eCALIBRATOR: A Comparative Tool to Identify Key Genes and Pathways for Eucalyptus Defense Against Biotic Stressors.
Identifieur interne : 000007 ( Main/Exploration ); précédent : 000006; suivant : 000008eCALIBRATOR: A Comparative Tool to Identify Key Genes and Pathways for Eucalyptus Defense Against Biotic Stressors.
Auteurs : Yves Du Toit [Afrique du Sud] ; Donovin William Coles [Afrique du Sud] ; Ritesh Mewalal [États-Unis] ; Nanette Christie [Afrique du Sud] ; Sanushka Naidoo [Afrique du Sud]Source :
- Frontiers in microbiology [ 1664-302X ] ; 2020.
Abstract
Many pests and pathogens threaten Eucalyptus plantations. The study of defense responses in this economically important wood and fiber crop enables the discovery of novel pathways and genes, which may be adopted to improve resistance. Various functional genomics experiments have been conducted in Eucalyptus-biotic stress interactions following the availability of the Eucalyptus grandis genome, however, comparisons between these studies were limited largely due to a lack of comparative tools. To this end, we developed eCALIBRATOR http://ecalibrator.bi.up.ac.za, a tool for the comparison of Eucalyptus biotic stress interaction. The tool, which is not limited to Eucalyptus, allows the comparison of various datasets, provides a visual output in the form of Venn diagrams and clustering and extraction of lists for gene ontology enrichment analyses. We also demonstrate the usefulness of the tool in revealing pathways and key gene targets to further functionally characterize. We identified 708 differentially expressed E. grandis genes in common among responses to the insect pest Leptocybe invasa, oomycete pathogen Phytophthora cinnamomi and fungus Chrysoporthe austroafricana. Within this set of genes, one of the Gene Ontology terms enriched was "response to organonitrogen compound," with NITRATE TRANSPORTER 2.5 (NRT2.5) being a key gene, up-regulated under susceptible interactions and down-regulated under resistant interactions. Although previous functional genetics studies in Arabidopsis thaliana support a role in nitrate acquisition and remobilization under long-term nitrate starvation, the importance of NRT2.5 in plant defense is unclear. The T-DNA mutants of AtNRT2.5 were more resistant to Pseudomonas syringae pv. tomato pv tomato DC3000 inoculation than the wild-type counterpart, supporting a direct role for NRT2.5 in plant defense. Future studies will focus on characterizing the Eucalyptus ortholog of NRT2.5.
DOI: 10.3389/fmicb.2020.00216
PubMed: 32127794
PubMed Central: PMC7039109
Affiliations:
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William" sort="Coles, Donovin William" uniqKey="Coles D" first="Donovin William" last="Coles">Donovin William Coles</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.</nlm:affiliation><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria</wicri:regionArea><wicri:noRegion>Pretoria</wicri:noRegion></affiliation></author><author><name sortKey="Mewalal, Ritesh" sort="Mewalal, Ritesh" uniqKey="Mewalal R" first="Ritesh" last="Mewalal">Ritesh Mewalal</name><affiliation wicri:level="2"><nlm:affiliation>Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA, United States.</nlm:affiliation><country 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sort="Naidoo, Sanushka" uniqKey="Naidoo S" first="Sanushka" last="Naidoo">Sanushka Naidoo</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.</nlm:affiliation><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria</wicri:regionArea><wicri:noRegion>Pretoria</wicri:noRegion></affiliation></author></analytic><series><title level="j">Frontiers in microbiology</title><idno type="ISSN">1664-302X</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Many pests and pathogens threaten Eucalyptus plantations. The study of defense responses in this economically important wood and fiber crop enables the discovery of novel pathways and genes, which may be adopted to improve resistance. Various functional genomics experiments have been conducted in Eucalyptus-biotic stress interactions following the availability of the <i>Eucalyptus grandis</i> genome, however, comparisons between these studies were limited largely due to a lack of comparative tools. To this end, we developed eCALIBRATOR http://ecalibrator.bi.up.ac.za, a tool for the comparison of Eucalyptus biotic stress interaction. The tool, which is not limited to Eucalyptus, allows the comparison of various datasets, provides a visual output in the form of Venn diagrams and clustering and extraction of lists for gene ontology enrichment analyses. We also demonstrate the usefulness of the tool in revealing pathways and key gene targets to further functionally characterize. We identified 708 differentially expressed <i>E. grandis</i> genes in common among responses to the insect pest <i>Leptocybe invasa</i>, oomycete pathogen <i>Phytophthora cinnamomi</i> and fungus <i>Chrysoporthe austroafricana</i>. Within this set of genes, one of the Gene Ontology terms enriched was "response to organonitrogen compound," with <i>NITRATE TRANSPORTER 2.5</i> (<i>NRT2.5</i>) being a key gene, up-regulated under susceptible interactions and down-regulated under resistant interactions. Although previous functional genetics studies in <i>Arabidopsis thaliana</i> support a role in nitrate acquisition and remobilization under long-term nitrate starvation, the importance of <i>NRT2.5</i> in plant defense is unclear. The T-DNA mutants of <i>AtNRT2.5</i> were more resistant to <i>Pseudomonas syringae</i> pv. <i>tomato pv tomato</i> DC3000 inoculation than the wild-type counterpart, supporting a direct role for <i>NRT2.5</i> in plant defense. Future studies will focus on characterizing the <i>Eucalyptus</i> ortholog of <i>NRT2.5</i>.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">32127794</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>28</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-302X</ISSN><JournalIssue CitedMedium="Print"><Volume>11</Volume><PubDate><Year>2020</Year></PubDate></JournalIssue><Title>Frontiers in microbiology</Title><ISOAbbreviation>Front Microbiol</ISOAbbreviation></Journal><ArticleTitle>eCALIBRATOR: A Comparative Tool to Identify Key Genes and Pathways for <i>Eucalyptus</i> Defense Against Biotic Stressors.</ArticleTitle><Pagination><MedlinePgn>216</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fmicb.2020.00216</ELocationID><Abstract><AbstractText>Many pests and pathogens threaten Eucalyptus plantations. The study of defense responses in this economically important wood and fiber crop enables the discovery of novel pathways and genes, which may be adopted to improve resistance. Various functional genomics experiments have been conducted in Eucalyptus-biotic stress interactions following the availability of the <i>Eucalyptus grandis</i> genome, however, comparisons between these studies were limited largely due to a lack of comparative tools. To this end, we developed eCALIBRATOR http://ecalibrator.bi.up.ac.za, a tool for the comparison of Eucalyptus biotic stress interaction. The tool, which is not limited to Eucalyptus, allows the comparison of various datasets, provides a visual output in the form of Venn diagrams and clustering and extraction of lists for gene ontology enrichment analyses. We also demonstrate the usefulness of the tool in revealing pathways and key gene targets to further functionally characterize. We identified 708 differentially expressed <i>E. grandis</i> genes in common among responses to the insect pest <i>Leptocybe invasa</i>, oomycete pathogen <i>Phytophthora cinnamomi</i> and fungus <i>Chrysoporthe austroafricana</i>. Within this set of genes, one of the Gene Ontology terms enriched was "response to organonitrogen compound," with <i>NITRATE TRANSPORTER 2.5</i> (<i>NRT2.5</i>) being a key gene, up-regulated under susceptible interactions and down-regulated under resistant interactions. Although previous functional genetics studies in <i>Arabidopsis thaliana</i> support a role in nitrate acquisition and remobilization under long-term nitrate starvation, the importance of <i>NRT2.5</i> in plant defense is unclear. The T-DNA mutants of <i>AtNRT2.5</i> were more resistant to <i>Pseudomonas syringae</i> pv. <i>tomato pv tomato</i> DC3000 inoculation than the wild-type counterpart, supporting a direct role for <i>NRT2.5</i> in plant defense. Future studies will focus on characterizing the <i>Eucalyptus</i> ortholog of <i>NRT2.5</i>.</AbstractText><CopyrightInformation>Copyright © 2020 du Toit, Coles, Mewalal, Christie and Naidoo.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>du Toit</LastName><ForeName>Yves</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Coles</LastName><ForeName>Donovin William</ForeName><Initials>DW</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mewalal</LastName><ForeName>Ritesh</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Christie</LastName><ForeName>Nanette</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Naidoo</LastName><ForeName>Sanushka</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>02</Month><Day>17</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Microbiol</MedlineTA><NlmUniqueID>101548977</NlmUniqueID><ISSNLinking>1664-302X</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Eucalyptus</Keyword><Keyword MajorTopicYN="N">comparative transcriptomics</Keyword><Keyword MajorTopicYN="N">defense</Keyword><Keyword MajorTopicYN="N">nitrate transporter</Keyword><Keyword MajorTopicYN="N">nitrogen</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>08</Month><Day>04</Day></PubMedPubDate><PubMedPubDate 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Toit">Yves Du Toit</name></noRegion><name sortKey="Christie, Nanette" sort="Christie, Nanette" uniqKey="Christie N" first="Nanette" last="Christie">Nanette Christie</name><name sortKey="Coles, Donovin William" sort="Coles, Donovin William" uniqKey="Coles D" first="Donovin William" last="Coles">Donovin William Coles</name><name sortKey="Naidoo, Sanushka" sort="Naidoo, Sanushka" uniqKey="Naidoo S" first="Sanushka" last="Naidoo">Sanushka Naidoo</name></country><country name="États-Unis"><region name="Californie"><name sortKey="Mewalal, Ritesh" sort="Mewalal, Ritesh" uniqKey="Mewalal R" first="Ritesh" last="Mewalal">Ritesh Mewalal</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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