Structure and expression analysis of seven salt-related ERF genes of Populus.
Identifieur interne : 000104 ( Main/Exploration ); précédent : 000103; suivant : 000105Structure and expression analysis of seven salt-related ERF genes of Populus.
Auteurs : Juanjuan Huang [République populaire de Chine] ; Shengji Wang [République populaire de Chine] ; Xingdou Wang [République populaire de Chine] ; Yan Fan [République populaire de Chine] ; Youzhi Han [République populaire de Chine]Source :
- PeerJ [ 2167-8359 ] ; 2020.
Abstract
Ethylene response factors (ERFs) are plant-specific transcription factors (TFs) that play important roles in plant growth and stress defense and have received a great amount of attention in recent years. In this study, seven ERF genes related to abiotic stress tolerance and response were identified in plants of the Populus genus. Systematic bioinformatics, including sequence phylogeny, genome organisation, gene structure, gene ontology (GO) annotation, etc. were detected. Expression-pattern of these seven ERF genes were analyzed using RT-qPCR and cross validated using RNA-Seq. Data from a phylogenetic tree and multiple alignment of protein sequences indicated that these seven ERF TFs belong to three subfamilies and contain AP2, YRG, and RAYD conserved domains, which may interact with downstream target genes to regulate the plant stress response. An analysis of the structure and promoter region of these seven ERF genes showed that they have multiple stress-related motifs and cis-elements, which may play roles in the plant stress-tolerance process through a transcriptional regulation mechanism; moreover, the cellular_component and molecular_function terms associated with these ERFs determined by GO annotation supported this hypothesis. In addition, the spatio-temporal expression pattern of these seven ERFs, as detected using RT-qPCR and RNA-seq, suggested that they play a critical role in mediating the salt response and tolerance in a dynamic and tissue-specific manner. The results of this study provide a solid basis to explore the functions of the stress-related ERF TFs in Populus abiotic stress tolerance and development process.
DOI: 10.7717/peerj.10206
PubMed: 33150090
PubMed Central: PMC7583627
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wicri:level="1"><nlm:affiliation>College of Forestry, Shanxi Agricultural University, Taigu, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Forestry, Shanxi Agricultural University, Taigu</wicri:regionArea><wicri:noRegion>Taigu</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Xingdou" sort="Wang, Xingdou" uniqKey="Wang X" first="Xingdou" last="Wang">Xingdou Wang</name><affiliation wicri:level="1"><nlm:affiliation>College of Forestry, Shanxi Agricultural University, Taigu, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Forestry, Shanxi Agricultural University, Taigu</wicri:regionArea><wicri:noRegion>Taigu</wicri:noRegion></affiliation></author><author><name sortKey="Fan, Yan" sort="Fan, Yan" uniqKey="Fan Y" first="Yan" last="Fan">Yan Fan</name><affiliation wicri:level="1"><nlm:affiliation>College of Forestry, Shanxi Agricultural University, Taigu, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Forestry, Shanxi Agricultural University, Taigu</wicri:regionArea><wicri:noRegion>Taigu</wicri:noRegion></affiliation></author><author><name sortKey="Han, Youzhi" sort="Han, Youzhi" uniqKey="Han Y" first="Youzhi" last="Han">Youzhi Han</name><affiliation wicri:level="1"><nlm:affiliation>College of Forestry, Shanxi Agricultural University, Taigu, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Forestry, Shanxi Agricultural University, Taigu</wicri:regionArea><wicri:noRegion>Taigu</wicri:noRegion></affiliation></author></analytic><series><title level="j">PeerJ</title><idno type="ISSN">2167-8359</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">Ethylene response factors (ERFs) are plant-specific transcription factors (TFs) that play important roles in plant growth and stress defense and have received a great amount of attention in recent years. In this study, seven <i>ERF</i> genes related to abiotic stress tolerance and response were identified in plants of the <i>Populus</i> genus. Systematic bioinformatics, including sequence phylogeny, genome organisation, gene structure, gene ontology (GO) annotation, etc. were detected. Expression-pattern of these seven <i>ERF</i> genes were analyzed using RT-qPCR and cross validated using RNA-Seq. Data from a phylogenetic tree and multiple alignment of protein sequences indicated that these seven ERF TFs belong to three subfamilies and contain AP2, YRG, and RAYD conserved domains, which may interact with downstream target genes to regulate the plant stress response. An analysis of the structure and promoter region of these seven <i>ERF</i> genes showed that they have multiple stress-related motifs and <i>cis</i>-elements, which may play roles in the plant stress-tolerance process through a transcriptional regulation mechanism; moreover, the cellular_component and molecular_function terms associated with these <i>ERFs</i> determined by GO annotation supported this hypothesis. In addition, the spatio-temporal expression pattern of these seven <i>ERFs</i>, as detected using RT-qPCR and RNA-seq, suggested that they play a critical role in mediating the salt response and tolerance in a dynamic and tissue-specific manner. The results of this study provide a solid basis to explore the functions of the stress-related ERF TFs in <i>Populus</i> abiotic stress tolerance and development process.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">33150090</PMID><DateRevised><Year>2020</Year><Month>11</Month><Day>06</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">2167-8359</ISSN><JournalIssue CitedMedium="Print"><Volume>8</Volume><PubDate><Year>2020</Year></PubDate></JournalIssue><Title>PeerJ</Title><ISOAbbreviation>PeerJ</ISOAbbreviation></Journal><ArticleTitle>Structure and expression analysis of seven salt-related <i>ERF</i> genes of <i>Populus</i>.</ArticleTitle><Pagination><MedlinePgn>e10206</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.7717/peerj.10206</ELocationID><Abstract><AbstractText>Ethylene response factors (ERFs) are plant-specific transcription factors (TFs) that play important roles in plant growth and stress defense and have received a great amount of attention in recent years. In this study, seven <i>ERF</i> genes related to abiotic stress tolerance and response were identified in plants of the <i>Populus</i> genus. Systematic bioinformatics, including sequence phylogeny, genome organisation, gene structure, gene ontology (GO) annotation, etc. were detected. Expression-pattern of these seven <i>ERF</i> genes were analyzed using RT-qPCR and cross validated using RNA-Seq. Data from a phylogenetic tree and multiple alignment of protein sequences indicated that these seven ERF TFs belong to three subfamilies and contain AP2, YRG, and RAYD conserved domains, which may interact with downstream target genes to regulate the plant stress response. An analysis of the structure and promoter region of these seven <i>ERF</i> genes showed that they have multiple stress-related motifs and <i>cis</i>-elements, which may play roles in the plant stress-tolerance process through a transcriptional regulation mechanism; moreover, the cellular_component and molecular_function terms associated with these <i>ERFs</i> determined by GO annotation supported this hypothesis. In addition, the spatio-temporal expression pattern of these seven <i>ERFs</i>, as detected using RT-qPCR and RNA-seq, suggested that they play a critical role in mediating the salt response and tolerance in a dynamic and tissue-specific manner. The results of this study provide a solid basis to explore the functions of the stress-related ERF TFs in <i>Populus</i> abiotic stress tolerance and development process.</AbstractText><CopyrightInformation>©2020 Huang et al.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y" EqualContrib="Y"><LastName>Huang</LastName><ForeName>Juanjuan</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>College of Forestry, Shanxi Agricultural University, Taigu, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y" EqualContrib="Y"><LastName>Wang</LastName><ForeName>Shengji</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>College of Forestry, Shanxi Agricultural University, Taigu, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Xingdou</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>College of Forestry, Shanxi Agricultural University, Taigu, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fan</LastName><ForeName>Yan</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>College of Forestry, Shanxi Agricultural University, Taigu, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Han</LastName><ForeName>Youzhi</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>College of Forestry, Shanxi Agricultural University, Taigu, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>10</Month><Day>20</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PeerJ</MedlineTA><NlmUniqueID>101603425</NlmUniqueID><ISSNLinking>2167-8359</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N"> Gene express</Keyword><Keyword MajorTopicYN="N"> Salt stress</Keyword><Keyword MajorTopicYN="N">ERF</Keyword><Keyword MajorTopicYN="N">Populus</Keyword><Keyword MajorTopicYN="N">Transcription factor</Keyword></KeywordList><CoiStatement>The authors declare there are no competing interests.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>07</Month><Day>03</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>09</Month><Day>28</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>11</Month><Day>5</Day><Hour>6</Hour><Minute>8</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>11</Month><Day>6</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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