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Genome-wide identification of AP2/EREBP in Fragaria vesca and expression pattern analysis of the FvDREB subfamily under drought stress
Drought is a common phenomenon worldwide. It is also one of the main abiotic factors that affect the growth and quality of strawberry. The dehydration-responsive element binding protein (DREB) members that belong to the APETALA2/ethylene-responsive element binding protein (AP2/EREBP) superfamily are...
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| Published in: | BMC plant biology 2021-06, Vol.21 (1), p.295-14, Article 295 |
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| creator | Dong, Chao Xi, Yue Chen, Xinlu Cheng, Zong-Ming |
| description | Drought is a common phenomenon worldwide. It is also one of the main abiotic factors that affect the growth and quality of strawberry. The dehydration-responsive element binding protein (DREB) members that belong to the APETALA2/ethylene-responsive element binding protein (AP2/EREBP) superfamily are unique transcription factors in plants that play important roles in the abiotic stress response.
Here, a total of 119 AP2/EREBP genes were identified in Fragaria vesca, and the AP2/EREBP superfamily was divided into AP2, RAV, ERF, DREB, and soloist subfamilies, containing 18, 7, 61, 32, and one member(s), respectively. The DREB subfamily was further divided into six subgroups (A-1 to A-6) based on phylogenetic analysis. Gene structure, conserved motifs, chromosomal location, and synteny analysis were conducted to comprehensively investigate the characteristics of FvDREBs. Furthermore, transcriptome analysis revealed distinctive expression patterns among the FvDREB genes in strawberry plants exposed to drought stress. The expression of FvDREB6 of the A-2 subgroup was down-regulated in old leaves and up-regulated in young leaves in response to drought. Furthermore, qRT-PCR analysis found that FvDREB8 from the A-2 subgroup had the highest expression level under drought stress. Together, analyses with the expression pattern, phylogenetic relationship, motif, and promoter suggest that FvDREB18 may play a critical role in the regulation of FvDREB1 and FvDREB2 expression.
Our findings provide new insights into the characteristics and potential functions of FvDREBs. These FvDREB genes should be further studied as they appear to be excellent candidates for drought tolerance improvement of strawberry. |
| doi_str_mv | 10.1186/s12870-021-03095-2 |
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Here, a total of 119 AP2/EREBP genes were identified in Fragaria vesca, and the AP2/EREBP superfamily was divided into AP2, RAV, ERF, DREB, and soloist subfamilies, containing 18, 7, 61, 32, and one member(s), respectively. The DREB subfamily was further divided into six subgroups (A-1 to A-6) based on phylogenetic analysis. Gene structure, conserved motifs, chromosomal location, and synteny analysis were conducted to comprehensively investigate the characteristics of FvDREBs. Furthermore, transcriptome analysis revealed distinctive expression patterns among the FvDREB genes in strawberry plants exposed to drought stress. The expression of FvDREB6 of the A-2 subgroup was down-regulated in old leaves and up-regulated in young leaves in response to drought. Furthermore, qRT-PCR analysis found that FvDREB8 from the A-2 subgroup had the highest expression level under drought stress. Together, analyses with the expression pattern, phylogenetic relationship, motif, and promoter suggest that FvDREB18 may play a critical role in the regulation of FvDREB1 and FvDREB2 expression.
Our findings provide new insights into the characteristics and potential functions of FvDREBs. These FvDREB genes should be further studied as they appear to be excellent candidates for drought tolerance improvement of strawberry.</description><identifier>ISSN: 1471-2229</identifier><identifier>EISSN: 1471-2229</identifier><identifier>DOI: 10.1186/s12870-021-03095-2</identifier><identifier>PMID: 34174836</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>Abiotic factors ; Agricultural research ; Chromosomes ; Conserved Sequence ; Dehydration ; DREB ; Drought resistance ; Drought stress ; Duplication ; Expression ; Food crops ; Fragaria - genetics ; Fragaria - metabolism ; Fragaria - physiology ; Fragaria vesca ; Gene expression ; Gene Expression Regulation, Plant - genetics ; Gene Expression Regulation, Plant - physiology ; Genes ; Genes, Plant - genetics ; Genes, Plant - physiology ; Genetic aspects ; Genome-Wide Association Study ; Genomes ; Hardiness ; Identification and classification ; Leaves ; Localization ; Pattern analysis ; Phylogenetics ; Phylogeny ; Physiological aspects ; Plant Proteins - genetics ; Plant Proteins - physiology ; Plants ; Proteins ; Real-Time Polymerase Chain Reaction ; Strawberries ; Structural characteristics ; Subgroups ; Synteny ; Transcription factors ; Transcription Factors - genetics ; Transcription Factors - physiology ; Transcriptome ; Transcriptomes ; Trees</subject><ispartof>BMC plant biology, 2021-06, Vol.21 (1), p.295-14, Article 295</ispartof><rights>COPYRIGHT 2021 BioMed Central Ltd.</rights><rights>2021. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>The Author(s) 2021</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c597t-18d1d91ec1388c33b09e476ed81923b8ee43f6ece2094335cc050407df242a883</citedby><cites>FETCH-LOGICAL-c597t-18d1d91ec1388c33b09e476ed81923b8ee43f6ece2094335cc050407df242a883</cites><orcidid>0000-0002-4575-3431</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8236174/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/2553224119?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,25752,27923,27924,37011,37012,44589,53790,53792</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34174836$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Dong, Chao</creatorcontrib><creatorcontrib>Xi, Yue</creatorcontrib><creatorcontrib>Chen, Xinlu</creatorcontrib><creatorcontrib>Cheng, Zong-Ming</creatorcontrib><title>Genome-wide identification of AP2/EREBP in Fragaria vesca and expression pattern analysis of the FvDREB subfamily under drought stress</title><title>BMC plant biology</title><addtitle>BMC Plant Biol</addtitle><description>Drought is a common phenomenon worldwide. It is also one of the main abiotic factors that affect the growth and quality of strawberry. The dehydration-responsive element binding protein (DREB) members that belong to the APETALA2/ethylene-responsive element binding protein (AP2/EREBP) superfamily are unique transcription factors in plants that play important roles in the abiotic stress response.
Here, a total of 119 AP2/EREBP genes were identified in Fragaria vesca, and the AP2/EREBP superfamily was divided into AP2, RAV, ERF, DREB, and soloist subfamilies, containing 18, 7, 61, 32, and one member(s), respectively. The DREB subfamily was further divided into six subgroups (A-1 to A-6) based on phylogenetic analysis. Gene structure, conserved motifs, chromosomal location, and synteny analysis were conducted to comprehensively investigate the characteristics of FvDREBs. Furthermore, transcriptome analysis revealed distinctive expression patterns among the FvDREB genes in strawberry plants exposed to drought stress. The expression of FvDREB6 of the A-2 subgroup was down-regulated in old leaves and up-regulated in young leaves in response to drought. Furthermore, qRT-PCR analysis found that FvDREB8 from the A-2 subgroup had the highest expression level under drought stress. Together, analyses with the expression pattern, phylogenetic relationship, motif, and promoter suggest that FvDREB18 may play a critical role in the regulation of FvDREB1 and FvDREB2 expression.
Our findings provide new insights into the characteristics and potential functions of FvDREBs. These FvDREB genes should be further studied as they appear to be excellent candidates for drought tolerance improvement of strawberry.</description><subject>Abiotic factors</subject><subject>Agricultural research</subject><subject>Chromosomes</subject><subject>Conserved Sequence</subject><subject>Dehydration</subject><subject>DREB</subject><subject>Drought resistance</subject><subject>Drought stress</subject><subject>Duplication</subject><subject>Expression</subject><subject>Food crops</subject><subject>Fragaria - genetics</subject><subject>Fragaria - metabolism</subject><subject>Fragaria - physiology</subject><subject>Fragaria vesca</subject><subject>Gene expression</subject><subject>Gene Expression Regulation, Plant - genetics</subject><subject>Gene Expression Regulation, Plant - physiology</subject><subject>Genes</subject><subject>Genes, Plant - genetics</subject><subject>Genes, Plant - physiology</subject><subject>Genetic aspects</subject><subject>Genome-Wide Association Study</subject><subject>Genomes</subject><subject>Hardiness</subject><subject>Identification and classification</subject><subject>Leaves</subject><subject>Localization</subject><subject>Pattern analysis</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Physiological aspects</subject><subject>Plant Proteins - genetics</subject><subject>Plant Proteins - physiology</subject><subject>Plants</subject><subject>Proteins</subject><subject>Real-Time Polymerase Chain Reaction</subject><subject>Strawberries</subject><subject>Structural characteristics</subject><subject>Subgroups</subject><subject>Synteny</subject><subject>Transcription factors</subject><subject>Transcription Factors - genetics</subject><subject>Transcription Factors - physiology</subject><subject>Transcriptome</subject><subject>Transcriptomes</subject><subject>Trees</subject><issn>1471-2229</issn><issn>1471-2229</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><sourceid>DOA</sourceid><recordid>eNptkl1v0zAUhiMEYmPwB7hAlriBi2z-SmLfIJXRjkqTmAZcW65zknpK4mI7Zf0D_G6cdYwVoShKdPKcJ_KrN8teE3xKiCjPAqGiwjmmJMcMyyKnT7JjwiuSU0rl00fvR9mLEG4wJpXg8nl2xDipuGDlcfbrAgbXQ_7T1oDSPUTbWKOjdQNyDZpd0bP59fzjFbIDWnjdam812kIwGumhRnC78RDCRG90jOCHNNbdLtgwrcc1oMX2UxKgMK4a3dtuh8ahBo9q78Z2HVGIk-Bl9qzRXYBX98-T7Pti_u38c3755WJ5PrvMTSGrmBNRk1oSMIQJYRhbYQm8KqEWRFK2EgCcNSUYoFhyxgpjcIE5ruqGcqqFYCfZcu-tnb5RG2977XfKaavuBs63SvtoTQcKdFkywYkwouCGCF0xQbAoGG4kAK6T68PetRlXPdQmZed1dyA9_DLYtWrdVgnKypR_Ery7F3j3Y4QQVW-Dga7TA7gxKFrwQkpKGE3o23_QGzf6lPREFYxSToj8S7U6HcAOjUv_NZNUzcqK0rLikiXq9D9UumrorXEDNDbNDxbeHywkJsJtbPUYglp-vT5k6Z413oXgoXnIg2A1tVbtW6tSa9Vda9V0ujePk3xY-VNT9htlxOVK</recordid><startdate>20210626</startdate><enddate>20210626</enddate><creator>Dong, Chao</creator><creator>Xi, Yue</creator><creator>Chen, Xinlu</creator><creator>Cheng, Zong-Ming</creator><general>BioMed Central Ltd</general><general>BioMed Central</general><general>BMC</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>ISR</scope><scope>3V.</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-4575-3431</orcidid></search><sort><creationdate>20210626</creationdate><title>Genome-wide identification of AP2/EREBP in Fragaria vesca and expression pattern analysis of the FvDREB subfamily under drought stress</title><author>Dong, Chao ; Xi, Yue ; Chen, Xinlu ; Cheng, Zong-Ming</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c597t-18d1d91ec1388c33b09e476ed81923b8ee43f6ece2094335cc050407df242a883</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Abiotic factors</topic><topic>Agricultural research</topic><topic>Chromosomes</topic><topic>Conserved Sequence</topic><topic>Dehydration</topic><topic>DREB</topic><topic>Drought resistance</topic><topic>Drought stress</topic><topic>Duplication</topic><topic>Expression</topic><topic>Food crops</topic><topic>Fragaria - genetics</topic><topic>Fragaria - metabolism</topic><topic>Fragaria - physiology</topic><topic>Fragaria vesca</topic><topic>Gene expression</topic><topic>Gene Expression Regulation, Plant - genetics</topic><topic>Gene Expression Regulation, Plant - physiology</topic><topic>Genes</topic><topic>Genes, Plant - genetics</topic><topic>Genes, Plant - physiology</topic><topic>Genetic aspects</topic><topic>Genome-Wide Association Study</topic><topic>Genomes</topic><topic>Hardiness</topic><topic>Identification and classification</topic><topic>Leaves</topic><topic>Localization</topic><topic>Pattern analysis</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Physiological aspects</topic><topic>Plant Proteins - genetics</topic><topic>Plant Proteins - physiology</topic><topic>Plants</topic><topic>Proteins</topic><topic>Real-Time Polymerase Chain Reaction</topic><topic>Strawberries</topic><topic>Structural characteristics</topic><topic>Subgroups</topic><topic>Synteny</topic><topic>Transcription factors</topic><topic>Transcription Factors - genetics</topic><topic>Transcription Factors - physiology</topic><topic>Transcriptome</topic><topic>Transcriptomes</topic><topic>Trees</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Dong, Chao</creatorcontrib><creatorcontrib>Xi, Yue</creatorcontrib><creatorcontrib>Chen, Xinlu</creatorcontrib><creatorcontrib>Cheng, Zong-Ming</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection (Proquest)</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>AUTh Library subscriptions: ProQuest Central</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Biological Sciences</collection><collection>Agriculture Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>PML(ProQuest Medical Library)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Publicly Available Content (ProQuest)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>BMC plant biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Dong, Chao</au><au>Xi, Yue</au><au>Chen, Xinlu</au><au>Cheng, Zong-Ming</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome-wide identification of AP2/EREBP in Fragaria vesca and expression pattern analysis of the FvDREB subfamily under drought stress</atitle><jtitle>BMC plant biology</jtitle><addtitle>BMC Plant Biol</addtitle><date>2021-06-26</date><risdate>2021</risdate><volume>21</volume><issue>1</issue><spage>295</spage><epage>14</epage><pages>295-14</pages><artnum>295</artnum><issn>1471-2229</issn><eissn>1471-2229</eissn><abstract>Drought is a common phenomenon worldwide. It is also one of the main abiotic factors that affect the growth and quality of strawberry. The dehydration-responsive element binding protein (DREB) members that belong to the APETALA2/ethylene-responsive element binding protein (AP2/EREBP) superfamily are unique transcription factors in plants that play important roles in the abiotic stress response.
Here, a total of 119 AP2/EREBP genes were identified in Fragaria vesca, and the AP2/EREBP superfamily was divided into AP2, RAV, ERF, DREB, and soloist subfamilies, containing 18, 7, 61, 32, and one member(s), respectively. The DREB subfamily was further divided into six subgroups (A-1 to A-6) based on phylogenetic analysis. Gene structure, conserved motifs, chromosomal location, and synteny analysis were conducted to comprehensively investigate the characteristics of FvDREBs. Furthermore, transcriptome analysis revealed distinctive expression patterns among the FvDREB genes in strawberry plants exposed to drought stress. The expression of FvDREB6 of the A-2 subgroup was down-regulated in old leaves and up-regulated in young leaves in response to drought. Furthermore, qRT-PCR analysis found that FvDREB8 from the A-2 subgroup had the highest expression level under drought stress. Together, analyses with the expression pattern, phylogenetic relationship, motif, and promoter suggest that FvDREB18 may play a critical role in the regulation of FvDREB1 and FvDREB2 expression.
Our findings provide new insights into the characteristics and potential functions of FvDREBs. These FvDREB genes should be further studied as they appear to be excellent candidates for drought tolerance improvement of strawberry.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>34174836</pmid><doi>10.1186/s12870-021-03095-2</doi><tpages>14</tpages><orcidid>https://orcid.org/0000-0002-4575-3431</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Abiotic factors Agricultural research Chromosomes Conserved Sequence Dehydration DREB Drought resistance Drought stress Duplication Expression Food crops Fragaria - genetics Fragaria - metabolism Fragaria - physiology Fragaria vesca Gene expression Gene Expression Regulation, Plant - genetics Gene Expression Regulation, Plant - physiology Genes Genes, Plant - genetics Genes, Plant - physiology Genetic aspects Genome-Wide Association Study Genomes Hardiness Identification and classification Leaves Localization Pattern analysis Phylogenetics Phylogeny Physiological aspects Plant Proteins - genetics Plant Proteins - physiology Plants Proteins Real-Time Polymerase Chain Reaction Strawberries Structural characteristics Subgroups Synteny Transcription factors Transcription Factors - genetics Transcription Factors - physiology Transcriptome Transcriptomes Trees |
| title | Genome-wide identification of AP2/EREBP in Fragaria vesca and expression pattern analysis of the FvDREB subfamily under drought stress |
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