Identification of conserved genes linked to responses to abiotic stresses in leaves among different plant species.
Identifieur interne : 000059 ( Main/Exploration ); précédent : 000058; suivant : 000060Identification of conserved genes linked to responses to abiotic stresses in leaves among different plant species.
Auteurs : Imen Balti ; Jubina Benny ; Anna Perrone ; Tiziano Caruso ; Donia Abdallah ; Amel Salhi-Hannachi ; Federico MartinelliSource :
- Functional plant biology : FPB [ 1445-4416 ] ; 2020.
Abstract
As a consequence of global climate change, certain stress factors that have a negative impact on crop productivity such as heat, cold, drought and salinity are becoming increasingly prevalent. We conducted a meta-analysis to identify genes conserved across plant species involved in (1) general abiotic stress conditions, and (2) specific and unique abiotic stress factors (drought, salinity, extreme temperature) in leaf tissues. We collected raw data and re-analysed eight RNA-Seq studies using our previously published bioinformatic pipeline. A total of 68 samples were analysed. Gene set enrichment analysis was performed using MapMan and PageMan whereas DAVID (Database for Annotation, Visualisation and Integrated Discovery) was used for metabolic process enrichment analysis. We identified of a total of 5122 differentially expressed genes when considering all abiotic stresses (3895 were upregulated and 1227 were downregulated). Jasmonate-related genes were more commonly upregulated by drought, whereas gibberellin downregulation was a key signal for drought and heat. In contrast, cold stress clearly upregulated genes involved in ABA (abscisic acid), cytokinin and gibberellins. A gene (non-phototrophic hypocotyl) involved in IAA (indoleacetic acid) response was induced by heat. Regarding secondary metabolism, as expected, MVA pathway (mevalonate pathway), terpenoids and alkaloids were generally upregulated by all different stresses. However, flavonoids, lignin and lignans were more repressed by heat (cinnamoyl coA reductase 1 and isopentenyl pyrophosphatase). Cold stress drastically modulated genes involved in terpenoid and alkaloids. Relating to transcription factors, AP2-EREBP, MADS-box, WRKY22, MYB, homoebox genes members were significantly modulated by drought stress whereas cold stress enhanced AP2-EREBPs, bZIP members, MYB7, BELL 1 and one bHLH member. C2C2-CO-LIKE, MADS-box and a homeobox (HOMEOBOX3) were mostly repressed in response to heat. Gene set enrichment analysis showed that ubiquitin-mediated protein degradation was enhanced by heat, which unexpectedly repressed glutaredoxin genes. Cold stress mostly upregulated MAP kinases (mitogen-activated protein kinase). Findings of this work will allow the identification of new molecular markers conserved across crops linked to major genes involved in quantitative agronomic traits affected by different abiotic stress.
DOI: 10.1071/FP20028
PubMed: 32727652
Affiliations:
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We conducted a meta-analysis to identify genes conserved across plant species involved in (1) general abiotic stress conditions, and (2) specific and unique abiotic stress factors (drought, salinity, extreme temperature) in leaf tissues. We collected raw data and re-analysed eight RNA-Seq studies using our previously published bioinformatic pipeline. A total of 68 samples were analysed. Gene set enrichment analysis was performed using MapMan and PageMan whereas DAVID (Database for Annotation, Visualisation and Integrated Discovery) was used for metabolic process enrichment analysis. We identified of a total of 5122 differentially expressed genes when considering all abiotic stresses (3895 were upregulated and 1227 were downregulated). Jasmonate-related genes were more commonly upregulated by drought, whereas gibberellin downregulation was a key signal for drought and heat. In contrast, cold stress clearly upregulated genes involved in ABA (abscisic acid), cytokinin and gibberellins. A gene (non-phototrophic hypocotyl) involved in IAA (indoleacetic acid) response was induced by heat. Regarding secondary metabolism, as expected, MVA pathway (mevalonate pathway), terpenoids and alkaloids were generally upregulated by all different stresses. However, flavonoids, lignin and lignans were more repressed by heat (cinnamoyl coA reductase 1 and isopentenyl pyrophosphatase). Cold stress drastically modulated genes involved in terpenoid and alkaloids. Relating to transcription factors, AP2-EREBP, MADS-box, WRKY22, MYB, homoebox genes members were significantly modulated by drought stress whereas cold stress enhanced AP2-EREBPs, bZIP members, MYB7, BELL 1 and one bHLH member. C2C2-CO-LIKE, MADS-box and a homeobox (HOMEOBOX3) were mostly repressed in response to heat. Gene set enrichment analysis showed that ubiquitin-mediated protein degradation was enhanced by heat, which unexpectedly repressed glutaredoxin genes. Cold stress mostly upregulated MAP kinases (mitogen-activated protein kinase). Findings of this work will allow the identification of new molecular markers conserved across crops linked to major genes involved in quantitative agronomic traits affected by different abiotic stress.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">32727652</PMID><DateRevised><Year>2020</Year><Month>07</Month><Day>30</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1445-4416</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2020</Year><Month>Jul</Month><Day>30</Day></PubDate></JournalIssue><Title>Functional plant biology : FPB</Title><ISOAbbreviation>Funct Plant Biol</ISOAbbreviation></Journal><ArticleTitle>Identification of conserved genes linked to responses to abiotic stresses in leaves among different plant species.</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.1071/FP20028</ELocationID><Abstract><AbstractText>As a consequence of global climate change, certain stress factors that have a negative impact on crop productivity such as heat, cold, drought and salinity are becoming increasingly prevalent. We conducted a meta-analysis to identify genes conserved across plant species involved in (1) general abiotic stress conditions, and (2) specific and unique abiotic stress factors (drought, salinity, extreme temperature) in leaf tissues. We collected raw data and re-analysed eight RNA-Seq studies using our previously published bioinformatic pipeline. A total of 68 samples were analysed. Gene set enrichment analysis was performed using MapMan and PageMan whereas DAVID (Database for Annotation, Visualisation and Integrated Discovery) was used for metabolic process enrichment analysis. We identified of a total of 5122 differentially expressed genes when considering all abiotic stresses (3895 were upregulated and 1227 were downregulated). Jasmonate-related genes were more commonly upregulated by drought, whereas gibberellin downregulation was a key signal for drought and heat. In contrast, cold stress clearly upregulated genes involved in ABA (abscisic acid), cytokinin and gibberellins. A gene (non-phototrophic hypocotyl) involved in IAA (indoleacetic acid) response was induced by heat. Regarding secondary metabolism, as expected, MVA pathway (mevalonate pathway), terpenoids and alkaloids were generally upregulated by all different stresses. However, flavonoids, lignin and lignans were more repressed by heat (cinnamoyl coA reductase 1 and isopentenyl pyrophosphatase). Cold stress drastically modulated genes involved in terpenoid and alkaloids. Relating to transcription factors, AP2-EREBP, MADS-box, WRKY22, MYB, homoebox genes members were significantly modulated by drought stress whereas cold stress enhanced AP2-EREBPs, bZIP members, MYB7, BELL 1 and one bHLH member. C2C2-CO-LIKE, MADS-box and a homeobox (HOMEOBOX3) were mostly repressed in response to heat. Gene set enrichment analysis showed that ubiquitin-mediated protein degradation was enhanced by heat, which unexpectedly repressed glutaredoxin genes. Cold stress mostly upregulated MAP kinases (mitogen-activated protein kinase). Findings of this work will allow the identification of new molecular markers conserved across crops linked to major genes involved in quantitative agronomic traits affected by different abiotic stress.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Balti</LastName><ForeName>Imen</ForeName><Initials>I</Initials></Author><Author ValidYN="Y"><LastName>Benny</LastName><ForeName>Jubina</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Perrone</LastName><ForeName>Anna</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Caruso</LastName><ForeName>Tiziano</ForeName><Initials>T</Initials></Author><Author ValidYN="Y"><LastName>Abdallah</LastName><ForeName>Donia</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Salhi-Hannachi</LastName><ForeName>Amel</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Martinelli</LastName><ForeName>Federico</ForeName><Initials>F</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>07</Month><Day>30</Day></ArticleDate></Article><MedlineJournalInfo><Country>Australia</Country><MedlineTA>Funct Plant Biol</MedlineTA><NlmUniqueID>101154361</NlmUniqueID><ISSNLinking>1445-4416</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>01</Month><Day>28</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>07</Month><Day>08</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>7</Month><Day>31</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>7</Month><Day>31</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>7</Month><Day>31</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32727652</ArticleId><ArticleId IdType="pii">FP20028</ArticleId><ArticleId IdType="doi">10.1071/FP20028</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list></list><tree><noCountry><name sortKey="Abdallah, Donia" sort="Abdallah, Donia" uniqKey="Abdallah D" first="Donia" last="Abdallah">Donia Abdallah</name><name sortKey="Balti, Imen" sort="Balti, Imen" uniqKey="Balti I" first="Imen" last="Balti">Imen Balti</name><name sortKey="Benny, Jubina" sort="Benny, Jubina" uniqKey="Benny J" first="Jubina" last="Benny">Jubina Benny</name><name sortKey="Caruso, Tiziano" sort="Caruso, Tiziano" uniqKey="Caruso T" first="Tiziano" last="Caruso">Tiziano Caruso</name><name sortKey="Martinelli, Federico" sort="Martinelli, Federico" uniqKey="Martinelli F" first="Federico" last="Martinelli">Federico Martinelli</name><name sortKey="Perrone, Anna" sort="Perrone, Anna" uniqKey="Perrone A" first="Anna" last="Perrone">Anna Perrone</name><name sortKey="Salhi Hannachi, Amel" sort="Salhi Hannachi, Amel" uniqKey="Salhi Hannachi A" first="Amel" last="Salhi-Hannachi">Amel Salhi-Hannachi</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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