Analysis of transcription factors among differentially expressed genes induced by drought stress in Populus davidiana.
Identifieur interne : 001524 ( Main/Exploration ); précédent : 001523; suivant : 001525Analysis of transcription factors among differentially expressed genes induced by drought stress in Populus davidiana.
Auteurs : Bong-Gyu Mun [Corée du Sud] ; Sang-Uk Lee [Corée du Sud] ; Eung-Jun Park [Corée du Sud] ; Hyun-Ho Kim [Corée du Sud] ; Adil Hussain [Corée du Sud, Pakistan] ; Qari Muhammad Imran [Corée du Sud] ; In-Jung Lee [Corée du Sud] ; Byung-Wook Yun [Corée du Sud]Source :
- 3 Biotech [ 2190-572X ] ; 2017.
Abstract
Populus davidiana is native to the Korean Peninsula and is one of the most dominant and abundantly growing forest trees in eastern Asia. Compared to other Populus species such as P. trichocarpa, P. euphratica, and P. tremula, relatively little is known about P. davidiana. Here, we performed transcriptomic analysis of P. davidiana under drought stress induced by 10% polyethylene glycol. A total of 12,403 and 12,414 differentially expressed genes (DEGs) were successfully annotated with the P. trichocarpa reference genome after 6 and 12 h of treatment, respectively. Of these, a total of 404 genes (238 up-regulated and 166 down-regulated) after 6 h and 359 genes (187 up-regulated and 172 down-regulated) after 12 h of treatment were identified as transcription factors. Transcription factors known to be key genes for drought stress response, such as AP2-EREB, WRKY, C2H2, and NAC, were identified. This results suggesting that early induction of these genes affected initiation of transcriptional regulation in response to drought stress. Quantitative real-time PCR results of selected genes showed highly significant (R = 0.93) correlation with RNA-Seq data. Interestingly, the expression pattern of some transcription factors was P. davidiana specific. The sequence of P. davidiana ortholog of P. trichocarpa gene POPTR_0018s10230, which plays an important role in plant response to drought, was further analyzed as our RNA-Seq results showed highly significant changes in the expression of this gene following the stress treatment. Sequence of the gene was compared to P. trichocarpa gene sequence using cloning-based sequencing. Additionally, we generated a predicted 3D protein structure for the gene product. Results indicated that the amino acid sequence of P. davidiana-specific POPTR_0018s10230 is different at six different positions compared to P. trichocarpa, resulting in a significantly different structure of the protein. Identifying the transcription factors expressed in P. davidiana under drought stress will not only offer clues for understanding the underlying mechanisms involved in drought stress physiology but also serve as a basis for future molecular studies on this species.
DOI: 10.1007/s13205-017-0858-7
PubMed: 28667649
PubMed Central: PMC5493580
Affiliations:
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uniqKey="Lee S" first="Sang-Uk" last="Lee">Sang-Uk Lee</name><affiliation wicri:level="1"><nlm:affiliation>School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>School of Applied Biosciences, Kyungpook National University, Daegu, 41566</wicri:regionArea><wicri:noRegion>41566</wicri:noRegion></affiliation></author><author><name sortKey="Park, Eung Jun" sort="Park, Eung Jun" uniqKey="Park E" first="Eung-Jun" last="Park">Eung-Jun Park</name><affiliation wicri:level="1"><nlm:affiliation>Division of Forest Biotechnology, Korea Forest Research Institute, Suwon, 16631, Republic of Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Division of Forest Biotechnology, Korea Forest Research Institute, Suwon, 16631</wicri:regionArea><wicri:noRegion>16631</wicri:noRegion></affiliation></author><author><name sortKey="Kim, Hyun Ho" sort="Kim, Hyun Ho" uniqKey="Kim H" first="Hyun-Ho" last="Kim">Hyun-Ho Kim</name><affiliation wicri:level="1"><nlm:affiliation>School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>School of Applied Biosciences, Kyungpook National University, Daegu, 41566</wicri:regionArea><wicri:noRegion>41566</wicri:noRegion></affiliation></author><author><name sortKey="Hussain, Adil" sort="Hussain, Adil" uniqKey="Hussain A" first="Adil" last="Hussain">Adil Hussain</name><affiliation wicri:level="1"><nlm:affiliation>School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>School of Applied Biosciences, Kyungpook National University, Daegu, 41566</wicri:regionArea><wicri:noRegion>41566</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Agriculture, Abdul Wali Khan University, Mardan, Pakistan.</nlm:affiliation><country xml:lang="fr">Pakistan</country><wicri:regionArea>Department of Agriculture, Abdul Wali Khan University, Mardan</wicri:regionArea><wicri:noRegion>Mardan</wicri:noRegion></affiliation></author><author><name sortKey="Imran, Qari Muhammad" sort="Imran, Qari Muhammad" uniqKey="Imran Q" first="Qari Muhammad" last="Imran">Qari Muhammad Imran</name><affiliation wicri:level="1"><nlm:affiliation>School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>School of Applied Biosciences, Kyungpook National University, Daegu, 41566</wicri:regionArea><wicri:noRegion>41566</wicri:noRegion></affiliation></author><author><name sortKey="Lee, In Jung" sort="Lee, In Jung" uniqKey="Lee I" first="In-Jung" last="Lee">In-Jung Lee</name><affiliation wicri:level="1"><nlm:affiliation>School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>School of Applied Biosciences, Kyungpook National University, Daegu, 41566</wicri:regionArea><wicri:noRegion>41566</wicri:noRegion></affiliation></author><author><name sortKey="Yun, Byung Wook" sort="Yun, Byung Wook" uniqKey="Yun B" first="Byung-Wook" last="Yun">Byung-Wook Yun</name><affiliation wicri:level="1"><nlm:affiliation>School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea. bwyun@knu.ac.kr.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>School of Applied Biosciences, Kyungpook National University, Daegu, 41566</wicri:regionArea><wicri:noRegion>41566</wicri:noRegion></affiliation></author></analytic><series><title level="j">3 Biotech</title><idno type="ISSN">2190-572X</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Populus davidiana is native to the Korean Peninsula and is one of the most dominant and abundantly growing forest trees in eastern Asia. Compared to other Populus species such as P. trichocarpa, P. euphratica, and P. tremula, relatively little is known about P. davidiana. Here, we performed transcriptomic analysis of P. davidiana under drought stress induced by 10% polyethylene glycol. A total of 12,403 and 12,414 differentially expressed genes (DEGs) were successfully annotated with the P. trichocarpa reference genome after 6 and 12 h of treatment, respectively. Of these, a total of 404 genes (238 up-regulated and 166 down-regulated) after 6 h and 359 genes (187 up-regulated and 172 down-regulated) after 12 h of treatment were identified as transcription factors. Transcription factors known to be key genes for drought stress response, such as AP2-EREB, WRKY, C2H2, and NAC, were identified. This results suggesting that early induction of these genes affected initiation of transcriptional regulation in response to drought stress. Quantitative real-time PCR results of selected genes showed highly significant (R = 0.93) correlation with RNA-Seq data. Interestingly, the expression pattern of some transcription factors was P. davidiana specific. The sequence of P. davidiana ortholog of P. trichocarpa gene POPTR_0018s10230, which plays an important role in plant response to drought, was further analyzed as our RNA-Seq results showed highly significant changes in the expression of this gene following the stress treatment. Sequence of the gene was compared to P. trichocarpa gene sequence using cloning-based sequencing. Additionally, we generated a predicted 3D protein structure for the gene product. Results indicated that the amino acid sequence of P. davidiana-specific POPTR_0018s10230 is different at six different positions compared to P. trichocarpa, resulting in a significantly different structure of the protein. Identifying the transcription factors expressed in P. davidiana under drought stress will not only offer clues for understanding the underlying mechanisms involved in drought stress physiology but also serve as a basis for future molecular studies on this species.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">28667649</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">2190-572X</ISSN><JournalIssue CitedMedium="Print"><Volume>7</Volume><Issue>3</Issue><PubDate><Year>2017</Year><Month>Jul</Month></PubDate></JournalIssue><Title>3 Biotech</Title><ISOAbbreviation>3 Biotech</ISOAbbreviation></Journal><ArticleTitle>Analysis of transcription factors among differentially expressed genes induced by drought stress in Populus davidiana.</ArticleTitle><Pagination><MedlinePgn>209</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s13205-017-0858-7</ELocationID><Abstract><AbstractText>Populus davidiana is native to the Korean Peninsula and is one of the most dominant and abundantly growing forest trees in eastern Asia. Compared to other Populus species such as P. trichocarpa, P. euphratica, and P. tremula, relatively little is known about P. davidiana. Here, we performed transcriptomic analysis of P. davidiana under drought stress induced by 10% polyethylene glycol. A total of 12,403 and 12,414 differentially expressed genes (DEGs) were successfully annotated with the P. trichocarpa reference genome after 6 and 12 h of treatment, respectively. Of these, a total of 404 genes (238 up-regulated and 166 down-regulated) after 6 h and 359 genes (187 up-regulated and 172 down-regulated) after 12 h of treatment were identified as transcription factors. Transcription factors known to be key genes for drought stress response, such as AP2-EREB, WRKY, C2H2, and NAC, were identified. This results suggesting that early induction of these genes affected initiation of transcriptional regulation in response to drought stress. Quantitative real-time PCR results of selected genes showed highly significant (R = 0.93) correlation with RNA-Seq data. Interestingly, the expression pattern of some transcription factors was P. davidiana specific. The sequence of P. davidiana ortholog of P. trichocarpa gene POPTR_0018s10230, which plays an important role in plant response to drought, was further analyzed as our RNA-Seq results showed highly significant changes in the expression of this gene following the stress treatment. Sequence of the gene was compared to P. trichocarpa gene sequence using cloning-based sequencing. Additionally, we generated a predicted 3D protein structure for the gene product. Results indicated that the amino acid sequence of P. davidiana-specific POPTR_0018s10230 is different at six different positions compared to P. trichocarpa, resulting in a significantly different structure of the protein. Identifying the transcription factors expressed in P. davidiana under drought stress will not only offer clues for understanding the underlying mechanisms involved in drought stress physiology but also serve as a basis for future molecular studies on this species.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Mun</LastName><ForeName>Bong-Gyu</ForeName><Initials>BG</Initials><AffiliationInfo><Affiliation>School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lee</LastName><ForeName>Sang-Uk</ForeName><Initials>SU</Initials><AffiliationInfo><Affiliation>School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Park</LastName><ForeName>Eung-Jun</ForeName><Initials>EJ</Initials><AffiliationInfo><Affiliation>Division of Forest Biotechnology, Korea Forest Research Institute, Suwon, 16631, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kim</LastName><ForeName>Hyun-Ho</ForeName><Initials>HH</Initials><AffiliationInfo><Affiliation>School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hussain</LastName><ForeName>Adil</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Agriculture, Abdul Wali Khan University, Mardan, Pakistan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Imran</LastName><ForeName>Qari Muhammad</ForeName><Initials>QM</Initials><AffiliationInfo><Affiliation>School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lee</LastName><ForeName>In-Jung</ForeName><Initials>IJ</Initials><AffiliationInfo><Affiliation>School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yun</LastName><ForeName>Byung-Wook</ForeName><Initials>BW</Initials><AffiliationInfo><Affiliation>School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea. bwyun@knu.ac.kr.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>06</Month><Day>30</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>3 Biotech</MedlineTA><NlmUniqueID>101565857</NlmUniqueID><ISSNLinking>2190-5738</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Drought stress</Keyword><Keyword MajorTopicYN="N">Poplar</Keyword><Keyword MajorTopicYN="N">Transcription factors</Keyword><Keyword MajorTopicYN="N">Transcriptome</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>04</Month><Day>25</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>06</Month><Day>17</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>7</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>7</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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last="Lee">In-Jung Lee</name><name sortKey="Lee, Sang Uk" sort="Lee, Sang Uk" uniqKey="Lee S" first="Sang-Uk" last="Lee">Sang-Uk Lee</name><name sortKey="Park, Eung Jun" sort="Park, Eung Jun" uniqKey="Park E" first="Eung-Jun" last="Park">Eung-Jun Park</name><name sortKey="Yun, Byung Wook" sort="Yun, Byung Wook" uniqKey="Yun B" first="Byung-Wook" last="Yun">Byung-Wook Yun</name></country><country name="Pakistan"><noRegion><name sortKey="Hussain, Adil" sort="Hussain, Adil" uniqKey="Hussain A" first="Adil" last="Hussain">Adil Hussain</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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