Transcriptome analysis of salt-responsive and wood-associated NACs in Populus simonii × Populus nigra.
Identifieur interne : 000042 ( Main/Exploration ); précédent : 000041; suivant : 000043Transcriptome analysis of salt-responsive and wood-associated NACs in Populus simonii × Populus nigra.
Auteurs : Wenjing Yao [République populaire de Chine] ; Chuanzhe Li [République populaire de Chine] ; Shuyan Lin [République populaire de Chine] ; Jianping Wang [États-Unis] ; Boru Zhou [République populaire de Chine] ; Tingbo Jiang [République populaire de Chine]Source :
- BMC plant biology [ 1471-2229 ] ; 2020.
Abstract
BACKGROUND
NAC (NAM, ATAF1-2, and CUC2) family is one of the largest plant-specific transcription factor families known to play significant roles in plant development processes and stress responses.
RESULTS
In the study, a total of 112 NACs were identified to be differentially expressed in the comparisons of leaves and stems, leaves and roots, roots and stems of Populus simonii×P. nigra among 289 members by RNA-Seq. And 148, 144 and 134 NACs were detected to be salt-responsive in the roots, stems and leaves under 150 mM NaCl stress, respectively. Among them, a total of 53 salt-responsive NACs were shared across the three tissues. Under salt stress, 41/37 NACs were identified to be up/down-regulated in the leaves of Populus simonii × P.nigra among 170 non-redundant NACs by RT-qPCR, which was similar with RNA-Seq results. The expression pattern analysis of 6 NACs including four randomly up-regulated genes (NAC86, NAC105, NAC139 and NAC163) and two down-regulated genes (NAC15 and NAC149) indicated a few NACs showed specific temporal and spatial expression patterns in the three tissues of Populus simonii×P.nigra. Based on transcriptome screening and phylogenic analysis of differentially expressed NACs in different tissues under salt stress, 18 potential NACs associated with wood formation and 20 involved in stress responses were identified in Populus simonii×P.nigra.
CONCLUSIONS
The study further gains an understanding of the connection of tissue specificity and gene function in poplar, and lays the foundation of functional analysis of poplar NACs in stress responses.
DOI: 10.1186/s12870-020-02507-z
PubMed: 32631231
PubMed Central: PMC7336439
Affiliations:
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tbjiang@yahoo.com.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin, 150040</wicri:regionArea><wicri:noRegion>150040</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:32631231</idno><idno type="pmid">32631231</idno><idno type="doi">10.1186/s12870-020-02507-z</idno><idno type="pmc">PMC7336439</idno><idno type="wicri:Area/Main/Corpus">000208</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000208</idno><idno type="wicri:Area/Main/Curation">000208</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000208</idno><idno type="wicri:Area/Main/Exploration">000208</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Transcriptome analysis of salt-responsive and wood-associated NACs in Populus simonii × Populus nigra.</title><author><name sortKey="Yao, Wenjing" sort="Yao, Wenjing" uniqKey="Yao W" first="Wenjing" last="Yao">Wenjing Yao</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin, 150040, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin, 150040</wicri:regionArea><wicri:noRegion>150040</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Co-Innovation Center for Sustainable Forestry in Southern China/Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Co-Innovation Center for Sustainable Forestry in Southern China/Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037</wicri:regionArea><wicri:noRegion>210037</wicri:noRegion></affiliation></author><author><name sortKey="Li, Chuanzhe" sort="Li, Chuanzhe" uniqKey="Li C" first="Chuanzhe" last="Li">Chuanzhe Li</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014</wicri:regionArea><wicri:noRegion>210014</wicri:noRegion></affiliation></author><author><name sortKey="Lin, Shuyan" sort="Lin, Shuyan" uniqKey="Lin S" first="Shuyan" last="Lin">Shuyan Lin</name><affiliation wicri:level="1"><nlm:affiliation>Co-Innovation Center for Sustainable Forestry in Southern China/Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Co-Innovation Center for Sustainable Forestry in Southern China/Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037</wicri:regionArea><wicri:noRegion>210037</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Jianping" sort="Wang, Jianping" uniqKey="Wang J" first="Jianping" last="Wang">Jianping Wang</name><affiliation wicri:level="2"><nlm:affiliation>Department of Agronomy, University of Florida, 2033 Mowry Road, Gainesville, FL32610, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Agronomy, University of Florida, 2033 Mowry Road, Gainesville, FL32610</wicri:regionArea><placeName><region type="state">Floride</region></placeName></affiliation></author><author><name sortKey="Zhou, Boru" sort="Zhou, Boru" uniqKey="Zhou B" first="Boru" last="Zhou">Boru Zhou</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin, 150040, China. 896099005@qq.com.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin, 150040</wicri:regionArea><wicri:noRegion>150040</wicri:noRegion></affiliation></author><author><name sortKey="Jiang, Tingbo" sort="Jiang, Tingbo" uniqKey="Jiang T" first="Tingbo" last="Jiang">Tingbo Jiang</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin, 150040, China. tbjiang@yahoo.com.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin, 150040</wicri:regionArea><wicri:noRegion>150040</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC plant biology</title><idno type="eISSN">1471-2229</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"><p><b>BACKGROUND</b></p><p>NAC (NAM, ATAF1-2, and CUC2) family is one of the largest plant-specific transcription factor families known to play significant roles in plant development processes and stress responses.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>In the study, a total of 112 NACs were identified to be differentially expressed in the comparisons of leaves and stems, leaves and roots, roots and stems of Populus simonii×P. nigra among 289 members by RNA-Seq. And 148, 144 and 134 NACs were detected to be salt-responsive in the roots, stems and leaves under 150 mM NaCl stress, respectively. Among them, a total of 53 salt-responsive NACs were shared across the three tissues. Under salt stress, 41/37 NACs were identified to be up/down-regulated in the leaves of Populus simonii × P.nigra among 170 non-redundant NACs by RT-qPCR, which was similar with RNA-Seq results. The expression pattern analysis of 6 NACs including four randomly up-regulated genes (NAC86, NAC105, NAC139 and NAC163) and two down-regulated genes (NAC15 and NAC149) indicated a few NACs showed specific temporal and spatial expression patterns in the three tissues of Populus simonii×P.nigra. Based on transcriptome screening and phylogenic analysis of differentially expressed NACs in different tissues under salt stress, 18 potential NACs associated with wood formation and 20 involved in stress responses were identified in Populus simonii×P.nigra.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>The study further gains an understanding of the connection of tissue specificity and gene function in poplar, and lays the foundation of functional analysis of poplar NACs in stress responses.</p></div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">32631231</PMID><DateRevised><Year>2020</Year><Month>07</Month><Day>09</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2229</ISSN><JournalIssue CitedMedium="Internet"><Volume>20</Volume><Issue>1</Issue><PubDate><Year>2020</Year><Month>Jul</Month><Day>06</Day></PubDate></JournalIssue><Title>BMC plant biology</Title><ISOAbbreviation>BMC Plant Biol</ISOAbbreviation></Journal><ArticleTitle>Transcriptome analysis of salt-responsive and wood-associated NACs in Populus simonii × Populus nigra.</ArticleTitle><Pagination><MedlinePgn>317</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12870-020-02507-z</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">NAC (NAM, ATAF1-2, and CUC2) family is one of the largest plant-specific transcription factor families known to play significant roles in plant development processes and stress responses.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">In the study, a total of 112 NACs were identified to be differentially expressed in the comparisons of leaves and stems, leaves and roots, roots and stems of Populus simonii×P. nigra among 289 members by RNA-Seq. And 148, 144 and 134 NACs were detected to be salt-responsive in the roots, stems and leaves under 150 mM NaCl stress, respectively. Among them, a total of 53 salt-responsive NACs were shared across the three tissues. Under salt stress, 41/37 NACs were identified to be up/down-regulated in the leaves of Populus simonii × P.nigra among 170 non-redundant NACs by RT-qPCR, which was similar with RNA-Seq results. The expression pattern analysis of 6 NACs including four randomly up-regulated genes (NAC86, NAC105, NAC139 and NAC163) and two down-regulated genes (NAC15 and NAC149) indicated a few NACs showed specific temporal and spatial expression patterns in the three tissues of Populus simonii×P.nigra. Based on transcriptome screening and phylogenic analysis of differentially expressed NACs in different tissues under salt stress, 18 potential NACs associated with wood formation and 20 involved in stress responses were identified in Populus simonii×P.nigra.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">The study further gains an understanding of the connection of tissue specificity and gene function in poplar, and lays the foundation of functional analysis of poplar NACs in stress responses.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Yao</LastName><ForeName>Wenjing</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin, 150040, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Co-Innovation Center for Sustainable Forestry in Southern China/Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Chuanzhe</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lin</LastName><ForeName>Shuyan</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Co-Innovation Center for Sustainable Forestry in Southern China/Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Jianping</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Agronomy, University of Florida, 2033 Mowry Road, Gainesville, FL32610, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhou</LastName><ForeName>Boru</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin, 150040, China. 896099005@qq.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jiang</LastName><ForeName>Tingbo</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin, 150040, China. tbjiang@yahoo.com.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>07</Month><Day>06</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Plant Biol</MedlineTA><NlmUniqueID>100967807</NlmUniqueID><ISSNLinking>1471-2229</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">NAC transcription factor</Keyword><Keyword MajorTopicYN="N">Phylogenic analysis</Keyword><Keyword MajorTopicYN="N">Populus simonii×P. nigra</Keyword><Keyword MajorTopicYN="N">Salt stress</Keyword><Keyword MajorTopicYN="N">Transcriptome analysis</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>12</Month><Day>30</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>06</Month><Day>19</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>7</Month><Day>8</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>7</Month><Day>8</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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IdType="pubmed">30727951</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li><li>États-Unis</li></country><region><li>Floride</li></region></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Yao, Wenjing" sort="Yao, Wenjing" uniqKey="Yao W" first="Wenjing" last="Yao">Wenjing Yao</name></noRegion><name sortKey="Jiang, Tingbo" sort="Jiang, Tingbo" uniqKey="Jiang T" first="Tingbo" last="Jiang">Tingbo Jiang</name><name sortKey="Li, Chuanzhe" sort="Li, Chuanzhe" uniqKey="Li C" first="Chuanzhe" last="Li">Chuanzhe Li</name><name sortKey="Lin, Shuyan" sort="Lin, Shuyan" uniqKey="Lin S" first="Shuyan" last="Lin">Shuyan Lin</name><name sortKey="Yao, Wenjing" sort="Yao, Wenjing" uniqKey="Yao W" first="Wenjing" last="Yao">Wenjing Yao</name><name sortKey="Zhou, Boru" sort="Zhou, Boru" uniqKey="Zhou B" first="Boru" last="Zhou">Boru Zhou</name></country><country name="États-Unis"><region name="Floride"><name sortKey="Wang, Jianping" sort="Wang, Jianping" uniqKey="Wang J" first="Jianping" last="Wang">Jianping Wang</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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