Genome-wide investigation and expression analysis of AP2-ERF gene family in salt tolerant common bean
Identifieur interne : 002018 ( Ncbi/Merge ); précédent : 002017; suivant : 002019Genome-wide investigation and expression analysis of AP2-ERF gene family in salt tolerant common bean
Auteurs : Musa Kavas [Turquie] ; Aslihan Kizildogan [Turquie] ; Gökhan Gökdemir [Turquie] ; Mehmet Cengiz Baloglu [Turquie]Source :
- EXCLI Journal [ 1611-2156 ] ; 2015.
Abstract
Apetala2-ethylene-responsive element binding factor (AP2-ERF) superfamily with common AP2-DNA binding domain have developmentally and physiologically important roles in plants. Since common bean genome project has been completed recently, it is possible to identify all of the
Url:
DOI: 10.17179/excli2015-600
PubMed: 27152109
PubMed Central: 4849109
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000284
- to stream Pmc, to step Curation: 000283
- to stream Pmc, to step Checkpoint: 000481
Links to Exploration step
PMC:4849109Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genome-wide investigation and expression analysis of AP2-ERF gene family in salt tolerant common bean</title><author><name sortKey="Kavas, Musa" sort="Kavas, Musa" uniqKey="Kavas M" first="Musa" last="Kavas">Musa Kavas</name><affiliation wicri:level="1"><nlm:aff id="A1">Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey</nlm:aff><country xml:lang="fr">Turquie</country><wicri:regionArea>Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun</wicri:regionArea><wicri:noRegion>Samsun</wicri:noRegion></affiliation></author><author><name sortKey="Kizildogan, Aslihan" sort="Kizildogan, Aslihan" uniqKey="Kizildogan A" first="Aslihan" last="Kizildogan">Aslihan Kizildogan</name><affiliation wicri:level="1"><nlm:aff id="A1">Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey</nlm:aff><country xml:lang="fr">Turquie</country><wicri:regionArea>Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun</wicri:regionArea><wicri:noRegion>Samsun</wicri:noRegion></affiliation></author><author><name sortKey="Gokdemir, Gokhan" sort="Gokdemir, Gokhan" uniqKey="Gokdemir G" first="Gökhan" last="Gökdemir">Gökhan Gökdemir</name><affiliation wicri:level="1"><nlm:aff id="A1">Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey</nlm:aff><country xml:lang="fr">Turquie</country><wicri:regionArea>Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun</wicri:regionArea><wicri:noRegion>Samsun</wicri:noRegion></affiliation></author><author><name sortKey="Baloglu, Mehmet Cengiz" sort="Baloglu, Mehmet Cengiz" uniqKey="Baloglu M" first="Mehmet Cengiz" last="Baloglu">Mehmet Cengiz Baloglu</name><affiliation wicri:level="1"><nlm:aff id="A2">Kastamonu University, Faculty of Engineering and Architecture, Department of Genetics and Bioengineering, Kastamonu, Turkey</nlm:aff><country xml:lang="fr">Turquie</country><wicri:regionArea>Kastamonu University, Faculty of Engineering and Architecture, Department of Genetics and Bioengineering, Kastamonu</wicri:regionArea><wicri:noRegion>Kastamonu</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27152109</idno><idno type="pmc">4849109</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4849109</idno><idno type="RBID">PMC:4849109</idno><idno type="doi">10.17179/excli2015-600</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000284</idno><idno type="wicri:Area/Pmc/Curation">000283</idno><idno type="wicri:Area/Pmc/Checkpoint">000481</idno><idno type="wicri:Area/Ncbi/Merge">002018</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Genome-wide investigation and expression analysis of AP2-ERF gene family in salt tolerant common bean</title><author><name sortKey="Kavas, Musa" sort="Kavas, Musa" uniqKey="Kavas M" first="Musa" last="Kavas">Musa Kavas</name><affiliation wicri:level="1"><nlm:aff id="A1">Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey</nlm:aff><country xml:lang="fr">Turquie</country><wicri:regionArea>Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun</wicri:regionArea><wicri:noRegion>Samsun</wicri:noRegion></affiliation></author><author><name sortKey="Kizildogan, Aslihan" sort="Kizildogan, Aslihan" uniqKey="Kizildogan A" first="Aslihan" last="Kizildogan">Aslihan Kizildogan</name><affiliation wicri:level="1"><nlm:aff id="A1">Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey</nlm:aff><country xml:lang="fr">Turquie</country><wicri:regionArea>Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun</wicri:regionArea><wicri:noRegion>Samsun</wicri:noRegion></affiliation></author><author><name sortKey="Gokdemir, Gokhan" sort="Gokdemir, Gokhan" uniqKey="Gokdemir G" first="Gökhan" last="Gökdemir">Gökhan Gökdemir</name><affiliation wicri:level="1"><nlm:aff id="A1">Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey</nlm:aff><country xml:lang="fr">Turquie</country><wicri:regionArea>Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun</wicri:regionArea><wicri:noRegion>Samsun</wicri:noRegion></affiliation></author><author><name sortKey="Baloglu, Mehmet Cengiz" sort="Baloglu, Mehmet Cengiz" uniqKey="Baloglu M" first="Mehmet Cengiz" last="Baloglu">Mehmet Cengiz Baloglu</name><affiliation wicri:level="1"><nlm:aff id="A2">Kastamonu University, Faculty of Engineering and Architecture, Department of Genetics and Bioengineering, Kastamonu, Turkey</nlm:aff><country xml:lang="fr">Turquie</country><wicri:regionArea>Kastamonu University, Faculty of Engineering and Architecture, Department of Genetics and Bioengineering, Kastamonu</wicri:regionArea><wicri:noRegion>Kastamonu</wicri:noRegion></affiliation></author></analytic><series><title level="j">EXCLI Journal</title><idno type="eISSN">1611-2156</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Apetala2-ethylene-responsive element binding factor (AP2-ERF) superfamily with common AP2-DNA binding domain have developmentally and physiologically important roles in plants. Since common bean genome project has been completed recently, it is possible to identify all of the <italic>AP2-ERF</italic> genes in the common bean genome. In this study, a comprehensive genome-wide in silico analysis identified 180 AP2-ERF superfamily genes in common bean (<italic>Phaseolus vulgaris</italic>). Based on the amino acid alignment and phylogenetic analyses, superfamily members were classified into four subfamilies: DREB (54), ERF (95), AP2 (27) and RAV (3), as well as one soloist. The physical and chemical characteristics of amino acids, interaction between AP2-ERF proteins, cis elements of promoter region of <italic>AP2-ERF</italic> genes and phylogenetic trees were predicted and analyzed. Additionally, expression levels of <italic>AP2-ERF</italic> genes were evaluated by in silico and qRT-PCR analyses. In silico micro-RNA target transcript analyses identified nearly all <italic>PvAP2-ERF</italic> genes as targets of by 44 different plant species' miRNAs were identified in this study. The most abundant target genes were <italic>PvAP2/ERF-20-25-62-78-113-173</italic>. miR156, miR172 and miR838 were the most important miRNAs found in targeting and BLAST analyses. Interactome analysis revealed that the transcription factor <italic>PvAP2-ERF78</italic>, an ortholog of Arabidopsis <italic>At2G28550</italic>, was potentially interacted with at least 15 proteins, indicating that it was very important in transcriptional regulation. Here we present the first study to identify and characterize the AP2-ERF transcription factors in common bean using whole-genome analysis, and the findings may serve as a references for future functional research on the transcription factors in common bean.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Baloglu, Mc" uniqKey="Baloglu M">MC Baloglu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Baloglu, Mc" uniqKey="Baloglu M">MC Baloglu</name></author><author><name sortKey="Eldem, V" uniqKey="Eldem V">V Eldem</name></author><author><name sortKey="Hajyzadeh, M" uniqKey="Hajyzadeh M">M Hajyzadeh</name></author><author><name sortKey="Unver, T" uniqKey="Unver T">T Unver</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Berman, Hm" uniqKey="Berman H">HM Berman</name></author><author><name sortKey="Westbrook, J" uniqKey="Westbrook J">J Westbrook</name></author><author><name sortKey="Feng, Z" uniqKey="Feng Z">Z Feng</name></author><author><name sortKey="Gilliland, G" uniqKey="Gilliland G">G Gilliland</name></author><author><name sortKey="Bhat, Tn" uniqKey="Bhat T">TN Bhat</name></author><author><name sortKey="Weissig, H" uniqKey="Weissig H">H Weissig</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Borges, A" uniqKey="Borges A">A Borges</name></author><author><name sortKey="Tsai, Sm" uniqKey="Tsai S">SM Tsai</name></author><author><name sortKey="Caldas, Dgg" uniqKey="Caldas D">DGG Caldas</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bouaziz, D" uniqKey="Bouaziz D">D Bouaziz</name></author><author><name sortKey="Charfeddine, M" uniqKey="Charfeddine M">M Charfeddine</name></author><author><name sortKey="Jbir, R" uniqKey="Jbir R">R Jbir</name></author><author><name sortKey="Saidi, M" uniqKey="Saidi M">M Saidi</name></author><author><name sortKey="Pirrello, J" uniqKey="Pirrello J">J Pirrello</name></author><author><name sortKey="Charfeddine, S" uniqKey="Charfeddine S">S Charfeddine</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Broughton, Wj" uniqKey="Broughton W">WJ Broughton</name></author><author><name sortKey="Hernandez, G" uniqKey="Hernandez G">G Hernandez</name></author><author><name sortKey="Blair, M" uniqKey="Blair M">M Blair</name></author><author><name sortKey="Beebe, S" uniqKey="Beebe S">S Beebe</name></author><author><name sortKey="Gepts, P" uniqKey="Gepts P">P Gepts</name></author><author><name sortKey="Vanderleyden, J" uniqKey="Vanderleyden J">J Vanderleyden</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cao, Pb" uniqKey="Cao P">PB Cao</name></author><author><name sortKey="Azar, S" uniqKey="Azar S">S Azar</name></author><author><name sortKey="Sanclemente, H" uniqKey="Sanclemente H">H SanClemente</name></author><author><name sortKey="Mounet, F" uniqKey="Mounet F">F Mounet</name></author><author><name sortKey="Dunand, C" uniqKey="Dunand C">C Dunand</name></author><author><name sortKey="Marque, G" uniqKey="Marque G">G Marque</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Caraux, G" uniqKey="Caraux G">G Caraux</name></author><author><name sortKey="Pinloche, S" uniqKey="Pinloche S">S Pinloche</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Charfeddine, M" uniqKey="Charfeddine M">M Charfeddine</name></author><author><name sortKey="Saidi, M" uniqKey="Saidi M">M Saïdi</name></author><author><name sortKey="Charfeddine, S" uniqKey="Charfeddine S">S Charfeddine</name></author><author><name sortKey="Hammami, A" uniqKey="Hammami A">A Hammami</name></author><author><name sortKey="Gargouri Bouzid, R" uniqKey="Gargouri Bouzid R">R Gargouri Bouzid</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chinnusamy, V" uniqKey="Chinnusamy V">V Chinnusamy</name></author><author><name sortKey="Jagendorf, A" uniqKey="Jagendorf A">A Jagendorf</name></author><author><name sortKey="Zhu, Jk" uniqKey="Zhu J">JK Zhu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Conesa, A" uniqKey="Conesa A">A Conesa</name></author><author><name sortKey="Gotz, S" uniqKey="Gotz S">S Götz</name></author><author><name sortKey="Garcia G Mez, Jm" uniqKey="Garcia G Mez J">JM García-Gómez</name></author><author><name sortKey="Terol, J" uniqKey="Terol J">J Terol</name></author><author><name sortKey="Tal N, M" uniqKey="Tal N M">M Talón</name></author><author><name sortKey="Robles, M" uniqKey="Robles M">M Robles</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Contreras Cubas, C" uniqKey="Contreras Cubas C">C Contreras-Cubas</name></author><author><name sortKey="Rabanal, F" uniqKey="Rabanal F">F Rabanal</name></author><author><name sortKey="Arenas Huertero, C" uniqKey="Arenas Huertero C">C Arenas-Huertero</name></author><author><name sortKey="Ortiz, M" uniqKey="Ortiz M">M Ortiz</name></author><author><name sortKey="Covarrubias, A" uniqKey="Covarrubias A">A Covarrubias</name></author><author><name sortKey="Reyes, J" uniqKey="Reyes J">J Reyes</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dasgan, Hy" uniqKey="Dasgan H">HY Dasgan</name></author><author><name sortKey="Koc, S" uniqKey="Koc S">S Koc</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Du, H" uniqKey="Du H">H Du</name></author><author><name sortKey="Huang, M" uniqKey="Huang M">M Huang</name></author><author><name sortKey="Zhang, Z" uniqKey="Zhang Z">Z Zhang</name></author><author><name sortKey="Cheng, S" uniqKey="Cheng S">S Cheng</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Eldem, V" uniqKey="Eldem V">V Eldem</name></author><author><name sortKey="Okay, S" uniqKey="Okay S">S Okay</name></author><author><name sortKey="Unver, T" uniqKey="Unver T">T Unver</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fang, Y" uniqKey="Fang Y">Y Fang</name></author><author><name sortKey="You, J" uniqKey="You J">J You</name></author><author><name sortKey="Xie, K" uniqKey="Xie K">K Xie</name></author><author><name sortKey="Xie, W" uniqKey="Xie W">W Xie</name></author><author><name sortKey="Xiong, L" uniqKey="Xiong L">L Xiong</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Formey, D" uniqKey="Formey D">D Formey</name></author><author><name sortKey="Iniguez, L" uniqKey="Iniguez L">L Iniguez</name></author><author><name sortKey="Pelaez, P" uniqKey="Pelaez P">P Pelaez</name></author><author><name sortKey="Li, Y F" uniqKey="Li Y">Y-F Li</name></author><author><name sortKey="Sunkar, R" uniqKey="Sunkar R">R Sunkar</name></author><author><name sortKey="Sanchez, F" uniqKey="Sanchez F">F Sanchez</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Girardi, Cl" uniqKey="Girardi C">CL Girardi</name></author><author><name sortKey="Rombaldi, Cv" uniqKey="Rombaldi C">CV Rombaldi</name></author><author><name sortKey="Dal Cero, J" uniqKey="Dal Cero J">J Dal Cero</name></author><author><name sortKey="Nobile, Pm" uniqKey="Nobile P">PM Nobile</name></author><author><name sortKey="Laurens, F" uniqKey="Laurens F">F Laurens</name></author><author><name sortKey="Bouzayen, M" uniqKey="Bouzayen M">M Bouzayen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Goodstein, Dm" uniqKey="Goodstein D">DM Goodstein</name></author><author><name sortKey="Shu, S" uniqKey="Shu S">S Shu</name></author><author><name sortKey="Howson, R" uniqKey="Howson R">R Howson</name></author><author><name sortKey="Neupane, R" uniqKey="Neupane R">R Neupane</name></author><author><name sortKey="Hayes, Rd" uniqKey="Hayes R">RD Hayes</name></author><author><name sortKey="Fazo, J" uniqKey="Fazo J">J Fazo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hiz, Mc" uniqKey="Hiz M">MC Hiz</name></author><author><name sortKey="Canher, B" uniqKey="Canher B">B Canher</name></author><author><name sortKey="Niron, H" uniqKey="Niron H">H Niron</name></author><author><name sortKey="Turet, M" uniqKey="Turet M">M Turet</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hoagland, Dr" uniqKey="Hoagland D">DR Hoagland</name></author><author><name sortKey="Arnon, Di" uniqKey="Arnon D">DI Arnon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hu, B" uniqKey="Hu B">B Hu</name></author><author><name sortKey="Jin, J" uniqKey="Jin J">J Jin</name></author><author><name sortKey="Guo, A Y" uniqKey="Guo A">A-Y Guo</name></author><author><name sortKey="Zhang, H" uniqKey="Zhang H">H Zhang</name></author><author><name sortKey="Luo, J" uniqKey="Luo J">J Luo</name></author><author><name sortKey="Gao, G" uniqKey="Gao G">G Gao</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hu, L" uniqKey="Hu L">L Hu</name></author><author><name sortKey="Liu, S" uniqKey="Liu S">S Liu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ito, Tm" uniqKey="Ito T">TM Ito</name></author><author><name sortKey="Polido, Pb" uniqKey="Polido P">PB Polido</name></author><author><name sortKey="Rampim, Mc" uniqKey="Rampim M">MC Rampim</name></author><author><name sortKey="Kaschuk, G" uniqKey="Kaschuk G">G Kaschuk</name></author><author><name sortKey="Souza, Sg" uniqKey="Souza S">SG Souza</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jin, J" uniqKey="Jin J">J Jin</name></author><author><name sortKey="Zhang, H" uniqKey="Zhang H">H Zhang</name></author><author><name sortKey="Kong, L" uniqKey="Kong L">L Kong</name></author><author><name sortKey="Gao, G" uniqKey="Gao G">G Gao</name></author><author><name sortKey="Luo, J" uniqKey="Luo J">J Luo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kalavacharla, V" uniqKey="Kalavacharla V">V Kalavacharla</name></author><author><name sortKey="Liu, Z" uniqKey="Liu Z">Z Liu</name></author><author><name sortKey="Meyers, B" uniqKey="Meyers B">B Meyers</name></author><author><name sortKey="Thimmapuram, J" uniqKey="Thimmapuram J">J Thimmapuram</name></author><author><name sortKey="Melmaiee, K" uniqKey="Melmaiee K">K Melmaiee</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kavas, M" uniqKey="Kavas M">M Kavas</name></author><author><name sortKey="Balo Lu, M" uniqKey="Balo Lu M">M Baloğlu</name></author><author><name sortKey="Atabay, E" uniqKey="Atabay E">E Atabay</name></author><author><name sortKey="Ziplar, U" uniqKey="Ziplar U">U Ziplar</name></author><author><name sortKey="Da Gan, H" uniqKey="Da Gan H">H Daşgan</name></author><author><name sortKey="Unver, T" uniqKey="Unver T">T Ünver</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kelley, La" uniqKey="Kelley L">LA Kelley</name></author><author><name sortKey="Sternberg, Mje" uniqKey="Sternberg M">MJE Sternberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lata, C" uniqKey="Lata C">C Lata</name></author><author><name sortKey="Mishra, Ak" uniqKey="Mishra A">AK Mishra</name></author><author><name sortKey="Muthamilarasan, M" uniqKey="Muthamilarasan M">M Muthamilarasan</name></author><author><name sortKey="Bonthala, Vs" uniqKey="Bonthala V">VS Bonthala</name></author><author><name sortKey="Khan, Y" uniqKey="Khan Y">Y Khan</name></author><author><name sortKey="Prasad, M" uniqKey="Prasad M">M Prasad</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Le, Dt" uniqKey="Le D">DT Le</name></author><author><name sortKey="Nishiyama, R" uniqKey="Nishiyama R">R Nishiyama</name></author><author><name sortKey="Watanabe, Y" uniqKey="Watanabe Y">Y Watanabe</name></author><author><name sortKey="Vankova, R" uniqKey="Vankova R">R Vankova</name></author><author><name sortKey="Tanaka, M" uniqKey="Tanaka M">M Tanaka</name></author><author><name sortKey="Seki, M" uniqKey="Seki M">M Seki</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Letunic, I" uniqKey="Letunic I">I Letunic</name></author><author><name sortKey="Bork, P" uniqKey="Bork P">P Bork</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, M Y" uniqKey="Li M">M-Y Li</name></author><author><name sortKey="Xu, Z S" uniqKey="Xu Z">Z-S Xu</name></author><author><name sortKey="Huang, Y" uniqKey="Huang Y">Y Huang</name></author><author><name sortKey="Tian, C" uniqKey="Tian C">C Tian</name></author><author><name sortKey="Wang, F" uniqKey="Wang F">F Wang</name></author><author><name sortKey="Xiong, A S" uniqKey="Xiong A">A-S Xiong</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Licausi, F" uniqKey="Licausi F">F Licausi</name></author><author><name sortKey="Giorgi, Fm" uniqKey="Giorgi F">FM Giorgi</name></author><author><name sortKey="Zenoni, S" uniqKey="Zenoni S">S Zenoni</name></author><author><name sortKey="Osti, F" uniqKey="Osti F">F Osti</name></author><author><name sortKey="Pezzotti, M" uniqKey="Pezzotti M">M Pezzotti</name></author><author><name sortKey="Perata, P" uniqKey="Perata P">P Perata</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Liu, Z" uniqKey="Liu Z">Z Liu</name></author><author><name sortKey="Crampton, M" uniqKey="Crampton M">M Crampton</name></author><author><name sortKey="Todd, A" uniqKey="Todd A">A Todd</name></author><author><name sortKey="Kalavacharla, V" uniqKey="Kalavacharla V">V Kalavacharla</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Liu, Z" uniqKey="Liu Z">Z Liu</name></author><author><name sortKey="Kong, L" uniqKey="Kong L">L Kong</name></author><author><name sortKey="Zhang, M" uniqKey="Zhang M">M Zhang</name></author><author><name sortKey="Lv, Y" uniqKey="Lv Y">Y Lv</name></author><author><name sortKey="Liu, Y" uniqKey="Liu Y">Y Liu</name></author><author><name sortKey="Zou, M" uniqKey="Zou M">M Zou</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Livak, Kj" uniqKey="Livak K">KJ Livak</name></author><author><name sortKey="Schmittgen, Td" uniqKey="Schmittgen T">TD Schmittgen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ma, Y" uniqKey="Ma Y">Y Ma</name></author><author><name sortKey="Zhang, F" uniqKey="Zhang F">F Zhang</name></author><author><name sortKey="Bade, R" uniqKey="Bade R">R Bade</name></author><author><name sortKey="Daxibater, A" uniqKey="Daxibater A">A Daxibater</name></author><author><name sortKey="Men, Z" uniqKey="Men Z">Z Men</name></author><author><name sortKey="Hasi, A" uniqKey="Hasi A">A Hasi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Massa, An" uniqKey="Massa A">AN Massa</name></author><author><name sortKey="Childs, Kl" uniqKey="Childs K">KL Childs</name></author><author><name sortKey="Lin, Hn" uniqKey="Lin H">HN Lin</name></author><author><name sortKey="Bryan, Gj" uniqKey="Bryan G">GJ Bryan</name></author><author><name sortKey="Giuliano, G" uniqKey="Giuliano G">G Giuliano</name></author><author><name sortKey="Buell, Cr" uniqKey="Buell C">CR Buell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mizoi, J" uniqKey="Mizoi J">J Mizoi</name></author><author><name sortKey="Shinozaki, K" uniqKey="Shinozaki K">K Shinozaki</name></author><author><name sortKey="Yamaguchi Shinozaki, K" uniqKey="Yamaguchi Shinozaki K">K Yamaguchi-Shinozaki</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mortazavi, A" uniqKey="Mortazavi A">A Mortazavi</name></author><author><name sortKey="Williams, Ba" uniqKey="Williams B">BA Williams</name></author><author><name sortKey="Mccue, K" uniqKey="Mccue K">K McCue</name></author><author><name sortKey="Schaeffer, L" uniqKey="Schaeffer L">L Schaeffer</name></author><author><name sortKey="Wold, B" uniqKey="Wold B">B Wold</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mousavi, A" uniqKey="Mousavi A">A Mousavi</name></author><author><name sortKey="Hotta, Y" uniqKey="Hotta Y">Y Hotta</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Munns, R" uniqKey="Munns R">R Munns</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nakano, T" uniqKey="Nakano T">T Nakano</name></author><author><name sortKey="Suzuki, K" uniqKey="Suzuki K">K Suzuki</name></author><author><name sortKey="Fujimura, T" uniqKey="Fujimura T">T Fujimura</name></author><author><name sortKey="Shinshi, H" uniqKey="Shinshi H">H Shinshi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nova Franco, B" uniqKey="Nova Franco B">B Nova-Franco</name></author><author><name sortKey="I Iguez, Lp" uniqKey="I Iguez L">LP Íñiguez</name></author><author><name sortKey="Valdes L Pez, O" uniqKey="Valdes L Pez O">O Valdés-López</name></author><author><name sortKey="Alvarado Affantranger, X" uniqKey="Alvarado Affantranger X">X Alvarado-Affantranger</name></author><author><name sortKey="Leija, A" uniqKey="Leija A">A Leija</name></author><author><name sortKey="Fuentes, Si" uniqKey="Fuentes S">SI Fuentes</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Parida, Ak" uniqKey="Parida A">AK Parida</name></author><author><name sortKey="Das, Ab" uniqKey="Das A">AB Das</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Qin, F" uniqKey="Qin F">F Qin</name></author><author><name sortKey="Shinozaki, K" uniqKey="Shinozaki K">K Shinozaki</name></author><author><name sortKey="Yamaguchi Shinozaki, K" uniqKey="Yamaguchi Shinozaki K">K Yamaguchi-Shinozaki</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rao, G" uniqKey="Rao G">G Rao</name></author><author><name sortKey="Sui, J" uniqKey="Sui J">J Sui</name></author><author><name sortKey="Zeng, Y" uniqKey="Zeng Y">Y Zeng</name></author><author><name sortKey="He, C" uniqKey="He C">C He</name></author><author><name sortKey="Zhang, J" uniqKey="Zhang J">J Zhang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Riano Pach N, Dm" uniqKey="Riano Pach N D">DM Riano-Pachón</name></author><author><name sortKey="Ruzicic, S" uniqKey="Ruzicic S">S Ruzicic</name></author><author><name sortKey="Dreyer, I" uniqKey="Dreyer I">I Dreyer</name></author><author><name sortKey="Mueller Roeber, B" uniqKey="Mueller Roeber B">B Mueller-Roeber</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sakuma, Y" uniqKey="Sakuma Y">Y Sakuma</name></author><author><name sortKey="Liu, Q" uniqKey="Liu Q">Q Liu</name></author><author><name sortKey="Dubouzet, Jg" uniqKey="Dubouzet J">JG Dubouzet</name></author><author><name sortKey="Abe, H" uniqKey="Abe H">H Abe</name></author><author><name sortKey="Shinozaki, K" uniqKey="Shinozaki K">K Shinozaki</name></author><author><name sortKey="Yamaguchi Shinozaki, K" uniqKey="Yamaguchi Shinozaki K">K Yamaguchi-Shinozaki</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schmutz, J" uniqKey="Schmutz J">J Schmutz</name></author><author><name sortKey="Mcclean, Pe" uniqKey="Mcclean P">PE McClean</name></author><author><name sortKey="Mamidi, S" uniqKey="Mamidi S">S Mamidi</name></author><author><name sortKey="Wu, Ga" uniqKey="Wu G">GA Wu</name></author><author><name sortKey="Cannon, Sb" uniqKey="Cannon S">SB Cannon</name></author><author><name sortKey="Grimwood, J" uniqKey="Grimwood J">J Grimwood</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sharma, Mk" uniqKey="Sharma M">MK Sharma</name></author><author><name sortKey="Kumar, R" uniqKey="Kumar R">R Kumar</name></author><author><name sortKey="Solanke, Au" uniqKey="Solanke A">AU Solanke</name></author><author><name sortKey="Sharma, R" uniqKey="Sharma R">R Sharma</name></author><author><name sortKey="Tyagi, Ak" uniqKey="Tyagi A">AK Tyagi</name></author><author><name sortKey="Sharma, Ak" uniqKey="Sharma A">AK Sharma</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shiu, Sh" uniqKey="Shiu S">SH Shiu</name></author><author><name sortKey="Bleecker, Ab" uniqKey="Bleecker A">AB Bleecker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Smialowski, P" uniqKey="Smialowski P">P Smialowski</name></author><author><name sortKey="Doose, G" uniqKey="Doose G">G Doose</name></author><author><name sortKey="Torkler, P" uniqKey="Torkler P">P Torkler</name></author><author><name sortKey="Kaufmann, S" uniqKey="Kaufmann S">S Kaufmann</name></author><author><name sortKey="Frishman, D" uniqKey="Frishman D">D Frishman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Soding, J" uniqKey="Soding J">J Soding</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Song, Xm" uniqKey="Song X">XM Song</name></author><author><name sortKey="Li, Y" uniqKey="Li Y">Y Li</name></author><author><name sortKey="Hou, Xl" uniqKey="Hou X">XL Hou</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tang, Hb" uniqKey="Tang H">HB Tang</name></author><author><name sortKey="Bowers, Je" uniqKey="Bowers J">JE Bowers</name></author><author><name sortKey="Wang, Xy" uniqKey="Wang X">XY Wang</name></author><author><name sortKey="Ming, R" uniqKey="Ming R">R Ming</name></author><author><name sortKey="Alam, M" uniqKey="Alam M">M Alam</name></author><author><name sortKey="Paterson, Ah" uniqKey="Paterson A">AH Paterson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Thamilarasan, Sk" uniqKey="Thamilarasan S">SK Thamilarasan</name></author><author><name sortKey="Park, Ji" uniqKey="Park J">JI Park</name></author><author><name sortKey="Jung, Hj" uniqKey="Jung H">HJ Jung</name></author><author><name sortKey="Nou, Is" uniqKey="Nou I">IS Nou</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, Jz" uniqKey="Wang J">JZ Wang</name></author><author><name sortKey="Zhou, Jx" uniqKey="Zhou J">JX Zhou</name></author><author><name sortKey="Zhang, Bl" uniqKey="Zhang B">BL Zhang</name></author><author><name sortKey="Vanitha, J" uniqKey="Vanitha J">J Vanitha</name></author><author><name sortKey="Ramachandran, S" uniqKey="Ramachandran S">S Ramachandran</name></author><author><name sortKey="Jiang, Sy" uniqKey="Jiang S">SY Jiang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, Yn" uniqKey="Wang Y">YN Wang</name></author><author><name sortKey="Wang, Lx" uniqKey="Wang L">LX Wang</name></author><author><name sortKey="Zou, Ym" uniqKey="Zou Y">YM Zou</name></author><author><name sortKey="Chen, L" uniqKey="Chen L">L Chen</name></author><author><name sortKey="Cai, Zm" uniqKey="Cai Z">ZM Cai</name></author><author><name sortKey="Zhang, Sl" uniqKey="Zhang S">SL Zhang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wessler, Sr" uniqKey="Wessler S">SR Wessler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wu, G" uniqKey="Wu G">G Wu</name></author><author><name sortKey="Park, My" uniqKey="Park M">MY Park</name></author><author><name sortKey="Conway, Sr" uniqKey="Conway S">SR Conway</name></author><author><name sortKey="Wang, J W" uniqKey="Wang J">J-W Wang</name></author><author><name sortKey="Weigel, D" uniqKey="Weigel D">D Weigel</name></author><author><name sortKey="Poethig, Rs" uniqKey="Poethig R">RS Poethig</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wu, Hl" uniqKey="Wu H">HL Wu</name></author><author><name sortKey="Lv, H" uniqKey="Lv H">H Lv</name></author><author><name sortKey="Li, L" uniqKey="Li L">L Li</name></author><author><name sortKey="Liu, J" uniqKey="Liu J">J Liu</name></author><author><name sortKey="Mu, Sh" uniqKey="Mu S">SH Mu</name></author><author><name sortKey="Li, Xp" uniqKey="Li X">XP Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Xu, W" uniqKey="Xu W">W Xu</name></author><author><name sortKey="Li, F" uniqKey="Li F">F Li</name></author><author><name sortKey="Ling, Lz" uniqKey="Ling L">LZ Ling</name></author><author><name sortKey="Liu, Az" uniqKey="Liu A">AZ Liu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yamaguchi Shinozaki, K" uniqKey="Yamaguchi Shinozaki K">K Yamaguchi-Shinozaki</name></author><author><name sortKey="Shinozaki, K" uniqKey="Shinozaki K">K Shinozaki</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yan, Z" uniqKey="Yan Z">Z Yan</name></author><author><name sortKey="Hossein, Ms" uniqKey="Hossein M">MS Hossein</name></author><author><name sortKey="Wang, J" uniqKey="Wang J">J Wang</name></author><author><name sortKey="Valdes Lopez, O" uniqKey="Valdes Lopez O">O Valdes-Lopez</name></author><author><name sortKey="Liang, Y" uniqKey="Liang Y">Y Liang</name></author><author><name sortKey="Libault, M" uniqKey="Libault M">M Libault</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, Y" uniqKey="Zhang Y">Y Zhang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhou, Ml" uniqKey="Zhou M">ML Zhou</name></author><author><name sortKey="Ma, Jt" uniqKey="Ma J">JT Ma</name></author><author><name sortKey="Pang, Jf" uniqKey="Pang J">JF Pang</name></author><author><name sortKey="Zhang, Zl" uniqKey="Zhang Z">ZL Zhang</name></author><author><name sortKey="Tang, Yx" uniqKey="Tang Y">YX Tang</name></author><author><name sortKey="Wu, Ym" uniqKey="Wu Y">YM Wu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhuang, J" uniqKey="Zhuang J">J Zhuang</name></author><author><name sortKey="Cai, B" uniqKey="Cai B">B Cai</name></author><author><name sortKey="Peng, Rh" uniqKey="Peng R">RH Peng</name></author><author><name sortKey="Zhu, B" uniqKey="Zhu B">B Zhu</name></author><author><name sortKey="Jin, Xf" uniqKey="Jin X">XF Jin</name></author><author><name sortKey="Xue, Y" uniqKey="Xue Y">Y Xue</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhuang, J" uniqKey="Zhuang J">J Zhuang</name></author><author><name sortKey="Chen, Jm" uniqKey="Chen J">JM Chen</name></author><author><name sortKey="Yao, Qh" uniqKey="Yao Q">QH Yao</name></author><author><name sortKey="Xiong, F" uniqKey="Xiong F">F Xiong</name></author><author><name sortKey="Sun, Cc" uniqKey="Sun C">CC Sun</name></author><author><name sortKey="Zhou, Xr" uniqKey="Zhou X">XR Zhou</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhuang, J" uniqKey="Zhuang J">J Zhuang</name></author><author><name sortKey="Yao, Qh" uniqKey="Yao Q">QH Yao</name></author><author><name sortKey="Xiong, As" uniqKey="Xiong A">AS Xiong</name></author><author><name sortKey="Zhang, Ja" uniqKey="Zhang J">JA Zhang</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">EXCLI J</journal-id><journal-id journal-id-type="iso-abbrev">EXCLI J</journal-id><journal-id journal-id-type="publisher-id">EXCLI J</journal-id><journal-title-group><journal-title>EXCLI Journal</journal-title></journal-title-group><issn pub-type="epub">1611-2156</issn><publisher><publisher-name>Leibniz Research Centre for Working Environment and Human Factors</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">27152109</article-id><article-id pub-id-type="pmc">4849109</article-id><article-id pub-id-type="publisher-id">2015-600</article-id><article-id pub-id-type="doi">10.17179/excli2015-600</article-id><article-id pub-id-type="publisher-id">Doc1187</article-id><article-categories><subj-group subj-group-type="heading"><subject>Original Article</subject></subj-group></article-categories><title-group><article-title>Genome-wide investigation and expression analysis of AP2-ERF gene family in salt tolerant common bean</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Kavas</surname><given-names>Musa</given-names></name><xref ref-type="corresp" rid="COR1">*</xref><xref ref-type="aff" rid="A1">1</xref></contrib><contrib contrib-type="author"><name><surname>Kizildogan</surname><given-names>Aslihan</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib><contrib contrib-type="author"><name><surname>Gökdemir</surname><given-names>Gökhan</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib><contrib contrib-type="author"><name><surname>Baloglu</surname><given-names>Mehmet Cengiz</given-names></name><xref ref-type="aff" rid="A2">2</xref></contrib></contrib-group><aff id="A1"><label>1</label>Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey</aff><aff id="A2"><label>2</label>Kastamonu University, Faculty of Engineering and Architecture, Department of Genetics and Bioengineering, Kastamonu, Turkey</aff><author-notes><corresp id="COR1">*To whom correspondence should be addressed: Musa Kavas, Ondokuz Mayıs University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey; Tel: +903623121919-1158; Fax: +903624576034, E-mail: <email>musa.kavas@omu.edu.tr</email></corresp></author-notes><pub-date pub-type="epub"><day>27</day><month>11</month><year>2015</year></pub-date><pub-date pub-type="collection"><year>2015</year></pub-date><volume>14</volume><fpage>1187</fpage><lpage>1206</lpage><history><date date-type="received"><day>26</day><month>9</month><year>2015</year></date><date date-type="accepted"><day>01</day><month>11</month><year>2015</year></date></history><permissions><copyright-statement>Copyright © 2015 Kavas et al.</copyright-statement><copyright-year>2015</copyright-year><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>This is an Open Access article distributed under the terms of the Creative Commons Attribution Licence (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>) You are free to copy, distribute and transmit the work, provided the original author and source are credited.</license-p></license></permissions><self-uri xlink:type="simple" xlink:href="http://www.excli.de/vol14/Kavas_27112015_proof.pdf">This article is available from http://www.excli.de/vol14/Kavas_27112015_proof.pdf</self-uri><abstract><p>Apetala2-ethylene-responsive element binding factor (AP2-ERF) superfamily with common AP2-DNA binding domain have developmentally and physiologically important roles in plants. Since common bean genome project has been completed recently, it is possible to identify all of the <italic>AP2-ERF</italic> genes in the common bean genome. In this study, a comprehensive genome-wide in silico analysis identified 180 AP2-ERF superfamily genes in common bean (<italic>Phaseolus vulgaris</italic>). Based on the amino acid alignment and phylogenetic analyses, superfamily members were classified into four subfamilies: DREB (54), ERF (95), AP2 (27) and RAV (3), as well as one soloist. The physical and chemical characteristics of amino acids, interaction between AP2-ERF proteins, cis elements of promoter region of <italic>AP2-ERF</italic> genes and phylogenetic trees were predicted and analyzed. Additionally, expression levels of <italic>AP2-ERF</italic> genes were evaluated by in silico and qRT-PCR analyses. In silico micro-RNA target transcript analyses identified nearly all <italic>PvAP2-ERF</italic> genes as targets of by 44 different plant species' miRNAs were identified in this study. The most abundant target genes were <italic>PvAP2/ERF-20-25-62-78-113-173</italic>. miR156, miR172 and miR838 were the most important miRNAs found in targeting and BLAST analyses. Interactome analysis revealed that the transcription factor <italic>PvAP2-ERF78</italic>, an ortholog of Arabidopsis <italic>At2G28550</italic>, was potentially interacted with at least 15 proteins, indicating that it was very important in transcriptional regulation. Here we present the first study to identify and characterize the AP2-ERF transcription factors in common bean using whole-genome analysis, and the findings may serve as a references for future functional research on the transcription factors in common bean.</p></abstract><kwd-group><kwd>AP2-ERF family</kwd><kwd>miRNA</kwd><kwd>interactome</kwd><kwd>salt resistance</kwd><kwd>transcriptome analyses</kwd></kwd-group></article-meta></front><floats-group><fig id="T1" position="float"><label>Table 1</label><caption><title>Summary of Ap2-ERF superfamily in common bean in compassion with <italic>Cucumis melo, Solanum lypersicon, Glycine max, Arabidopsis thaliana</italic></title></caption><graphic xlink:href="EXCLI-14-1187-t-001"></graphic></fig><fig id="F1" position="float"><label>Figure 1</label><caption><title>Chromosomal distribution of 180 <italic>PvAP2-ERF</italic> genes. The chromosome number is indicated above each chromosome. Numbers on the left site of each chromosome indicate the physical position (in Mb).The graph below represents percentage of <italic>PvAP2-ERF</italic> gene distribution among 11 Phaseolus chromosome and a scaffold.</title></caption><graphic xlink:href="EXCLI-14-1187-g-001"></graphic></fig><fig id="F2" position="float"><label>Figure 2</label><caption><title>Phylogenetic tree of aligned 180 AP2-ERF subfamily proteins constructed using CLC Genomics Workbench via the Neighbor-Joining (NJ) method. The different classes of PvAP2-ERF proteins are highlighted in different colors.</title></caption><graphic xlink:href="EXCLI-14-1187-g-002"></graphic></fig><fig id="F3" position="float"><label>Figure 3</label><caption><title>Predicted 3D structures of three selected PvAP2-ERF proteins namely, PvERF49, PvERF89 and PvERF94, modelled at >90 % confidence level by using Phyre2 server.</title></caption><graphic xlink:href="EXCLI-14-1187-g-003"></graphic></fig><fig id="F4" position="float"><label>Figure 4</label><caption><title>Figure 4: The interaction network of <italic>AP2-ERF</italic> genes in common bean according to the orthologs in Arabidopsis. Ellipse in purple represent common bean genes and rectangle in yellow color <italic>PvAP2-ERFs</italic>.</title></caption><graphic xlink:href="EXCLI-14-1187-g-004"></graphic></fig><fig id="F5" position="float"><label>Figure 5</label><caption><title>Gene ontology (GO) and functional annotation of PvAP2-ERF proteins using Blast2GO. CC (cellular compartment) was represented as yellow bars, MF (molecular function) was indicated as purple bars and BP (biological process) was given as green bars on the graph.</title></caption><graphic xlink:href="EXCLI-14-1187-g-005"></graphic></fig><fig id="F6" position="float"><label>Figure 6</label><caption><title>Representation of Heat map and hierarchical clustering of all <italic>PvAP2-ERF</italic> genes in leaves and roots upon high salinity treatment. The RPKM values retrieved from published RNA-seq data were log2 transformed and the heat map generated using PermutMatrix . CL; control leaf, SL; salt leaf, CR; control root, ST; salt root. Color scale in the dendrogram represents relative expression levels: green represents low level (down regulated of genes), red indicates high level (up-regulated ones) and black represents unchanged gene expression level. The color scales for fold-change values are shown above the dendogram.</title></caption><graphic xlink:href="EXCLI-14-1187-g-006"></graphic></fig><fig id="F7" position="float"><label>Figure 7</label><caption><title>Relative expression levels of nine selected PvAP2-ERF genes in salt stressed leaf and root tissues as compared to the control by qRT-PCR . Relative expression represents log2 expression values. Standard error (SE) was determined from three independent biological replicates.</title></caption><graphic xlink:href="EXCLI-14-1187-g-007"></graphic></fig></floats-group></pmc><affiliations><list><country><li>Turquie</li></country></list><tree><country name="Turquie"><noRegion><name sortKey="Kavas, Musa" sort="Kavas, Musa" uniqKey="Kavas M" first="Musa" last="Kavas">Musa Kavas</name></noRegion><name sortKey="Baloglu, Mehmet Cengiz" sort="Baloglu, Mehmet Cengiz" uniqKey="Baloglu M" first="Mehmet Cengiz" last="Baloglu">Mehmet Cengiz Baloglu</name><name sortKey="Gokdemir, Gokhan" sort="Gokdemir, Gokhan" uniqKey="Gokdemir G" first="Gökhan" last="Gökdemir">Gökhan Gökdemir</name><name sortKey="Kizildogan, Aslihan" sort="Kizildogan, Aslihan" uniqKey="Kizildogan A" first="Aslihan" last="Kizildogan">Aslihan Kizildogan</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Bois/explor/OrangerV1/Data/Ncbi/Merge
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002018 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Ncbi/Merge/biblio.hfd -nk 002018 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/Bois
|area= OrangerV1
|flux= Ncbi
|étape= Merge
|type= RBID
|clé= PMC:4849109
|texte= Genome-wide investigation and expression analysis of AP2-ERF gene family in salt tolerant common bean
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Merge/RBID.i -Sk "pubmed:27152109" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Merge/biblio.hfd \
| NlmPubMed2Wicri -a OrangerV1
| This area was generated with Dilib version V0.6.25. |  |