by the pathogens in established infections, although the leaf tissues sampled were asymptomatic. There were greater similarities between the sweet orange in response to CTV-B6 and CaLas-B232 than between the two CTV strains, reflecting the similar physiological changes caused by both CTV-B6 and CaLas-B232. The circadian rhythm system of plants was perturbed by all three pathogens, especially by CTV-B6, and the ion balance was also disrupted by all three pathogens, especially by CaLas-B232. Defense responses related to cell wall modification, transcriptional regulation, hormones, secondary metabolites, kinases and stress were activated by all three pathogens but with different patterns. The transcriptome profiles of
The online version of this article (doi:10.1186/s12864-016-2663-9) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12864-016-2663-9
PubMed: 27169471
PubMed Central: 4865098
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Transcriptome analysis of sweet orange trees infected with ‘<italic>Candidatus</italic> Liberibacter asiaticus’ and two strains of <italic>Citrus Tristeza Virus</italic></title><author><name sortKey="Fu, Shimin" sort="Fu, Shimin" uniqKey="Fu S" first="Shimin" last="Fu">Shimin Fu</name><affiliation wicri:level="1"><nlm:aff id="Aff1">College of Plant Protection/Citrus Research Institute, Southwest University, Chongqing, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Plant Protection/Citrus Research Institute, Southwest University, Chongqing</wicri:regionArea><wicri:noRegion>Chongqing</wicri:noRegion></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff2">Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Maryland</region></placeName><wicri:cityArea>Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville</wicri:cityArea></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff3">Lingnan Normal University, Zhanjian, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Lingnan Normal University, Zhanjian</wicri:regionArea><wicri:noRegion>Zhanjian</wicri:noRegion></affiliation></author><author><name sortKey="Shao, Jonathan" sort="Shao, Jonathan" uniqKey="Shao J" first="Jonathan" last="Shao">Jonathan Shao</name><affiliation wicri:level="2"><nlm:aff id="Aff2">Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Maryland</region></placeName><wicri:cityArea>Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville</wicri:cityArea></affiliation></author><author><name sortKey="Zhou, Changyong" sort="Zhou, Changyong" uniqKey="Zhou C" first="Changyong" last="Zhou">Changyong Zhou</name><affiliation wicri:level="1"><nlm:aff id="Aff1">College of Plant Protection/Citrus Research Institute, Southwest University, Chongqing, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Plant Protection/Citrus Research Institute, Southwest University, Chongqing</wicri:regionArea><wicri:noRegion>Chongqing</wicri:noRegion></affiliation></author><author><name sortKey="Hartung, John S" sort="Hartung, John S" uniqKey="Hartung J" first="John S." last="Hartung">John S. Hartung</name><affiliation wicri:level="2"><nlm:aff id="Aff2">Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Maryland</region></placeName><wicri:cityArea>Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville</wicri:cityArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27169471</idno><idno type="pmc">4865098</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4865098</idno><idno type="RBID">PMC:4865098</idno><idno type="doi">10.1186/s12864-016-2663-9</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000605</idno><idno type="wicri:Area/Pmc/Curation">000604</idno><idno type="wicri:Area/Pmc/Checkpoint">000012</idno><idno type="wicri:source">PubMed</idno><idno type="wicri:Area/PubMed/Corpus">000047</idno><idno type="wicri:Area/PubMed/Curation">000047</idno><idno type="wicri:Area/PubMed/Checkpoint">000047</idno><idno type="wicri:Area/Ncbi/Merge">002025</idno><idno type="wicri:Area/Ncbi/Curation">002025</idno><idno type="wicri:Area/Ncbi/Checkpoint">002025</idno><idno type="wicri:Area/Main/Merge">000017</idno><idno type="wicri:Area/Main/Curation">000017</idno><idno type="wicri:Area/Main/Exploration">000017</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Transcriptome analysis of sweet orange trees infected with ‘<italic>Candidatus</italic> Liberibacter asiaticus’ and two strains of <italic>Citrus Tristeza Virus</italic></title><author><name sortKey="Fu, Shimin" sort="Fu, Shimin" uniqKey="Fu S" first="Shimin" last="Fu">Shimin Fu</name><affiliation wicri:level="1"><nlm:aff id="Aff1">College of Plant Protection/Citrus Research Institute, Southwest University, Chongqing, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Plant Protection/Citrus Research Institute, Southwest University, Chongqing</wicri:regionArea><wicri:noRegion>Chongqing</wicri:noRegion></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff2">Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Maryland</region></placeName><wicri:cityArea>Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville</wicri:cityArea></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff3">Lingnan Normal University, Zhanjian, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Lingnan Normal University, Zhanjian</wicri:regionArea><wicri:noRegion>Zhanjian</wicri:noRegion></affiliation></author><author><name sortKey="Shao, Jonathan" sort="Shao, Jonathan" uniqKey="Shao J" first="Jonathan" last="Shao">Jonathan Shao</name><affiliation wicri:level="2"><nlm:aff id="Aff2">Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Maryland</region></placeName><wicri:cityArea>Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville</wicri:cityArea></affiliation></author><author><name sortKey="Zhou, Changyong" sort="Zhou, Changyong" uniqKey="Zhou C" first="Changyong" last="Zhou">Changyong Zhou</name><affiliation wicri:level="1"><nlm:aff id="Aff1">College of Plant Protection/Citrus Research Institute, Southwest University, Chongqing, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Plant Protection/Citrus Research Institute, Southwest University, Chongqing</wicri:regionArea><wicri:noRegion>Chongqing</wicri:noRegion></affiliation></author><author><name sortKey="Hartung, John S" sort="Hartung, John S" uniqKey="Hartung J" first="John S." last="Hartung">John S. Hartung</name><affiliation wicri:level="2"><nlm:aff id="Aff2">Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Maryland</region></placeName><wicri:cityArea>Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville</wicri:cityArea></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2016">2016</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) and tristeza, are diseases of citrus caused by a member of the α-proteobacteria, ‘<italic>Candidatus</italic> Liberibacter asiaticus’ (CaLas), and <italic>Citrus tristeza virus</italic> (CTV) respectively. HLB is a devastating disease, but CTV strains vary from very severe to very mild. Both CaLas and CTV are phloem-restricted. The CaLas-B232 strain and CTV-B6 cause a wide range of severe and similar symptoms. The mild strain CTV-B2 doesn’t induce significant symptoms or damage to plants.</p></sec><sec><title>Results</title><p>Transcriptome profiles obtained through RNA-seq revealed 611, 404 and 285 differentially expressed transcripts (DETs) after infection with CaLas-B232, CTV-B6 and CTV-B2. These DETs were components of a wide range of pathways involved in circadian rhythm, cell wall modification and cell organization, as well as transcription factors, transport, hormone response and secondary metabolism, signaling and stress response. The number of transcripts that responded to both CTV-B6 and CaLas-B232 was much larger than the number of transcripts that responded to both strains of CTV or to both CTV-B2 and CaLas-B232. A total of 38 genes were assayed by RT-qPCR and the correlation coefficients between Gfold and RT-qPCR were 0.82, 0.69, 0.81 for sweet orange plants infected with CTV-B2, CTV-B6 and CaLas-B232, respectively.</p></sec><sec><title>Conclusions</title><p>The number and composition of DETs reflected the complexity of symptoms caused by the pathogens in established infections, although the leaf tissues sampled were asymptomatic. There were greater similarities between the sweet orange in response to CTV-B6 and CaLas-B232 than between the two CTV strains, reflecting the similar physiological changes caused by both CTV-B6 and CaLas-B232. The circadian rhythm system of plants was perturbed by all three pathogens, especially by CTV-B6, and the ion balance was also disrupted by all three pathogens, especially by CaLas-B232. Defense responses related to cell wall modification, transcriptional regulation, hormones, secondary metabolites, kinases and stress were activated by all three pathogens but with different patterns. The transcriptome profiles of <italic>Citrus sinensis</italic> identified host genes whose expression is affected by the presence of a pathogen in the phloem without producing symptoms (CTV-B2), and host genes whose expression leads to induction of symptoms in the plant (CTV-B6, CaLas-B232).</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12864-016-2663-9) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Moreno, P" uniqKey="Moreno P">P Moreno</name></author><author><name sortKey="Ambros, S" uniqKey="Ambros S">S Ambros</name></author><author><name sortKey="Albiach Marti, Mr" uniqKey="Albiach Marti M">MR Albiach-Marti</name></author><author><name sortKey="Guerri, J" uniqKey="Guerri J">J Guerri</name></author><author><name sortKey="Pena, L" uniqKey="Pena L">L 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Z" uniqKey="Du Z">Z Du</name></author><author><name sortKey="Su, Z" uniqKey="Su Z">Z Su</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Thimm, O" uniqKey="Thimm O">O Thimm</name></author><author><name sortKey="Bl Sing, O" uniqKey="Bl Sing O">O Bläsing</name></author><author><name sortKey="Gibon, Y" uniqKey="Gibon Y">Y Gibon</name></author><author><name sortKey="Nagel, A" uniqKey="Nagel A">A Nagel</name></author><author><name sortKey="Meyer, S" uniqKey="Meyer S">S Meyer</name></author><author><name sortKey="Kruger, P" uniqKey="Kruger P">P Krüger</name></author><author><name sortKey="Selbig, J" uniqKey="Selbig J">J Selbig</name></author><author><name sortKey="Muller, La" uniqKey="Muller L">LA Müller</name></author><author><name sortKey="Rhee, Sy" uniqKey="Rhee S">SY Rhee</name></author><author><name sortKey="Stitt, M" uniqKey="Stitt M">M Stitt</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Livak, Kj" uniqKey="Livak K">KJ Livak</name></author><author><name sortKey="Schmittgen, Td" uniqKey="Schmittgen T">TD Schmittgen</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>République populaire de Chine</li><li>États-Unis</li></country><region><li>Maryland</li></region></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Fu, Shimin" sort="Fu, Shimin" uniqKey="Fu S" first="Shimin" last="Fu">Shimin Fu</name></noRegion><name sortKey="Fu, Shimin" sort="Fu, Shimin" uniqKey="Fu S" first="Shimin" last="Fu">Shimin Fu</name><name sortKey="Zhou, Changyong" sort="Zhou, Changyong" uniqKey="Zhou C" first="Changyong" last="Zhou">Changyong Zhou</name></country><country name="États-Unis"><region name="Maryland"><name sortKey="Fu, Shimin" sort="Fu, Shimin" uniqKey="Fu S" first="Shimin" last="Fu">Shimin Fu</name></region><name sortKey="Hartung, John S" sort="Hartung, John S" uniqKey="Hartung J" first="John S." last="Hartung">John S. 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