Confirmation of the sequence of 'Candidatus Liberibacter asiaticus' and assessment of microbial diversity in Huanglongbing-infected citrus phloem using a metagenomic approach.
Identifieur interne : 000253 ( Main/Exploration ); précédent : 000252; suivant : 000254Confirmation of the sequence of 'Candidatus Liberibacter asiaticus' and assessment of microbial diversity in Huanglongbing-infected citrus phloem using a metagenomic approach.
Auteurs : Heather L. Tyler [États-Unis] ; Luiz F W. Roesch ; Siddarame Gowda ; William O. Dawson ; Eric W. TriplettSource :
- Molecular plant-microbe interactions : MPMI [ 0894-0282 ] ; 2009.
Descripteurs français
- KwdFr :
- ARN ribosomique 16S (génétique), Analyse de profil d'expression de gènes (MeSH), Citrus (microbiologie), Données de séquences moléculaires (MeSH), Génomique (MeSH), Interactions hôte-pathogène (MeSH), Maladies des plantes (microbiologie), Phloème (microbiologie), Rhizobiaceae (classification), Rhizobiaceae (génétique), Rhizobiaceae (isolement et purification), Régulation de l'expression des gènes bactériens (MeSH), Variation génétique (MeSH), Virus à ADN (isolement et purification).
- MESH :
- génétique : ARN ribosomique 16S, Rhizobiaceae.
- isolement et purification : Rhizobiaceae, Virus à ADN.
- microbiologie : Citrus, Maladies des plantes, Phloème.
- Analyse de profil d'expression de gènes, Données de séquences moléculaires, Génomique, Interactions hôte-pathogène, Régulation de l'expression des gènes bactériens, Variation génétique.
English descriptors
- KwdEn :
- Citrus (microbiology), DNA Viruses (isolation & purification), Gene Expression Profiling (MeSH), Gene Expression Regulation, Bacterial (MeSH), Genetic Variation (MeSH), Genomics (MeSH), Host-Pathogen Interactions (MeSH), Molecular Sequence Data (MeSH), Phloem (microbiology), Plant Diseases (microbiology), RNA, Ribosomal, 16S (genetics), Rhizobiaceae (classification), Rhizobiaceae (genetics), Rhizobiaceae (isolation & purification).
- MESH :
- chemical , genetics : RNA, Ribosomal, 16S.
- classification : Rhizobiaceae.
- genetics : Rhizobiaceae.
- isolation & purification : DNA Viruses, Rhizobiaceae.
- microbiology : Citrus, Phloem, Plant Diseases.
- Gene Expression Profiling, Gene Expression Regulation, Bacterial, Genetic Variation, Genomics, Host-Pathogen Interactions, Molecular Sequence Data.
Abstract
The citrus disease Huanglongbing (HLB) is highly destructive in many citrus-growing regions of the world. The putative causal agent of this disease, 'Candidatus Liberibacter asiaticus', is difficult to culture, and Koch's postulates have not yet been fulfilled. As a result, efforts have focused on obtaining the genome sequence of 'Ca. L. asiaticus' in order to give insight on the physiology of this organism. In this work, three next-generation high-throughput sequencing platforms, 454, Solexa, and SOLiD, were used to obtain metagenomic DNA sequences from phloem tissue of Florida citrus trees infected with HLB. A culture-independent, polymerase chain reaction (PCR)-independent analysis of 16S ribosomal RNA sequences showed that the only bacterium present within the phloem metagenome was 'Ca L. asiaticus'. No viral or viroid sequences were identified within the metagenome. By reference assembly, the phloem metagenome contained sequences that provided 26-fold coverage of the 'Ca. L. asiaticus' contigs in GenBank. By the same approach, phloem metagenomic data yielded less than 0.2-fold coverage of five other alphaproteobacterial genomes. Thus, phloem metagenomic DNA provided a PCR-independent means of verifying the presence of 'Ca L. asiaticus' in infected tissue and strongly suggests that no other disease agent was present in phloem. Analysis of these metagenomic data suggest that this approach has a detection limit of one 'Ca. Liberibacter' cell for every 52 phloem cells. The phloem sample sequenced here is estimated to have contained 1.7 'Ca. Liberibacter' cells per phloem cell.
DOI: 10.1094/MPMI-22-12-1624
PubMed: 19888827
Affiliations:
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Tyler</name><affiliation wicri:level="2"><nlm:affiliation>Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611</wicri:regionArea><placeName><region type="state">Floride</region></placeName></affiliation></author><author><name sortKey="Roesch, Luiz F W" sort="Roesch, Luiz F W" uniqKey="Roesch L" first="Luiz F W" last="Roesch">Luiz F W. Roesch</name></author><author><name sortKey="Gowda, Siddarame" sort="Gowda, Siddarame" uniqKey="Gowda S" first="Siddarame" last="Gowda">Siddarame Gowda</name></author><author><name sortKey="Dawson, William O" sort="Dawson, William O" uniqKey="Dawson W" first="William O" last="Dawson">William O. Dawson</name></author><author><name sortKey="Triplett, Eric W" sort="Triplett, Eric W" uniqKey="Triplett E" first="Eric W" last="Triplett">Eric W. Triplett</name></author></analytic><series><title level="j">Molecular plant-microbe interactions : MPMI</title><idno type="ISSN">0894-0282</idno><imprint><date when="2009" type="published">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Citrus (microbiology)</term><term>DNA Viruses (isolation & purification)</term><term>Gene Expression Profiling (MeSH)</term><term>Gene Expression Regulation, Bacterial (MeSH)</term><term>Genetic Variation (MeSH)</term><term>Genomics (MeSH)</term><term>Host-Pathogen Interactions (MeSH)</term><term>Molecular Sequence Data (MeSH)</term><term>Phloem (microbiology)</term><term>Plant Diseases (microbiology)</term><term>RNA, Ribosomal, 16S (genetics)</term><term>Rhizobiaceae (classification)</term><term>Rhizobiaceae (genetics)</term><term>Rhizobiaceae (isolation & purification)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN ribosomique 16S (génétique)</term><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Citrus (microbiologie)</term><term>Données de séquences moléculaires (MeSH)</term><term>Génomique (MeSH)</term><term>Interactions hôte-pathogène (MeSH)</term><term>Maladies des plantes (microbiologie)</term><term>Phloème (microbiologie)</term><term>Rhizobiaceae (classification)</term><term>Rhizobiaceae (génétique)</term><term>Rhizobiaceae (isolement et purification)</term><term>Régulation de l'expression des gènes bactériens (MeSH)</term><term>Variation génétique (MeSH)</term><term>Virus à ADN (isolement et purification)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Ribosomal, 16S</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Rhizobiaceae</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Rhizobiaceae</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN ribosomique 16S</term><term>Rhizobiaceae</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>DNA Viruses</term><term>Rhizobiaceae</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Rhizobiaceae</term><term>Virus à ADN</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Citrus</term><term>Maladies des plantes</term><term>Phloème</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Citrus</term><term>Phloem</term><term>Plant Diseases</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Bacterial</term><term>Genetic Variation</term><term>Genomics</term><term>Host-Pathogen Interactions</term><term>Molecular Sequence Data</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Données de séquences moléculaires</term><term>Génomique</term><term>Interactions hôte-pathogène</term><term>Régulation de l'expression des gènes bactériens</term><term>Variation génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The citrus disease Huanglongbing (HLB) is highly destructive in many citrus-growing regions of the world. The putative causal agent of this disease, 'Candidatus Liberibacter asiaticus', is difficult to culture, and Koch's postulates have not yet been fulfilled. As a result, efforts have focused on obtaining the genome sequence of 'Ca. L. asiaticus' in order to give insight on the physiology of this organism. In this work, three next-generation high-throughput sequencing platforms, 454, Solexa, and SOLiD, were used to obtain metagenomic DNA sequences from phloem tissue of Florida citrus trees infected with HLB. A culture-independent, polymerase chain reaction (PCR)-independent analysis of 16S ribosomal RNA sequences showed that the only bacterium present within the phloem metagenome was 'Ca L. asiaticus'. No viral or viroid sequences were identified within the metagenome. By reference assembly, the phloem metagenome contained sequences that provided 26-fold coverage of the 'Ca. L. asiaticus' contigs in GenBank. By the same approach, phloem metagenomic data yielded less than 0.2-fold coverage of five other alphaproteobacterial genomes. Thus, phloem metagenomic DNA provided a PCR-independent means of verifying the presence of 'Ca L. asiaticus' in infected tissue and strongly suggests that no other disease agent was present in phloem. Analysis of these metagenomic data suggest that this approach has a detection limit of one 'Ca. Liberibacter' cell for every 52 phloem cells. The phloem sample sequenced here is estimated to have contained 1.7 'Ca. Liberibacter' cells per phloem cell.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">19888827</PMID><DateCompleted><Year>2010</Year><Month>03</Month><Day>12</Day></DateCompleted><DateRevised><Year>2009</Year><Month>11</Month><Day>05</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0894-0282</ISSN><JournalIssue CitedMedium="Print"><Volume>22</Volume><Issue>12</Issue><PubDate><Year>2009</Year><Month>Dec</Month></PubDate></JournalIssue><Title>Molecular plant-microbe interactions : MPMI</Title><ISOAbbreviation>Mol Plant Microbe Interact</ISOAbbreviation></Journal><ArticleTitle>Confirmation of the sequence of 'Candidatus Liberibacter asiaticus' and assessment of microbial diversity in Huanglongbing-infected citrus phloem using a metagenomic approach.</ArticleTitle><Pagination><MedlinePgn>1624-34</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1094/MPMI-22-12-1624</ELocationID><Abstract><AbstractText>The citrus disease Huanglongbing (HLB) is highly destructive in many citrus-growing regions of the world. The putative causal agent of this disease, 'Candidatus Liberibacter asiaticus', is difficult to culture, and Koch's postulates have not yet been fulfilled. As a result, efforts have focused on obtaining the genome sequence of 'Ca. L. asiaticus' in order to give insight on the physiology of this organism. In this work, three next-generation high-throughput sequencing platforms, 454, Solexa, and SOLiD, were used to obtain metagenomic DNA sequences from phloem tissue of Florida citrus trees infected with HLB. A culture-independent, polymerase chain reaction (PCR)-independent analysis of 16S ribosomal RNA sequences showed that the only bacterium present within the phloem metagenome was 'Ca L. asiaticus'. No viral or viroid sequences were identified within the metagenome. By reference assembly, the phloem metagenome contained sequences that provided 26-fold coverage of the 'Ca. L. asiaticus' contigs in GenBank. By the same approach, phloem metagenomic data yielded less than 0.2-fold coverage of five other alphaproteobacterial genomes. Thus, phloem metagenomic DNA provided a PCR-independent means of verifying the presence of 'Ca L. asiaticus' in infected tissue and strongly suggests that no other disease agent was present in phloem. Analysis of these metagenomic data suggest that this approach has a detection limit of one 'Ca. Liberibacter' cell for every 52 phloem cells. The phloem sample sequenced here is estimated to have contained 1.7 'Ca. Liberibacter' cells per phloem cell.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Tyler</LastName><ForeName>Heather L</ForeName><Initials>HL</Initials><AffiliationInfo><Affiliation>Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Roesch</LastName><ForeName>Luiz F W</ForeName><Initials>LF</Initials></Author><Author ValidYN="Y"><LastName>Gowda</LastName><ForeName>Siddarame</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Dawson</LastName><ForeName>William O</ForeName><Initials>WO</Initials></Author><Author ValidYN="Y"><LastName>Triplett</LastName><ForeName>Eric W</ForeName><Initials>EW</Initials></Author></AuthorList><Language>eng</Language><DataBankList 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Dawson</name><name sortKey="Gowda, Siddarame" sort="Gowda, Siddarame" uniqKey="Gowda S" first="Siddarame" last="Gowda">Siddarame Gowda</name><name sortKey="Roesch, Luiz F W" sort="Roesch, Luiz F W" uniqKey="Roesch L" first="Luiz F W" last="Roesch">Luiz F W. Roesch</name><name sortKey="Triplett, Eric W" sort="Triplett, Eric W" uniqKey="Triplett E" first="Eric W" last="Triplett">Eric W. Triplett</name></noCountry><country name="États-Unis"><region name="Floride"><name sortKey="Tyler, Heather L" sort="Tyler, Heather L" uniqKey="Tyler H" first="Heather L" last="Tyler">Heather L. Tyler</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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