Transcriptome analysis of the white pine blister rust pathogen Cronartium ribicola: de novo assembly, expression profiling, and identification of candidate effectors.
Identifieur interne : 000443 ( Main/Exploration ); précédent : 000442; suivant : 000444Transcriptome analysis of the white pine blister rust pathogen Cronartium ribicola: de novo assembly, expression profiling, and identification of candidate effectors.
Auteurs : Jun-Jun Liu [Canada] ; Rona N. Sturrock [Canada] ; Richard A. Sniezko [États-Unis] ; Holly Williams [Canada] ; Ross Benton [Canada] ; Arezoo Zamany [Canada]Source :
- BMC genomics [ 1471-2164 ] ; 2015.
Descripteurs français
- KwdFr :
- Analyse de profil d'expression de gènes (MeSH), Analyse de regroupements (MeSH), Annotation de séquence moléculaire (MeSH), Basidiomycota (génétique), Biologie informatique (méthodes), Données de séquences moléculaires (MeSH), Maladies des plantes (microbiologie), Pinus (microbiologie), Protéines fongiques (génétique), Régulation de l'expression des gènes fongiques (MeSH), Transcriptome (MeSH).
- MESH :
- génétique : Basidiomycota, Protéines fongiques.
- microbiologie : Maladies des plantes, Pinus.
- méthodes : Biologie informatique.
- Analyse de profil d'expression de gènes, Analyse de regroupements, Annotation de séquence moléculaire, Données de séquences moléculaires, Régulation de l'expression des gènes fongiques, Transcriptome.
English descriptors
- KwdEn :
- Basidiomycota (genetics), Cluster Analysis (MeSH), Computational Biology (methods), Fungal Proteins (genetics), Gene Expression Profiling (MeSH), Gene Expression Regulation, Fungal (MeSH), Molecular Sequence Annotation (MeSH), Molecular Sequence Data (MeSH), Pinus (microbiology), Plant Diseases (microbiology), Transcriptome (MeSH).
- MESH :
- chemical , genetics : Fungal Proteins.
- genetics : Basidiomycota.
- methods : Computational Biology.
- microbiology : Pinus, Plant Diseases.
- Cluster Analysis, Gene Expression Profiling, Gene Expression Regulation, Fungal, Molecular Sequence Annotation, Molecular Sequence Data, Transcriptome.
Abstract
BACKGROUND
The fungus Cronartium ribicola (Cri) is an economically and ecologically important forest pathogen that causes white pine blister rust (WPBR) disease on five-needle pines. To cause stem cankers and kill white pine trees the fungus elaborates a life cycle with five stages of spore development on five-needle pines and the alternate host Ribes plants. To increase our understanding of molecular WP-BR interactions, here we report genome-wide transcriptional profile analysis of C. ribicola using RNA-seq.
RESULTS
cDNA libraries were constructed from aeciospore, urediniospore, and western white pine (Pinus monticola) tissues post Cri infection. Over 200 million RNA-seq 100-bp paired-end (PE) reads from rust fungal spores were de novo assembled and a reference transcriptome was generated with 17,880 transcripts that were expressed from 13,629 unigenes. A total of 734 unique proteins were predicted as a part of the Cri secretome from complete open reading frames (ORFs), and 41 % of them were Cronartium-specific. This study further identified a repertoire of candidate effectors and other pathogenicity determinants. Differentially expressed genes (DEGs) were identified to gain an understanding of molecular events important during the WPBR fungus life cycle by comparing Cri transcriptomes at different infection stages. Large-scale changes of in planta gene expression profiles were observed, revealing that multiple fungal biosynthetic pathways were enhanced during mycelium growth inside infected pine stem tissues. Conversely, many fungal genes that were up-regulated at the urediniospore stage appeared to be signalling components and transporters. The secreted fungal protein genes that were up-regulated in pine needle tissues during early infection were primarily associated with cell wall modifications, possibly to mask the rust pathogen from plant defenses.
CONCLUSION
This comprehensive transcriptome profiling substantially improves our current understanding of molecular WP-BR interactions. The repertoire of candidate effectors and other putative pathogenicity determinants identified here are valuable for future functional analysis of Cri virulence and pathogenicity.
DOI: 10.1186/s12864-015-1861-1
PubMed: 26338692
PubMed Central: PMC4559923
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Transcriptome analysis of the white pine blister rust pathogen Cronartium ribicola: de novo assembly, expression profiling, and identification of candidate effectors.</title><author><name sortKey="Liu, Jun Jun" sort="Liu, Jun Jun" uniqKey="Liu J" first="Jun-Jun" last="Liu">Jun-Jun Liu</name><affiliation wicri:level="1"><nlm:affiliation>Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada. Jun-Jun.Liu@NRCan-RNCan.gc.ca.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5</wicri:regionArea><wicri:noRegion>V8Z 1M5</wicri:noRegion></affiliation></author><author><name sortKey="Sturrock, Rona N" sort="Sturrock, Rona N" uniqKey="Sturrock R" first="Rona N" last="Sturrock">Rona N. Sturrock</name><affiliation wicri:level="1"><nlm:affiliation>Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada. Rona.Sturrock@NRCan-RNCan.gc.ca.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5</wicri:regionArea><wicri:noRegion>V8Z 1M5</wicri:noRegion></affiliation></author><author><name sortKey="Sniezko, Richard A" sort="Sniezko, Richard A" uniqKey="Sniezko R" first="Richard A" last="Sniezko">Richard A. Sniezko</name><affiliation wicri:level="1"><nlm:affiliation>USDA Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Road, Cottage Grove, OR, 97424, USA. rsniezko@fs.fed.us.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Road, Cottage Grove, OR, 97424</wicri:regionArea><wicri:noRegion>97424</wicri:noRegion></affiliation></author><author><name sortKey="Williams, Holly" sort="Williams, Holly" uniqKey="Williams H" first="Holly" last="Williams">Holly Williams</name><affiliation wicri:level="1"><nlm:affiliation>Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada. Holly.Williams@NRCan-RNCan.gc.ca.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5</wicri:regionArea><wicri:noRegion>V8Z 1M5</wicri:noRegion></affiliation></author><author><name sortKey="Benton, Ross" sort="Benton, Ross" uniqKey="Benton R" first="Ross" last="Benton">Ross Benton</name><affiliation wicri:level="1"><nlm:affiliation>Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada. Ross.Benton@NRCan-RNCan.gc.ca.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5</wicri:regionArea><wicri:noRegion>V8Z 1M5</wicri:noRegion></affiliation></author><author><name sortKey="Zamany, Arezoo" sort="Zamany, Arezoo" uniqKey="Zamany A" first="Arezoo" last="Zamany">Arezoo Zamany</name><affiliation wicri:level="1"><nlm:affiliation>Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada. Arezoo.Zamany@NRCan-RNCan.gc.ca.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5</wicri:regionArea><wicri:noRegion>V8Z 1M5</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:26338692</idno><idno type="pmid">26338692</idno><idno type="doi">10.1186/s12864-015-1861-1</idno><idno type="pmc">PMC4559923</idno><idno type="wicri:Area/Main/Corpus">000448</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000448</idno><idno type="wicri:Area/Main/Curation">000448</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000448</idno><idno type="wicri:Area/Main/Exploration">000448</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Transcriptome analysis of the white pine blister rust pathogen Cronartium ribicola: de novo assembly, expression profiling, and identification of candidate effectors.</title><author><name sortKey="Liu, Jun Jun" sort="Liu, Jun Jun" uniqKey="Liu J" first="Jun-Jun" last="Liu">Jun-Jun Liu</name><affiliation wicri:level="1"><nlm:affiliation>Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada. Jun-Jun.Liu@NRCan-RNCan.gc.ca.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5</wicri:regionArea><wicri:noRegion>V8Z 1M5</wicri:noRegion></affiliation></author><author><name sortKey="Sturrock, Rona N" sort="Sturrock, Rona N" uniqKey="Sturrock R" first="Rona N" last="Sturrock">Rona N. Sturrock</name><affiliation wicri:level="1"><nlm:affiliation>Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada. Rona.Sturrock@NRCan-RNCan.gc.ca.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5</wicri:regionArea><wicri:noRegion>V8Z 1M5</wicri:noRegion></affiliation></author><author><name sortKey="Sniezko, Richard A" sort="Sniezko, Richard A" uniqKey="Sniezko R" first="Richard A" last="Sniezko">Richard A. Sniezko</name><affiliation wicri:level="1"><nlm:affiliation>USDA Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Road, Cottage Grove, OR, 97424, USA. rsniezko@fs.fed.us.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Road, Cottage Grove, OR, 97424</wicri:regionArea><wicri:noRegion>97424</wicri:noRegion></affiliation></author><author><name sortKey="Williams, Holly" sort="Williams, Holly" uniqKey="Williams H" first="Holly" last="Williams">Holly Williams</name><affiliation wicri:level="1"><nlm:affiliation>Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada. Holly.Williams@NRCan-RNCan.gc.ca.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5</wicri:regionArea><wicri:noRegion>V8Z 1M5</wicri:noRegion></affiliation></author><author><name sortKey="Benton, Ross" sort="Benton, Ross" uniqKey="Benton R" first="Ross" last="Benton">Ross Benton</name><affiliation wicri:level="1"><nlm:affiliation>Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada. Ross.Benton@NRCan-RNCan.gc.ca.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5</wicri:regionArea><wicri:noRegion>V8Z 1M5</wicri:noRegion></affiliation></author><author><name sortKey="Zamany, Arezoo" sort="Zamany, Arezoo" uniqKey="Zamany A" first="Arezoo" last="Zamany">Arezoo Zamany</name><affiliation wicri:level="1"><nlm:affiliation>Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada. Arezoo.Zamany@NRCan-RNCan.gc.ca.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5</wicri:regionArea><wicri:noRegion>V8Z 1M5</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Basidiomycota (genetics)</term><term>Cluster Analysis (MeSH)</term><term>Computational Biology (methods)</term><term>Fungal Proteins (genetics)</term><term>Gene Expression Profiling (MeSH)</term><term>Gene Expression Regulation, Fungal (MeSH)</term><term>Molecular Sequence Annotation (MeSH)</term><term>Molecular Sequence Data (MeSH)</term><term>Pinus (microbiology)</term><term>Plant Diseases (microbiology)</term><term>Transcriptome (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Analyse de regroupements (MeSH)</term><term>Annotation de séquence moléculaire (MeSH)</term><term>Basidiomycota (génétique)</term><term>Biologie informatique (méthodes)</term><term>Données de séquences moléculaires (MeSH)</term><term>Maladies des plantes (microbiologie)</term><term>Pinus (microbiologie)</term><term>Protéines fongiques (génétique)</term><term>Régulation de l'expression des gènes fongiques (MeSH)</term><term>Transcriptome (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Fungal Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Basidiomycota</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Basidiomycota</term><term>Protéines fongiques</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Maladies des plantes</term><term>Pinus</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Pinus</term><term>Plant Diseases</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Biologie informatique</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Cluster Analysis</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Fungal</term><term>Molecular Sequence Annotation</term><term>Molecular Sequence Data</term><term>Transcriptome</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Analyse de regroupements</term><term>Annotation de séquence moléculaire</term><term>Données de séquences moléculaires</term><term>Régulation de l'expression des gènes fongiques</term><term>Transcriptome</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>The fungus Cronartium ribicola (Cri) is an economically and ecologically important forest pathogen that causes white pine blister rust (WPBR) disease on five-needle pines. To cause stem cankers and kill white pine trees the fungus elaborates a life cycle with five stages of spore development on five-needle pines and the alternate host Ribes plants. To increase our understanding of molecular WP-BR interactions, here we report genome-wide transcriptional profile analysis of C. ribicola using RNA-seq.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>cDNA libraries were constructed from aeciospore, urediniospore, and western white pine (Pinus monticola) tissues post Cri infection. Over 200 million RNA-seq 100-bp paired-end (PE) reads from rust fungal spores were de novo assembled and a reference transcriptome was generated with 17,880 transcripts that were expressed from 13,629 unigenes. A total of 734 unique proteins were predicted as a part of the Cri secretome from complete open reading frames (ORFs), and 41 % of them were Cronartium-specific. This study further identified a repertoire of candidate effectors and other pathogenicity determinants. Differentially expressed genes (DEGs) were identified to gain an understanding of molecular events important during the WPBR fungus life cycle by comparing Cri transcriptomes at different infection stages. Large-scale changes of in planta gene expression profiles were observed, revealing that multiple fungal biosynthetic pathways were enhanced during mycelium growth inside infected pine stem tissues. Conversely, many fungal genes that were up-regulated at the urediniospore stage appeared to be signalling components and transporters. The secreted fungal protein genes that were up-regulated in pine needle tissues during early infection were primarily associated with cell wall modifications, possibly to mask the rust pathogen from plant defenses.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSION</b></p><p>This comprehensive transcriptome profiling substantially improves our current understanding of molecular WP-BR interactions. The repertoire of candidate effectors and other putative pathogenicity determinants identified here are valuable for future functional analysis of Cri virulence and pathogenicity.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26338692</PMID><DateCompleted><Year>2016</Year><Month>06</Month><Day>02</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>16</Volume><PubDate><Year>2015</Year><Month>Sep</Month><Day>04</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Transcriptome analysis of the white pine blister rust pathogen Cronartium ribicola: de novo assembly, expression profiling, and identification of candidate effectors.</ArticleTitle><Pagination><MedlinePgn>678</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12864-015-1861-1</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">The fungus Cronartium ribicola (Cri) is an economically and ecologically important forest pathogen that causes white pine blister rust (WPBR) disease on five-needle pines. To cause stem cankers and kill white pine trees the fungus elaborates a life cycle with five stages of spore development on five-needle pines and the alternate host Ribes plants. To increase our understanding of molecular WP-BR interactions, here we report genome-wide transcriptional profile analysis of C. ribicola using RNA-seq.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">cDNA libraries were constructed from aeciospore, urediniospore, and western white pine (Pinus monticola) tissues post Cri infection. Over 200 million RNA-seq 100-bp paired-end (PE) reads from rust fungal spores were de novo assembled and a reference transcriptome was generated with 17,880 transcripts that were expressed from 13,629 unigenes. A total of 734 unique proteins were predicted as a part of the Cri secretome from complete open reading frames (ORFs), and 41 % of them were Cronartium-specific. This study further identified a repertoire of candidate effectors and other pathogenicity determinants. Differentially expressed genes (DEGs) were identified to gain an understanding of molecular events important during the WPBR fungus life cycle by comparing Cri transcriptomes at different infection stages. Large-scale changes of in planta gene expression profiles were observed, revealing that multiple fungal biosynthetic pathways were enhanced during mycelium growth inside infected pine stem tissues. Conversely, many fungal genes that were up-regulated at the urediniospore stage appeared to be signalling components and transporters. The secreted fungal protein genes that were up-regulated in pine needle tissues during early infection were primarily associated with cell wall modifications, possibly to mask the rust pathogen from plant defenses.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">This comprehensive transcriptome profiling substantially improves our current understanding of molecular WP-BR interactions. The repertoire of candidate effectors and other putative pathogenicity determinants identified here are valuable for future functional analysis of Cri virulence and pathogenicity.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Jun-Jun</ForeName><Initials>JJ</Initials><AffiliationInfo><Affiliation>Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada. Jun-Jun.Liu@NRCan-RNCan.gc.ca.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sturrock</LastName><ForeName>Rona N</ForeName><Initials>RN</Initials><AffiliationInfo><Affiliation>Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada. Rona.Sturrock@NRCan-RNCan.gc.ca.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sniezko</LastName><ForeName>Richard A</ForeName><Initials>RA</Initials><AffiliationInfo><Affiliation>USDA Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Road, Cottage Grove, OR, 97424, USA. rsniezko@fs.fed.us.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Williams</LastName><ForeName>Holly</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada. Holly.Williams@NRCan-RNCan.gc.ca.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Benton</LastName><ForeName>Ross</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada. Ross.Benton@NRCan-RNCan.gc.ca.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zamany</LastName><ForeName>Arezoo</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada. Arezoo.Zamany@NRCan-RNCan.gc.ca.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>GENBANK</DataBankName><AccessionNumberList><AccessionNumber>GBSG01000000</AccessionNumber></AccessionNumberList></DataBank><DataBank><DataBankName>SRA</DataBankName><AccessionNumberList><AccessionNumber>SRR1583540</AccessionNumber><AccessionNumber>SRR1583545</AccessionNumber><AccessionNumber>SRR1583552</AccessionNumber><AccessionNumber>SRR1583557</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2015</Year><Month>09</Month><Day>04</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Genomics</MedlineTA><NlmUniqueID>100965258</NlmUniqueID><ISSNLinking>1471-2164</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005656">Fungal Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001487" MajorTopicYN="N">Basidiomycota</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016000" MajorTopicYN="N">Cluster Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005656" MajorTopicYN="N">Fungal Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="Y">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015966" MajorTopicYN="N">Gene Expression Regulation, Fungal</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058977" MajorTopicYN="N">Molecular Sequence Annotation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D028223" MajorTopicYN="N">Pinus</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059467" MajorTopicYN="Y">Transcriptome</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>03</Month><Day>09</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2015</Year><Month>08</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>9</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>9</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>6</Month><Day>3</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26338692</ArticleId><ArticleId IdType="doi">10.1186/s12864-015-1861-1</ArticleId><ArticleId IdType="pii">10.1186/s12864-015-1861-1</ArticleId><ArticleId IdType="pmc">PMC4559923</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Nucleic Acids Res. 2014 Jan;42(Database issue):D705-10</Citation><ArticleIdList><ArticleId IdType="pubmed">24194595</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Physiol. 2008 Jun;147(2):779-89</Citation><ArticleIdList><ArticleId IdType="pubmed">18400936</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Plant Pathol. 2012 Jun;13(5):454-66</Citation><ArticleIdList><ArticleId IdType="pubmed">22112294</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2013;14:270</Citation><ArticleIdList><ArticleId IdType="pubmed">23607900</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Plant Microbe Interact. 2007 Jun;20(6):637-47</Citation><ArticleIdList><ArticleId IdType="pubmed">17555272</ArticleId></ArticleIdList></Reference><Reference><Citation>J Mol Biol. 2001 Jan 19;305(3):567-80</Citation><ArticleIdList><ArticleId IdType="pubmed">11152613</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Genet. 2012 Sep;44(9):1060-5</Citation><ArticleIdList><ArticleId IdType="pubmed">22885923</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Plant Biol. 2014;14:380</Citation><ArticleIdList><ArticleId IdType="pubmed">25547170</ArticleId></ArticleIdList></Reference><Reference><Citation>Phytopathology. 2004 Jul;94(7):751-8</Citation><ArticleIdList><ArticleId IdType="pubmed">18943908</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS Pathog. 2014 Sep;10(9):e1004329</Citation><ArticleIdList><ArticleId IdType="pubmed">25211126</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2012 Jul;40(Web Server issue):W445-51</Citation><ArticleIdList><ArticleId IdType="pubmed">22645317</ArticleId></ArticleIdList></Reference><Reference><Citation>Pharmacogenetics. 1996 Feb;6(1):1-42</Citation><ArticleIdList><ArticleId IdType="pubmed">8845856</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2013;14:21</Citation><ArticleIdList><ArticleId IdType="pubmed">23324402</ArticleId></ArticleIdList></Reference><Reference><Citation>Phytopathology. 2002 Mar;92(3):278-80</Citation><ArticleIdList><ArticleId IdType="pubmed">18943999</ArticleId></ArticleIdList></Reference><Reference><Citation>Front Plant Sci. 2014 Aug 20;5:416</Citation><ArticleIdList><ArticleId IdType="pubmed">25191335</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS Pathog. 2011 Jul;7(7):e1002147</Citation><ArticleIdList><ArticleId IdType="pubmed">21829350</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2013;8(4):e62460</Citation><ArticleIdList><ArticleId IdType="pubmed">23638091</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Cell. 2006 Jan;18(1):243-56</Citation><ArticleIdList><ArticleId IdType="pubmed">16326930</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2003 Sep;13(9):2178-89</Citation><ArticleIdList><ArticleId IdType="pubmed">12952885</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Methods. 2011;8(10):785-6</Citation><ArticleIdList><ArticleId IdType="pubmed">21959131</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2013;8(6):e67150</Citation><ArticleIdList><ArticleId IdType="pubmed">23840606</ArticleId></ArticleIdList></Reference><Reference><Citation>J Mol Biol. 2000 Jul 21;300(4):1005-16</Citation><ArticleIdList><ArticleId IdType="pubmed">10891285</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS Pathog. 2012 Feb;8(2):e1002514</Citation><ArticleIdList><ArticleId IdType="pubmed">22346750</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2014 Aug 1;30(15):2114-20</Citation><ArticleIdList><ArticleId IdType="pubmed">24695404</ArticleId></ArticleIdList></Reference><Reference><Citation>Phytopathology. 2014 Feb;104(2):163-73</Citation><ArticleIdList><ArticleId IdType="pubmed">23941780</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Plant Pathol. 2013 Jan;14(1):96-107</Citation><ArticleIdList><ArticleId IdType="pubmed">22998218</ArticleId></ArticleIdList></Reference><Reference><Citation>Front Plant Sci. 2014 Jun 26;5:299</Citation><ArticleIdList><ArticleId IdType="pubmed">25018762</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Protoc. 2013 Aug;8(8):1494-512</Citation><ArticleIdList><ArticleId IdType="pubmed">23845962</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS Pathog. 2012;8(3):e1002515</Citation><ArticleIdList><ArticleId IdType="pubmed">22396640</ArticleId></ArticleIdList></Reference><Reference><Citation>Annu Rev Phytopathol. 2009;47:233-63</Citation><ArticleIdList><ArticleId IdType="pubmed">19400631</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2012;7(11):e49423</Citation><ArticleIdList><ArticleId IdType="pubmed">23139845</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Cell. 2004 Mar;16(3):755-68</Citation><ArticleIdList><ArticleId IdType="pubmed">14973158</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2005 Sep 15;21(18):3674-6</Citation><ArticleIdList><ArticleId IdType="pubmed">16081474</ArticleId></ArticleIdList></Reference><Reference><Citation>Front Plant Sci. 2014 Oct 31;5:594</Citation><ArticleIdList><ArticleId IdType="pubmed">25400655</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2012 Mar;40(5):2020-31</Citation><ArticleIdList><ArticleId IdType="pubmed">22080557</ArticleId></ArticleIdList></Reference><Reference><Citation>Database (Oxford). 2011;2011:bar020</Citation><ArticleIdList><ArticleId IdType="pubmed">21622642</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2013;8(1):e53937</Citation><ArticleIdList><ArticleId IdType="pubmed">23349770</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2008 Jan;36(Database issue):D572-6</Citation><ArticleIdList><ArticleId IdType="pubmed">17942425</ArticleId></ArticleIdList></Reference><Reference><Citation>Microbiology. 2013 May;159(Pt 5):833-47</Citation><ArticleIdList><ArticleId IdType="pubmed">23519157</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2014 Jan;42(Database issue):D251-8</Citation><ArticleIdList><ArticleId IdType="pubmed">24225317</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Plant Pathol. 2012 Jan;13(1):17-37</Citation><ArticleIdList><ArticleId IdType="pubmed">21726390</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2007 May 1;23(9):1061-7</Citation><ArticleIdList><ArticleId IdType="pubmed">17332020</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Plant Microbe Interact. 2014 Mar;27(3):255-64</Citation><ArticleIdList><ArticleId IdType="pubmed">24156769</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2011;6(8):e24230</Citation><ArticleIdList><ArticleId IdType="pubmed">21909385</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2011 May 31;108(22):9166-71</Citation><ArticleIdList><ArticleId IdType="pubmed">21536894</ArticleId></ArticleIdList></Reference><Reference><Citation>Front Plant Sci. 2014 Sep 03;5:435</Citation><ArticleIdList><ArticleId IdType="pubmed">25232357</ArticleId></ArticleIdList></Reference><Reference><Citation>MBio. 2014;5(1):e01087-13</Citation><ArticleIdList><ArticleId IdType="pubmed">24496797</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Plant Pathol. 2014 Sep;15(7):711-29</Citation><ArticleIdList><ArticleId IdType="pubmed">24612180</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Plant Pathol. 2011 Jan;12(1):93-102</Citation><ArticleIdList><ArticleId IdType="pubmed">21118351</ArticleId></ArticleIdList></Reference><Reference><Citation>Front Plant Sci. 2014 Jan 13;4:520</Citation><ArticleIdList><ArticleId IdType="pubmed">24454317</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS Pathog. 2013;9(6):e1003475</Citation><ArticleIdList><ArticleId IdType="pubmed">23825955</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Cell. 2008 Jan;20(1):228-40</Citation><ArticleIdList><ArticleId IdType="pubmed">18192436</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2014;15:164</Citation><ArticleIdList><ArticleId IdType="pubmed">24571091</ArticleId></ArticleIdList></Reference><Reference><Citation>Cold Spring Harb Symp Quant Biol. 2012;77:235-47</Citation><ArticleIdList><ArticleId IdType="pubmed">23223409</ArticleId></ArticleIdList></Reference><Reference><Citation>Fungal Genet Biol. 2006 Sep;43(9):605-17</Citation><ArticleIdList><ArticleId IdType="pubmed">16731015</ArticleId></ArticleIdList></Reference><Reference><Citation>Fungal Genet Biol. 2002 Feb;35(1):53-66</Citation><ArticleIdList><ArticleId IdType="pubmed">11860265</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant J. 2013 Sep;75(5):767-80</Citation><ArticleIdList><ArticleId IdType="pubmed">23663217</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2013;14:884</Citation><ArticleIdList><ArticleId IdType="pubmed">24341615</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2012;7(4):e34728</Citation><ArticleIdList><ArticleId IdType="pubmed">22529930</ArticleId></ArticleIdList></Reference><Reference><Citation>J Proteomics. 2014 May 6;102:28-43</Citation><ArticleIdList><ArticleId IdType="pubmed">24631824</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2007 Jan 16;104(3):997-1002</Citation><ArticleIdList><ArticleId IdType="pubmed">17215377</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Rev Microbiol. 2013 Nov;11(11):800-14</Citation><ArticleIdList><ArticleId IdType="pubmed">24129511</ArticleId></ArticleIdList></Reference><Reference><Citation>Front Plant Sci. 2014 Mar 24;5:98</Citation><ArticleIdList><ArticleId IdType="pubmed">24715894</ArticleId></ArticleIdList></Reference><Reference><Citation>Front Plant Sci. 2014 Mar 14;5:88</Citation><ArticleIdList><ArticleId IdType="pubmed">24672531</ArticleId></ArticleIdList></Reference><Reference><Citation>Proteomics. 2013 Feb;13(3-4):597-608</Citation><ArticleIdList><ArticleId IdType="pubmed">23349114</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Commun. 2013;4:2673</Citation><ArticleIdList><ArticleId IdType="pubmed">24150273</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioessays. 2014 Apr;36(4):335-45</Citation><ArticleIdList><ArticleId IdType="pubmed">24531982</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Genet Genomics. 2005 Feb;272(6):639-50</Citation><ArticleIdList><ArticleId IdType="pubmed">15578222</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>Canada</li><li>États-Unis</li></country></list><tree><country name="Canada"><noRegion><name sortKey="Liu, Jun Jun" sort="Liu, Jun Jun" uniqKey="Liu J" first="Jun-Jun" last="Liu">Jun-Jun Liu</name></noRegion><name sortKey="Benton, Ross" sort="Benton, Ross" uniqKey="Benton R" first="Ross" last="Benton">Ross Benton</name><name sortKey="Sturrock, Rona N" sort="Sturrock, Rona N" uniqKey="Sturrock R" first="Rona N" last="Sturrock">Rona N. Sturrock</name><name sortKey="Williams, Holly" sort="Williams, Holly" uniqKey="Williams H" first="Holly" last="Williams">Holly Williams</name><name sortKey="Zamany, Arezoo" sort="Zamany, Arezoo" uniqKey="Zamany A" first="Arezoo" last="Zamany">Arezoo Zamany</name></country><country name="États-Unis"><noRegion><name sortKey="Sniezko, Richard A" sort="Sniezko, Richard A" uniqKey="Sniezko R" first="Richard A" last="Sniezko">Richard A. Sniezko</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Bois/explor/RustFungiGenomicsV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000443 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000443 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Bois
|area= RustFungiGenomicsV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:26338692
|texte= Transcriptome analysis of the white pine blister rust pathogen Cronartium ribicola: de novo assembly, expression profiling, and identification of candidate effectors.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:26338692" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a RustFungiGenomicsV1
| This area was generated with Dilib version V0.6.38. |  |