Identification of genes expressed by Phakopsora pachyrhizi, the pathogen causing soybean rust, at a late stage of infection of susceptible soybean leaves
Identifieur interne : 002414 ( Istex/Corpus ); précédent : 002413; suivant : 002415Identification of genes expressed by Phakopsora pachyrhizi, the pathogen causing soybean rust, at a late stage of infection of susceptible soybean leaves
Auteurs : A. Tremblay ; P. Hosseini ; S. Li ; N. W. Alkharouf ; B. F. MatthewsSource :
- Plant Pathology [ 0032-0862 ] ; 2012-08.
English descriptors
- Teeft :
- Acid, Amino, Amino acid metabolism, Amino acid sequences, Amino acids, Aspergillus, Canadian journal, Carbohydrate, Cdna, Central schema, Citrate cycle, Contigs, Database, Encoding, Fabb, Fabf, Fabg, Fabi, Fabk, Fabl, Fabz, Fas1, Fas2, Fasn, Fasn fas1, Fasn fas1 fabz, Fasn fas2, Fatty acid metabolism, Fungal, Fungal development, Fungal growth, Fungal structures, Fungi, Fungicide, Fungus, Galactose metabolism, Gene, Gene expression, Genome, Genomic, Glycogen, High number, Homologue, Illumina, Infection process, Late stage, Lipid, Many mrnas, Metabolism, Microbiology, Molecular biology, Molecular interactions, Molecular plant pathology, Mrna, Mrnas encoding, Mrnas encoding enzymes, Mrnas encoding proteins, Mutase, Ncbi, Ncbi database, Other fungi, Pachyrhizi, Pachyrhizi ests, Pachyrhizi genes, Pachyrhizi mrnas, Pachyrhizi sequences, Pathogen, Pathway, Peptide, Phakopsora, Phakopsora pachyrhizi, Phakopsora pachyrhizi genes, Plant host, Plant pathology, Plant rusts, Present data, Protein synthesis, Schematize bioinformatics data, Sequencing, Signal peptide, Signal peptides, Similarity searches, Simplistic representation, Solomon oliver, Soybean, Soybean infection, Soybean rust, Spore, Sporulation, Study gene expression, Tremblay, Tulloch, Urediniospores, Uredinium.
Abstract
Soybean is one of the top five agricultural products in the United States and is highly susceptible to Phakopsora pachyrhizi, an exotic obligate biotrophic fungus. The little amount of genomic information about P. pachyrhizi limits understanding of the soybean–soybean rust pathogen interaction and the possibility of engineering resistance to this pathogen in soybean. Illumina mRNA‐Seq analysis revealed P. pachyrhizi genes expressed during a biotrophic interaction between P. pachyrhizi and soybean during fungal sporulation 10 days after inoculation. Approximately 2·4 million DNA sequences representing portions of potential P. pachyrhizi genes were assembled into 32 940 contigs that were used to search against expressed sequence tag (EST), protein and conserved domain databases. About 7500 contigs represent newly discovered P. pachyrhizi sequences. Of these, 527 shared similarity to genes encoding fungal proteins involved in different metabolic pathways such as galactose and glycogen metabolism, glycolysis, the citrate cycle, fatty acid metabolism, amino acid metabolism, proteolysis, protein synthesis, cell cycle division and mitosis, and cell wall biogenesis. Almost 7000 potential P. pachyrhizi genes are still of unknown function. Such information may be useful in the development of new methods of broadening resistance of soybean to P. pachyrhizi, including the silencing of important P. pachyrhizi genes, and also to understand the molecular basis of soybean–P. pachyrhizi interactions.
Url:
DOI: 10.1111/j.1365-3059.2011.02550.x
Links to Exploration step
ISTEX:719CFF62BA79F1AFEC7ADBA8FC4B07D03E9BA95BLe document en format XML
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The little amount of genomic information about P. pachyrhizi limits understanding of the soybean–soybean rust pathogen interaction and the possibility of engineering resistance to this pathogen in soybean. Illumina mRNA‐Seq analysis revealed P. pachyrhizi genes expressed during a biotrophic interaction between P. pachyrhizi and soybean during fungal sporulation 10 days after inoculation. Approximately 2·4 million DNA sequences representing portions of potential P. pachyrhizi genes were assembled into 32 940 contigs that were used to search against expressed sequence tag (EST), protein and conserved domain databases. About 7500 contigs represent newly discovered P. pachyrhizi sequences. Of these, 527 shared similarity to genes encoding fungal proteins involved in different metabolic pathways such as galactose and glycogen metabolism, glycolysis, the citrate cycle, fatty acid metabolism, amino acid metabolism, proteolysis, protein synthesis, cell cycle division and mitosis, and cell wall biogenesis. Almost 7000 potential P. pachyrhizi genes are still of unknown function. Such information may be useful in the development of new methods of broadening resistance of soybean to P. pachyrhizi, including the silencing of important P. pachyrhizi genes, and also to understand the molecular basis of soybean–P. pachyrhizi interactions.</div></front></TEI><istex><corpusName>wiley</corpusName><keywords><teeft><json:string>mrna</json:string><json:string>pachyrhizi</json:string><json:string>encoding</json:string><json:string>fasn</json:string><json:string>contigs</json:string><json:string>cdna</json:string><json:string>phakopsora</json:string><json:string>fungal</json:string><json:string>database</json:string><json:string>spore</json:string><json:string>fungi</json:string><json:string>genome</json:string><json:string>uredinium</json:string><json:string>fas1</json:string><json:string>pathogen</json:string><json:string>fas2</json:string><json:string>sequencing</json:string><json:string>phakopsora pachyrhizi</json:string><json:string>glycogen</json:string><json:string>ncbi</json:string><json:string>tremblay</json:string><json:string>urediniospores</json:string><json:string>pathway</json:string><json:string>present data</json:string><json:string>soybean rust</json:string><json:string>metabolism</json:string><json:string>illumina</json:string><json:string>late stage</json:string><json:string>pachyrhizi mrnas</json:string><json:string>soybean</json:string><json:string>tulloch</json:string><json:string>fabk</json:string><json:string>fabz</json:string><json:string>fabi</json:string><json:string>fabb</json:string><json:string>fabf</json:string><json:string>homologue</json:string><json:string>mrnas encoding</json:string><json:string>gene expression</json:string><json:string>fabg</json:string><json:string>fungicide</json:string><json:string>plant pathology</json:string><json:string>amino</json:string><json:string>pachyrhizi genes</json:string><json:string>microbiology</json:string><json:string>phakopsora pachyrhizi genes</json:string><json:string>mutase</json:string><json:string>fabl</json:string><json:string>sporulation</json:string><json:string>lipid</json:string><json:string>genomic</json:string><json:string>mrnas encoding proteins</json:string><json:string>aspergillus</json:string><json:string>fungal growth</json:string><json:string>fasn fas2</json:string><json:string>fungal structures</json:string><json:string>fatty acid metabolism</json:string><json:string>amino acid metabolism</json:string><json:string>canadian journal</json:string><json:string>protein synthesis</json:string><json:string>fungus</json:string><json:string>carbohydrate</json:string><json:string>study gene expression</json:string><json:string>many mrnas</json:string><json:string>other fungi</json:string><json:string>high number</json:string><json:string>pachyrhizi ests</json:string><json:string>signal peptide</json:string><json:string>plant rusts</json:string><json:string>mrnas encoding enzymes</json:string><json:string>amino acids</json:string><json:string>citrate cycle</json:string><json:string>ncbi database</json:string><json:string>signal peptides</json:string><json:string>fungal development</json:string><json:string>similarity searches</json:string><json:string>peptide</json:string><json:string>gene</json:string><json:string>solomon oliver</json:string><json:string>amino acid sequences</json:string><json:string>fasn fas1</json:string><json:string>galactose metabolism</json:string><json:string>schematize bioinformatics data</json:string><json:string>pachyrhizi sequences</json:string><json:string>soybean infection</json:string><json:string>plant host</json:string><json:string>infection process</json:string><json:string>simplistic representation</json:string><json:string>molecular plant pathology</json:string><json:string>molecular interactions</json:string><json:string>molecular biology</json:string><json:string>central schema</json:string><json:string>fasn fas1 fabz</json:string><json:string>acid</json:string></teeft></keywords><author><json:item><name>A. Tremblay</name><affiliations><json:string>Soybean Genomics and Improvement Laboratory, United States Department of Agriculture‐Agricultural Research Service (USDA‐ARS), Beltsville, MD 20705</json:string><json:string>E-mail: arianne@umbc.edu</json:string></affiliations></json:item><json:item><name>P. Hosseini</name><affiliations><json:string>Soybean Genomics and Improvement Laboratory, United States Department of Agriculture‐Agricultural Research Service (USDA‐ARS), Beltsville, MD 20705</json:string></affiliations></json:item><json:item><name>S. Li</name><affiliations><json:string>USDA‐ARS, Crop Genetics Research Unit, Stoneville, MS 38776</json:string></affiliations></json:item><json:item><name>N. W. Alkharouf</name><affiliations><json:string>Towson University, 8000 York Road, Towson, MD 21252, USA</json:string></affiliations></json:item><json:item><name>B. F. Matthews</name><affiliations><json:string>Soybean Genomics and Improvement Laboratory, United States Department of Agriculture‐Agricultural Research Service (USDA‐ARS), Beltsville, MD 20705</json:string></affiliations></json:item></author><subject><json:item><lang><json:string>eng</json:string></lang><value>deep sequencing</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>gene expression</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Glycine max</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Phakopsora pachyrhizi</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>soybean</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>soybean rust</value></json:item></subject><articleId><json:string>PPA2550</json:string></articleId><arkIstex>ark:/67375/WNG-14T8VTM2-1</arkIstex><language><json:string>eng</json:string></language><originalGenre><json:string>article</json:string></originalGenre><abstract>Soybean is one of the top five agricultural products in the United States and is highly susceptible to Phakopsora pachyrhizi, an exotic obligate biotrophic fungus. The little amount of genomic information about P. pachyrhizi limits understanding of the soybean–soybean rust pathogen interaction and the possibility of engineering resistance to this pathogen in soybean. Illumina mRNA‐Seq analysis revealed P. pachyrhizi genes expressed during a biotrophic interaction between P. pachyrhizi and soybean during fungal sporulation 10 days after inoculation. Approximately 2·4 million DNA sequences representing portions of potential P. pachyrhizi genes were assembled into 32 940 contigs that were used to search against expressed sequence tag (EST), protein and conserved domain databases. About 7500 contigs represent newly discovered P. pachyrhizi sequences. Of these, 527 shared similarity to genes encoding fungal proteins involved in different metabolic pathways such as galactose and glycogen metabolism, glycolysis, the citrate cycle, fatty acid metabolism, amino acid metabolism, proteolysis, protein synthesis, cell cycle division and mitosis, and cell wall biogenesis. Almost 7000 potential P. pachyrhizi genes are still of unknown function. Such information may be useful in the development of new methods of broadening resistance of soybean to P. pachyrhizi, including the silencing of important P. pachyrhizi genes, and also to understand the molecular basis of soybean–P. pachyrhizi interactions.</abstract><qualityIndicators><score>9.388</score><pdfWordCount>7586</pdfWordCount><pdfCharCount>55603</pdfCharCount><pdfVersion>1.3</pdfVersion><pdfPageCount>14</pdfPageCount><pdfPageSize>595.276 x 782.362 pts</pdfPageSize><pdfWordsPerPage>542</pdfWordsPerPage><pdfText>true</pdfText><refBibsNative>true</refBibsNative><abstractWordCount>199</abstractWordCount><abstractCharCount>1508</abstractCharCount><keywordCount>6</keywordCount></qualityIndicators><title>Identification of genes expressed by Phakopsora pachyrhizi, the pathogen causing soybean rust, at a late stage of infection of susceptible soybean leaves</title><genre><json:string>article</json:string></genre><host><title>Plant Pathology</title><language><json:string>unknown</json:string></language><doi><json:string>10.1111/(ISSN)1365-3059</json:string></doi><issn><json:string>0032-0862</json:string></issn><eissn><json:string>1365-3059</json:string></eissn><publisherId><json:string>PPA</json:string></publisherId><volume>61</volume><issue>4</issue><pages><first>773</first><last>786</last><total>14</total></pages><genre><json:string>journal</json:string></genre></host><namedEntities><unitex><date><json:string>2009</json:string><json:string>1930</json:string><json:string>1997</json:string><json:string>2012</json:string><json:string>2006</json:string><json:string>2007</json:string><json:string>1995</json:string><json:string>7500</json:string></date><geogName></geogName><orgName><json:string>US Government</json:string><json:string>United States Department of Agriculture-Agricultural Research Service Stoneville Research Quarantine Facility</json:string><json:string>Mississippi State University</json:string><json:string>Department of Energy</json:string><json:string>Consortium for the Functional Genomics</json:string><json:string>Crop Genetics Research Unit, Stoneville, MS</json:string><json:string>Stoneville Research Quarantine Facility</json:string><json:string>USDAARS</json:string><json:string>Burkard Manufacturing Co.</json:string></orgName><orgName_funder></orgName_funder><orgName_provider></orgName_provider><persName><json:string>Eric Brewer</json:string><json:string>S.Sulfo</json:string><json:string>Richard Jones</json:string><json:string>N. W. Alkharoufc</json:string><json:string>Results</json:string><json:string>Alicia Beavers</json:string><json:string>B. F. Matthewsa</json:string><json:string>S. Lib</json:string><json:string>P. Hosseinia</json:string><json:string>Richard Joost</json:string><json:string>Serine L-Homocysteine</json:string></persName><placeName><json:string>Jefferson County</json:string><json:string>United States</json:string><json:string>Taiwan</json:string></placeName><ref_url><json:string>http://www.cbs.dtu.dk/services/SignalP/</json:string><json:string>http://www.illumina.com</json:string></ref_url><ref_bibl><json:string>Duplessis et al. (2009)</json:string><json:string>Tulloch & Ledingham, 1960, 1962, 1964</json:string><json:string>Marchetti et al., 1975</json:string><json:string>Bonde et al., 1976</json:string><json:string>Ragsdale et al., 2008</json:string><json:string>Breakspear & Momany, 2007</json:string><json:string>Bonfante & Genre, 2010</json:string><json:string>Nowara et al. 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E‐mail: <email>arianne@umbc.edu</email></correspondenceTo><linkGroup><link type="toTypesetVersion" href="file:PPA.PPA2550.pdf"></link></linkGroup></publicationMeta><contentMeta><unparsedEditorialHistory>Published online 16 November 2011</unparsedEditorialHistory><countGroup><count type="figureTotal" number="7"></count><count type="tableTotal" number="1"></count></countGroup><titleGroup><title type="main">Identification of genes expressed by <i>Phakopsora pachyrhizi</i>, the pathogen causing soybean rust, at a late stage of infection of susceptible soybean leaves</title><title type="shortAuthors"><i>A. Tremblay</i> et al.</title><title type="short">Phakopsora pachyrhizi <i>genes expressed during soybean infection</i></title></titleGroup><creators><creator creatorRole="author" xml:id="cr1" affiliationRef="#a1" corresponding="yes"><personName><givenNames>A.</givenNames><familyName>Tremblay</familyName></personName></creator><creator creatorRole="author" xml:id="cr2" affiliationRef="#a1"><personName><givenNames>P.</givenNames><familyName>Hosseini</familyName></personName></creator><creator creatorRole="author" xml:id="cr3" affiliationRef="#a2"><personName><givenNames>S.</givenNames><familyName>Li</familyName></personName></creator><creator creatorRole="author" xml:id="cr4" affiliationRef="#a3"><personName><givenNames>N. W.</givenNames><familyName>Alkharouf</familyName></personName></creator><creator creatorRole="author" xml:id="cr5" affiliationRef="#a1"><personName><givenNames>B. F.</givenNames><familyName>Matthews</familyName></personName></creator></creators><affiliationGroup><affiliation xml:id="a1" countryCode="US"><unparsedAffiliation>Soybean Genomics and Improvement Laboratory, United States Department of Agriculture‐Agricultural Research Service (USDA‐ARS), Beltsville, MD 20705</unparsedAffiliation></affiliation><affiliation xml:id="a2"><unparsedAffiliation>USDA‐ARS, Crop Genetics Research Unit, Stoneville, MS 38776</unparsedAffiliation></affiliation><affiliation xml:id="a3" countryCode="US"><unparsedAffiliation>Towson University, 8000 York Road, Towson, MD 21252, USA</unparsedAffiliation></affiliation></affiliationGroup><keywordGroup xml:lang="en"><keyword xml:id="k1">deep sequencing</keyword><keyword xml:id="k2">gene expression</keyword><keyword xml:id="k3"><i>Glycine max</i></keyword><keyword xml:id="k4"><i>Phakopsora pachyrhizi</i></keyword><keyword xml:id="k5">soybean</keyword><keyword xml:id="k6">soybean rust</keyword></keywordGroup><supportingInformation><p><b>Table S1.</b> Contigs sharing similarity to
<i>Phakopsora pachyrhizi</i> ESTs and proteins from NCBI databases.</p><p><b>Table S2.</b> Potential new <i>Phakopsora
pachyrhizi</i> genes including their similarity to proteins from diverse databases.</p><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:00320862:media:ppa2550:PPA_2550_sm_TableS1"></mediaResource><caption>Supporting info item</caption></supportingInfoItem><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:00320862:media:ppa2550:PPA_2550_sm_TableS2"></mediaResource><caption>Supporting info item</caption></supportingInfoItem></supportingInformation><abstractGroup><abstract type="main" xml:lang="en"><p>Soybean is one of the top five agricultural products in the United States and is highly susceptible to <i>Phakopsora pachyrhizi</i>, an exotic obligate biotrophic fungus. The little amount of genomic information about <i>P. pachyrhizi</i> limits understanding of the soybean–soybean rust pathogen interaction and the possibility of engineering resistance to this pathogen in soybean. Illumina mRNA‐Seq analysis revealed <i>P. pachyrhizi</i> genes expressed during a biotrophic interaction between <i>P. pachyrhizi</i> and soybean during fungal sporulation 10 days after inoculation. Approximately 2·4 million DNA sequences representing portions of potential <i>P. pachyrhizi</i> genes were assembled into 32 940 contigs that were used to search against expressed sequence tag (EST), protein and conserved domain databases. About 7500 contigs represent newly discovered <i>P. pachyrhizi</i> sequences. Of these, 527 shared similarity to genes encoding fungal proteins involved in different metabolic pathways such as galactose and glycogen metabolism, glycolysis, the citrate cycle, fatty acid metabolism, amino acid metabolism, proteolysis, protein synthesis, cell cycle division and mitosis, and cell wall biogenesis. Almost 7000 potential <i>P. pachyrhizi</i> genes are still of unknown function. Such information may be useful in the development of new methods of broadening resistance of soybean to <i>P. pachyrhizi</i>, including the silencing of important <i>P. pachyrhizi</i> genes, and also to understand the molecular basis of soybean–<i>P. pachyrhizi</i> interactions.</p></abstract></abstractGroup></contentMeta></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Identification of genes expressed by Phakopsora pachyrhizi, the pathogen causing soybean rust, at a late stage of infection of susceptible soybean leaves</title></titleInfo><titleInfo type="abbreviated" lang="en"><title>Phakopsora pachyrhizi genes expressed during soybean infection</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>Identification of genes expressed by Phakopsora pachyrhizi, the pathogen causing soybean rust, at a late stage of infection of susceptible soybean leaves</title></titleInfo><name type="personal"><namePart type="given">A.</namePart><namePart type="family">Tremblay</namePart><affiliation>Soybean Genomics and Improvement Laboratory, United States Department of Agriculture‐Agricultural Research Service (USDA‐ARS), Beltsville, MD 20705</affiliation><affiliation>E-mail: arianne@umbc.edu</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">P.</namePart><namePart type="family">Hosseini</namePart><affiliation>Soybean Genomics and Improvement Laboratory, United States Department of Agriculture‐Agricultural Research Service (USDA‐ARS), Beltsville, MD 20705</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">S.</namePart><namePart type="family">Li</namePart><affiliation>USDA‐ARS, Crop Genetics Research Unit, Stoneville, MS 38776</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">N. W.</namePart><namePart type="family">Alkharouf</namePart><affiliation>Towson University, 8000 York Road, Towson, MD 21252, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">B. F.</namePart><namePart type="family">Matthews</namePart><affiliation>Soybean Genomics and Improvement Laboratory, United States Department of Agriculture‐Agricultural Research Service (USDA‐ARS), Beltsville, MD 20705</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="article" displayLabel="article" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-6N5SZHKN-D">article</genre><originInfo><publisher>Blackwell Publishing Ltd</publisher><place><placeTerm type="text">Oxford, UK</placeTerm></place><dateIssued encoding="w3cdtf">2012-08</dateIssued><edition>Published online 16 November 2011</edition><copyrightDate encoding="w3cdtf">2012</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><physicalDescription><extent unit="figures">7</extent><extent unit="tables">1</extent></physicalDescription><abstract lang="en">Soybean is one of the top five agricultural products in the United States and is highly susceptible to Phakopsora pachyrhizi, an exotic obligate biotrophic fungus. The little amount of genomic information about P. pachyrhizi limits understanding of the soybean–soybean rust pathogen interaction and the possibility of engineering resistance to this pathogen in soybean. Illumina mRNA‐Seq analysis revealed P. pachyrhizi genes expressed during a biotrophic interaction between P. pachyrhizi and soybean during fungal sporulation 10 days after inoculation. Approximately 2·4 million DNA sequences representing portions of potential P. pachyrhizi genes were assembled into 32 940 contigs that were used to search against expressed sequence tag (EST), protein and conserved domain databases. About 7500 contigs represent newly discovered P. pachyrhizi sequences. Of these, 527 shared similarity to genes encoding fungal proteins involved in different metabolic pathways such as galactose and glycogen metabolism, glycolysis, the citrate cycle, fatty acid metabolism, amino acid metabolism, proteolysis, protein synthesis, cell cycle division and mitosis, and cell wall biogenesis. Almost 7000 potential P. pachyrhizi genes are still of unknown function. Such information may be useful in the development of new methods of broadening resistance of soybean to P. pachyrhizi, including the silencing of important P. pachyrhizi genes, and also to understand the molecular basis of soybean–P. pachyrhizi interactions.</abstract><subject lang="en"><genre>keywords</genre><topic>deep sequencing</topic><topic>gene expression</topic><topic>Glycine max</topic><topic>Phakopsora pachyrhizi</topic><topic>soybean</topic><topic>soybean rust</topic></subject><relatedItem type="host"><titleInfo><title>Plant Pathology</title></titleInfo><genre type="journal" authority="ISTEX" authorityURI="https://publication-type.data.istex.fr" valueURI="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</genre><note type="content"> Table S1. Contigs sharing similarity to Phakopsora pachyrhizi ESTs and proteins from NCBI databases. Table S2. Potential new Phakopsora pachyrhizi genes including their similarity to proteins from diverse databases. Table S1. Contigs sharing similarity to Phakopsora pachyrhizi ESTs and proteins from NCBI databases. Table S2. 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