Genome-wide identification and expression analysis of the NF-Y transcription factor family in Populus.
Identifieur interne : 000370 ( Main/Exploration ); précédent : 000369; suivant : 000371Genome-wide identification and expression analysis of the NF-Y transcription factor family in Populus.
Auteurs : Rui Liu [République populaire de Chine] ; Min Wu [République populaire de Chine] ; Huan-Long Liu [République populaire de Chine] ; Ya-Meng Gao [République populaire de Chine] ; Jun Chen [République populaire de Chine] ; Han-Wei Yan [République populaire de Chine] ; Yan Xiang [République populaire de Chine]Source :
- Physiologia plantarum [ 1399-3054 ] ; 2020.
Abstract
In the past few years, many studies have reported that the transcription factor Nuclear Factor Y (NF-Y) gene family plays important roles in embryonic development, photosynthesis, flowering time regulation and stress response, in various plants. Although the NF-Y gene family has been systematically studied in many species, little is known about NF-Y genes in Populus. In this study, the NF-Y gene family in the Populus genome was identified and its structural characteristics were described. Fifty-two NF-Y genes were authenticated in the Populus trichocarpa genome and categorized into three subfamilies (NF-YA/B/C) by phylogenetic analysis. Chromosomal localization of these genes revealed that they were distributed randomly across 17 of the 19 chromosomes. Segmental duplication played a vital role in the amplification of Populus NF-Y gene family. Moreover, microsynteny analysis indicated that, among Populus trichocarpa, Arabidopsis thaliana, Vitis vinifera and Carica papaya, NF-Y duplicated regions were more conserved between Populus trichocarpa and Vitis vinifera. Redundant stress-related cis-elements were also found in the promoters of most 13 NF-YA genes and their expression levels varied widely following drought, salt, ABA and cold treatments. Subcellular localization experiments in tobacco showed that PtNF-YA3 was localized in nucleus and cytomembrane, while PtNF-YA4 was only in the nucleus in tobacco. According to the transcriptional activity experiments, neither of them had transcriptional activity in yeast. In summary, a comprehensive analysis of the Populus NF-Y gene family was performed to establish a theoretical basis for further functional studies on this family.
DOI: 10.1111/ppl.13084
PubMed: 32134494
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School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036</wicri:regionArea><wicri:noRegion>230036</wicri:noRegion></affiliation></author><author><name sortKey="Liu, Huan Long" sort="Liu, Huan Long" uniqKey="Liu H" first="Huan-Long" last="Liu">Huan-Long Liu</name><affiliation wicri:level="1"><nlm:affiliation>National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 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China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036</wicri:regionArea><wicri:noRegion>230036</wicri:noRegion></affiliation></author><author><name sortKey="Yan, Han Wei" sort="Yan, Han Wei" uniqKey="Yan H" first="Han-Wei" last="Yan">Han-Wei Yan</name><affiliation wicri:level="1"><nlm:affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036</wicri:regionArea><wicri:noRegion>230036</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036</wicri:regionArea><wicri:noRegion>230036</wicri:noRegion></affiliation></author><author><name sortKey="Xiang, Yan" sort="Xiang, Yan" uniqKey="Xiang Y" first="Yan" last="Xiang">Yan Xiang</name><affiliation wicri:level="1"><nlm:affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036</wicri:regionArea><wicri:noRegion>230036</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036</wicri:regionArea><wicri:noRegion>230036</wicri:noRegion></affiliation></author></analytic><series><title level="j">Physiologia plantarum</title><idno type="eISSN">1399-3054</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">In the past few years, many studies have reported that the transcription factor Nuclear Factor Y (NF-Y) gene family plays important roles in embryonic development, photosynthesis, flowering time regulation and stress response, in various plants. Although the NF-Y gene family has been systematically studied in many species, little is known about NF-Y genes in Populus. In this study, the NF-Y gene family in the Populus genome was identified and its structural characteristics were described. Fifty-two NF-Y genes were authenticated in the Populus trichocarpa genome and categorized into three subfamilies (NF-YA/B/C) by phylogenetic analysis. Chromosomal localization of these genes revealed that they were distributed randomly across 17 of the 19 chromosomes. Segmental duplication played a vital role in the amplification of Populus NF-Y gene family. Moreover, microsynteny analysis indicated that, among Populus trichocarpa, Arabidopsis thaliana, Vitis vinifera and Carica papaya, NF-Y duplicated regions were more conserved between Populus trichocarpa and Vitis vinifera. Redundant stress-related cis-elements were also found in the promoters of most 13 NF-YA genes and their expression levels varied widely following drought, salt, ABA and cold treatments. Subcellular localization experiments in tobacco showed that PtNF-YA3 was localized in nucleus and cytomembrane, while PtNF-YA4 was only in the nucleus in tobacco. According to the transcriptional activity experiments, neither of them had transcriptional activity in yeast. In summary, a comprehensive analysis of the Populus NF-Y gene family was performed to establish a theoretical basis for further functional studies on this family.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">32134494</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>14</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1399-3054</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2020</Year><Month>Mar</Month><Day>05</Day></PubDate></JournalIssue><Title>Physiologia plantarum</Title><ISOAbbreviation>Physiol Plant</ISOAbbreviation></Journal><ArticleTitle>Genome-wide identification and expression analysis of the NF-Y transcription factor family in Populus.</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.1111/ppl.13084</ELocationID><Abstract><AbstractText>In the past few years, many studies have reported that the transcription factor Nuclear Factor Y (NF-Y) gene family plays important roles in embryonic development, photosynthesis, flowering time regulation and stress response, in various plants. Although the NF-Y gene family has been systematically studied in many species, little is known about NF-Y genes in Populus. In this study, the NF-Y gene family in the Populus genome was identified and its structural characteristics were described. Fifty-two NF-Y genes were authenticated in the Populus trichocarpa genome and categorized into three subfamilies (NF-YA/B/C) by phylogenetic analysis. Chromosomal localization of these genes revealed that they were distributed randomly across 17 of the 19 chromosomes. Segmental duplication played a vital role in the amplification of Populus NF-Y gene family. Moreover, microsynteny analysis indicated that, among Populus trichocarpa, Arabidopsis thaliana, Vitis vinifera and Carica papaya, NF-Y duplicated regions were more conserved between Populus trichocarpa and Vitis vinifera. Redundant stress-related cis-elements were also found in the promoters of most 13 NF-YA genes and their expression levels varied widely following drought, salt, ABA and cold treatments. Subcellular localization experiments in tobacco showed that PtNF-YA3 was localized in nucleus and cytomembrane, while PtNF-YA4 was only in the nucleus in tobacco. According to the transcriptional activity experiments, neither of them had transcriptional activity in yeast. In summary, a comprehensive analysis of the Populus NF-Y gene family was performed to establish a theoretical basis for further functional studies on this family.</AbstractText><CopyrightInformation>© 2020 Scandinavian Plant Physiology Society.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Rui</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Min</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Huan-Long</ForeName><Initials>HL</Initials><AffiliationInfo><Affiliation>National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gao</LastName><ForeName>Ya-Meng</ForeName><Initials>YM</Initials><AffiliationInfo><Affiliation>National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Jun</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yan</LastName><ForeName>Han-Wei</ForeName><Initials>HW</Initials><AffiliationInfo><Affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xiang</LastName><ForeName>Yan</ForeName><Initials>Y</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-6124-9876</Identifier><AffiliationInfo><Affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>2019ysj-14</GrantID><Agency>Graduate Innovation Foundation of Anhui Agricultural University</Agency><Country></Country></Grant><Grant><GrantID>Grant No.31370561</GrantID><Agency>The National Natural Science Foundation of China</Agency><Country></Country></Grant><Grant><Agency>The National Science and Technology Support Planning Subjects</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>03</Month><Day>05</Day></ArticleDate></Article><MedlineJournalInfo><Country>Denmark</Country><MedlineTA>Physiol Plant</MedlineTA><NlmUniqueID>1256322</NlmUniqueID><ISSNLinking>0031-9317</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>04</Month><Day>19</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2019</Year><Month>10</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>11</Month><Day>01</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>3</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>3</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>3</Month><Day>6</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32134494</ArticleId><ArticleId IdType="doi">10.1111/ppl.13084</ArticleId></ArticleIdList><ReferenceList><Title>References</Title><Reference><Citation>Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 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