454‐pyrosequencing of Coffea arabica leaves infected by the rust fungus Hemileia vastatrix reveals in planta‐expressed pathogen‐secreted proteins and plant functions in a late compatible plant–rust interaction
Identifieur interne : 001E71 ( Main/Exploration ); précédent : 001E70; suivant : 001E72454‐pyrosequencing of Coffea arabica leaves infected by the rust fungus Hemileia vastatrix reveals in planta‐expressed pathogen‐secreted proteins and plant functions in a late compatible plant–rust interaction
Auteurs : Diana Fernandez [France] ; Emilie Tisserant [France] ; Pedro Talhinhas [Portugal] ; Helena Azinheira [Portugal] ; Ana Vieira [Portugal] ; Anne-Sophie Petitot [France] ; Andreia Loureiro [Portugal] ; Julie Poulain [France] ; Corinne Da Silva [France] ; Maria Do Céu Silva [Portugal] ; Sébastien Duplessis [France]Source :
- Molecular Plant Pathology [ 1464-6722 ] ; 2012-01.
English descriptors
- Teeft :
- Abundant contigs, Amino, Amino acid transport, Amino acids, Arabica, Arabica leaf tissues, Asparagine synthase, Avirulence, Avirulence genes, Basidiomycete, Bean rust fungus, Best blast, Bicolor, Bioinformatic, Bioinformatic procedure, Biotechnology information, Blackwell publishing, Blast hits, Blastx, Blastx searches, Bspp, Cahv, Cahv contigs, Carbohydrate, Carbohydrate transport, Catanzariti, Cdna, Coffea, Coffea arabica, Coffee plants, Coffee rust, Coffee rust fungus, Columns detail, Compatible interaction, Contig, Contig sequences, Contigs, Database, Dehydrogenase, Distinct patterns, Duplessis, Effector, Encoding, Est, Est3, Est3 program, Eukaryotic orthologous group, Experimental procedures, Fabae, Fernandez, Fungal, Fungal contigs, Fungal origin, Fungal sequences, Fungal transcripts, Fungi, Fungus, Gene, Gene models, Genome, Genome sequences, Genomic, Glutamine hydrolysing, Graminis, Hacquard, Hahn, Haustorium, Hemileia, Hemileia vastatrix, Homologues, Homology, Homology searches, Hypothetical protein, Independent replicates, International databases, Intracellular secretion, Joint genome institute, Kemen, Laccaria, Laccaria bicolor, Late stage, Lini, Mannitol, Mannitol dehydrogenase, Melampsora, Mendgen, Mesophyll cells, Metabolism, Molecular plant pathology, National center, Nicole, Nonredundant nucleotide, Nucleic acids, Nucleotide, Order pucciniales, Oryza, Oryza sativa, Pathogen, Pathol, Petitot, Phakopsora pachyrhizi, Plant cell, Plant cells, Plant contigs, Plant host, Plant pathol, Plant pathology, Plant sequences, Poplar, Populus, Populus trichocarpa, Populus trichocarpa populus deltoides, Protein, Protein sequences, Public databases, Puccinia, Puccinia graminis tritici, Puccinia triticina, Pucciniales, Puthoff, Pyrosequencing, Ramiro, Relative abundance, Ribosomal structure, Rodrigues, Rtp1, Rust, Rust contigs, Rust effectors, Rust fungi, Rust fungus, Rust fungus hemileia vastatrix, Rust fungus uromyces fabae, Rust genes, Rust homologues, Rust species, Rust transcripts, Sativa, Secretion prediction, Sequence tags, Sequencing, Silva, Sporulation, Stringent criteria, Time course, Time point, Titanium pyrosequencing, Total number, Transcript, Transcript accumulation, Translation elongation factor, Transporter, Trichocarpa, Trinucleotide frequencies, Tritici, Uredinial stage, Uredinium, Uromyces, Uromyces appendiculatus, Uromyces fabae, Vastatrix, Vastatrix contigs, Vastatrix genes, Vastatrix races, Vastatrix transcripts, Vesicular transport, Vitis vinifera, Voegele.
Abstract
Coffee (Coffea arabica L.), one of the key export and cash crops in tropical and subtropical countries, suffers severe losses from the rust fungus Hemileia vastatrix. The transcriptome of H. vastatrix was analysed during a compatible interaction with coffee to obtain an exhaustive repertoire of the genes expressed during infection and to identify potential effector genes. Large‐scale sequencing (454‐GS‐FLEX Titanium) of mixed coffee and rust cDNAs obtained from 21‐day rust‐infected leaves generated 352 146 sequences which assembled into 22 774 contigs. In the absence of any reference genomic sequences for Coffea or Hemileia, specific trinucleotide frequencies within expressed sequence tags (ESTs) and blast homology against a set of dicots and basidiomycete genomes were used to distinguish pathogen from plant sequences. About 30% (6763) of the contigs were assigned to H. vastatrix and 61% (13 951) to C. arabica. The majority (60%) of the rust sequences did not show homology to any genomic database, indicating that they were potential novel fungal genes. In silico analyses of the 6763 H. vastatrix contigs predicted 382 secreted proteins and identified homologues of the flax rust haustorially expressed secreted proteins (HESPs) and bean rust transferred protein 1 (RTP1). These rust candidate effectors showed conserved amino‐acid domains and conserved patterns of cysteine positions suggestive of conserved functions during infection of host plants. Quantitative reverse transcription‐polymerase chain reaction profiling of selected rust genes revealed dynamic expression patterns during the time course of infection of coffee leaves. This study provides the first valuable genomic resource for the agriculturally important plant pathogen H. vastatrix and the first comprehensive C. arabica EST dataset.
Url:
DOI: 10.1111/j.1364-3703.2011.00723.x
Affiliations:
- France, Portugal
- Grand Est, Languedoc-Roussillon, Lorraine (région), Occitanie (région administrative), Île-de-France
- Champenoux, Montpellier, Évry (Essonne)
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Le document en format XML
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nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region><settlement type="city">Champenoux</settlement></placeName></affiliation><affiliation wicri:level="1"><country wicri:rule="url">France</country></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">Molecular Plant Pathology</title><title level="j" type="alt">MOLECULAR PLANT PATHOLOGY</title><idno type="ISSN">1464-6722</idno><idno type="eISSN">1364-3703</idno><imprint><biblScope unit="vol">13</biblScope><biblScope unit="issue">1</biblScope><biblScope unit="page" from="17">17</biblScope><biblScope unit="page" to="37">37</biblScope><biblScope unit="page-count">21</biblScope><publisher>Blackwell Publishing Ltd</publisher><pubPlace>Oxford, UK</pubPlace><date type="published" when="2012-01">2012-01</date></imprint><idno type="ISSN">1464-6722</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1464-6722</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="Teeft" xml:lang="en"><term>Abundant contigs</term><term>Amino</term><term>Amino acid transport</term><term>Amino acids</term><term>Arabica</term><term>Arabica leaf tissues</term><term>Asparagine synthase</term><term>Avirulence</term><term>Avirulence genes</term><term>Basidiomycete</term><term>Bean rust fungus</term><term>Best blast</term><term>Bicolor</term><term>Bioinformatic</term><term>Bioinformatic procedure</term><term>Biotechnology information</term><term>Blackwell publishing</term><term>Blast hits</term><term>Blastx</term><term>Blastx searches</term><term>Bspp</term><term>Cahv</term><term>Cahv contigs</term><term>Carbohydrate</term><term>Carbohydrate transport</term><term>Catanzariti</term><term>Cdna</term><term>Coffea</term><term>Coffea arabica</term><term>Coffee plants</term><term>Coffee rust</term><term>Coffee rust fungus</term><term>Columns detail</term><term>Compatible interaction</term><term>Contig</term><term>Contig sequences</term><term>Contigs</term><term>Database</term><term>Dehydrogenase</term><term>Distinct patterns</term><term>Duplessis</term><term>Effector</term><term>Encoding</term><term>Est</term><term>Est3</term><term>Est3 program</term><term>Eukaryotic orthologous group</term><term>Experimental procedures</term><term>Fabae</term><term>Fernandez</term><term>Fungal</term><term>Fungal contigs</term><term>Fungal origin</term><term>Fungal sequences</term><term>Fungal transcripts</term><term>Fungi</term><term>Fungus</term><term>Gene</term><term>Gene models</term><term>Genome</term><term>Genome sequences</term><term>Genomic</term><term>Glutamine hydrolysing</term><term>Graminis</term><term>Hacquard</term><term>Hahn</term><term>Haustorium</term><term>Hemileia</term><term>Hemileia vastatrix</term><term>Homologues</term><term>Homology</term><term>Homology searches</term><term>Hypothetical protein</term><term>Independent replicates</term><term>International databases</term><term>Intracellular secretion</term><term>Joint genome institute</term><term>Kemen</term><term>Laccaria</term><term>Laccaria bicolor</term><term>Late stage</term><term>Lini</term><term>Mannitol</term><term>Mannitol dehydrogenase</term><term>Melampsora</term><term>Mendgen</term><term>Mesophyll cells</term><term>Metabolism</term><term>Molecular plant pathology</term><term>National center</term><term>Nicole</term><term>Nonredundant nucleotide</term><term>Nucleic acids</term><term>Nucleotide</term><term>Order pucciniales</term><term>Oryza</term><term>Oryza sativa</term><term>Pathogen</term><term>Pathol</term><term>Petitot</term><term>Phakopsora pachyrhizi</term><term>Plant cell</term><term>Plant cells</term><term>Plant contigs</term><term>Plant host</term><term>Plant pathol</term><term>Plant pathology</term><term>Plant sequences</term><term>Poplar</term><term>Populus</term><term>Populus trichocarpa</term><term>Populus trichocarpa populus deltoides</term><term>Protein</term><term>Protein sequences</term><term>Public databases</term><term>Puccinia</term><term>Puccinia graminis tritici</term><term>Puccinia triticina</term><term>Pucciniales</term><term>Puthoff</term><term>Pyrosequencing</term><term>Ramiro</term><term>Relative abundance</term><term>Ribosomal structure</term><term>Rodrigues</term><term>Rtp1</term><term>Rust</term><term>Rust contigs</term><term>Rust effectors</term><term>Rust fungi</term><term>Rust fungus</term><term>Rust fungus hemileia vastatrix</term><term>Rust fungus uromyces fabae</term><term>Rust genes</term><term>Rust homologues</term><term>Rust species</term><term>Rust transcripts</term><term>Sativa</term><term>Secretion prediction</term><term>Sequence tags</term><term>Sequencing</term><term>Silva</term><term>Sporulation</term><term>Stringent criteria</term><term>Time course</term><term>Time point</term><term>Titanium pyrosequencing</term><term>Total number</term><term>Transcript</term><term>Transcript accumulation</term><term>Translation elongation factor</term><term>Transporter</term><term>Trichocarpa</term><term>Trinucleotide frequencies</term><term>Tritici</term><term>Uredinial stage</term><term>Uredinium</term><term>Uromyces</term><term>Uromyces appendiculatus</term><term>Uromyces fabae</term><term>Vastatrix</term><term>Vastatrix contigs</term><term>Vastatrix genes</term><term>Vastatrix races</term><term>Vastatrix transcripts</term><term>Vesicular transport</term><term>Vitis vinifera</term><term>Voegele</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Coffee (Coffea arabica L.), one of the key export and cash crops in tropical and subtropical countries, suffers severe losses from the rust fungus Hemileia vastatrix. The transcriptome of H. vastatrix was analysed during a compatible interaction with coffee to obtain an exhaustive repertoire of the genes expressed during infection and to identify potential effector genes. Large‐scale sequencing (454‐GS‐FLEX Titanium) of mixed coffee and rust cDNAs obtained from 21‐day rust‐infected leaves generated 352 146 sequences which assembled into 22 774 contigs. In the absence of any reference genomic sequences for Coffea or Hemileia, specific trinucleotide frequencies within expressed sequence tags (ESTs) and blast homology against a set of dicots and basidiomycete genomes were used to distinguish pathogen from plant sequences. About 30% (6763) of the contigs were assigned to H. vastatrix and 61% (13 951) to C. arabica. The majority (60%) of the rust sequences did not show homology to any genomic database, indicating that they were potential novel fungal genes. In silico analyses of the 6763 H. vastatrix contigs predicted 382 secreted proteins and identified homologues of the flax rust haustorially expressed secreted proteins (HESPs) and bean rust transferred protein 1 (RTP1). These rust candidate effectors showed conserved amino‐acid domains and conserved patterns of cysteine positions suggestive of conserved functions during infection of host plants. Quantitative reverse transcription‐polymerase chain reaction profiling of selected rust genes revealed dynamic expression patterns during the time course of infection of coffee leaves. This study provides the first valuable genomic resource for the agriculturally important plant pathogen H. vastatrix and the first comprehensive C. arabica EST dataset.</div></front></TEI><affiliations><list><country><li>France</li><li>Portugal</li></country><region><li>Grand Est</li><li>Languedoc-Roussillon</li><li>Lorraine (région)</li><li>Occitanie (région administrative)</li><li>Île-de-France</li></region><settlement><li>Champenoux</li><li>Montpellier</li><li>Évry (Essonne)</li></settlement></list><tree><country name="France"><region name="Occitanie (région administrative)"><name sortKey="Fernandez, Diana" sort="Fernandez, Diana" uniqKey="Fernandez D" first="Diana" last="Fernandez">Diana Fernandez</name></region><name sortKey="Da Silva, Corinne" sort="Da Silva, Corinne" uniqKey="Da Silva C" first="Corinne" last="Da Silva">Corinne Da Silva</name><name sortKey="Duplessis, Sebastien" sort="Duplessis, Sebastien" uniqKey="Duplessis S" first="Sébastien" last="Duplessis">Sébastien Duplessis</name><name sortKey="Duplessis, Sebastien" sort="Duplessis, Sebastien" uniqKey="Duplessis S" first="Sébastien" last="Duplessis">Sébastien Duplessis</name><name sortKey="Petitot, Anne Ophie" sort="Petitot, Anne Ophie" uniqKey="Petitot A" first="Anne-Sophie" last="Petitot">Anne-Sophie Petitot</name><name sortKey="Poulain, Julie" sort="Poulain, Julie" uniqKey="Poulain J" first="Julie" last="Poulain">Julie Poulain</name><name sortKey="Tisserant, Emilie" sort="Tisserant, Emilie" uniqKey="Tisserant E" first="Emilie" last="Tisserant">Emilie Tisserant</name></country><country name="Portugal"><noRegion><name sortKey="Talhinhas, Pedro" sort="Talhinhas, Pedro" uniqKey="Talhinhas P" first="Pedro" last="Talhinhas">Pedro Talhinhas</name></noRegion><name sortKey="Azinheira, Helena" sort="Azinheira, Helena" uniqKey="Azinheira H" first="Helena" last="Azinheira">Helena Azinheira</name><name sortKey="Loureiro, Andreia" sort="Loureiro, Andreia" uniqKey="Loureiro A" first="Andreia" last="Loureiro">Andreia Loureiro</name><name sortKey="Silva, Maria Do Ceu" sort="Silva, Maria Do Ceu" uniqKey="Silva M" first="Maria Do Céu" last="Silva">Maria Do Céu Silva</name><name sortKey="Vieira, Ana" sort="Vieira, Ana" uniqKey="Vieira A" first="Ana" last="Vieira">Ana Vieira</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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