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<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><nlm:aff id="A1">Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey</nlm:aff></affiliation></author><author><name sortKey="Kizildogan, Aslihan" sort="Kizildogan, Aslihan" uniqKey="Kizildogan A" first="Aslihan" last="Kizildogan">Aslihan Kizildogan</name><affiliation><nlm:aff id="A1">Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey</nlm:aff></affiliation></author><author><name sortKey="Gokdemir, Gokhan" sort="Gokdemir, Gokhan" uniqKey="Gokdemir G" first="Gökhan" last="Gökdemir">Gökhan Gökdemir</name><affiliation><nlm:aff id="A1">Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey</nlm:aff></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><nlm:aff id="A2">Kastamonu University, Faculty of Engineering and Architecture, Department of Genetics and Bioengineering, Kastamonu, Turkey</nlm:aff></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></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><nlm:aff id="A1">Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey</nlm:aff></affiliation></author><author><name sortKey="Kizildogan, Aslihan" sort="Kizildogan, Aslihan" uniqKey="Kizildogan A" first="Aslihan" last="Kizildogan">Aslihan Kizildogan</name><affiliation><nlm:aff id="A1">Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey</nlm:aff></affiliation></author><author><name sortKey="Gokdemir, Gokhan" sort="Gokdemir, Gokhan" uniqKey="Gokdemir G" first="Gökhan" last="Gökdemir">Gökhan Gökdemir</name><affiliation><nlm:aff id="A1">Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey</nlm:aff></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><nlm:aff id="A2">Kastamonu University, Faculty of Engineering and Architecture, Department of Genetics and Bioengineering, Kastamonu, Turkey</nlm:aff></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><body><sec sec-type="intro"><title>Introduction</title><p>Pulse crops are very well known species with their nitrogen fixation capacity via nodulation in symbiosis with rhizobia. Common bean, <italic>Phaseolus vulgaris</italic> L., is the most important leguminous crop in human diet as a natural nutritional source with its high protein, complex carbohydrate and micronutrients content. It is marketed in different forms such as canned beans, green beans or dried beans and it is consumed mostly in grain form worldwide (Broughton et al., 2003[<xref rid="R6" ref-type="bibr">6</xref>]). As a crucial nutritional source, the global production of common bean is estimated to be 23 million metric tons and India is in first rank with 3.3 million tons annual bean production (FAO, 2014[<xref rid="R17" ref-type="bibr">17</xref>]). Due to its economic value especially for developing countries, studies have focused on improvement of agronomic and nutritional traits of this legume. Analysis of gene expression upon exposure to biotic and abiotic stresses (Liu et al., 2012[<xref rid="R35" ref-type="bibr">35</xref>]; Hiz et al., 2014[<xref rid="R21" ref-type="bibr">21</xref>]) or post-transcriptional regulation of gene expression (Contreras-Cubas et al., 2012[<xref rid="R12" ref-type="bibr">12</xref>]) are among the common approaches performed. Meanwhile, the complete genome sequence of common bean has been recently published (Schmutz et al., 2014[<xref rid="R51" ref-type="bibr">51</xref>]). Its release further extended genome-wide identification and expression analyses of genes and their regulatory networks to improve knowledge about common bean (Formey et al., 2015[<xref rid="R18" ref-type="bibr">18</xref>]). High-salt content in soil is an adverse environmental factor that threatens growth and productivity of plants thereby reducing agricultural sustainability in affected lands (Munns, 2002[<xref rid="R43" ref-type="bibr">43</xref>]; Qin et al., 2011[<xref rid="R47" ref-type="bibr">47</xref>]). Soil salinity exerts its effect on plants by causing ionic and osmotic stresses, which disturb plant's main metabolic processes such as photosynthesis, lipid metabolism and protein synthesis (Parida and Das, 2005[<xref rid="R46" ref-type="bibr">46</xref>]). Being a glycophyte, <italic>P. vulgaris</italic> is negatively influenced even in the presence of 1 dS/m salinity level (Chinnusamy et al., 2005[<xref rid="R10" ref-type="bibr">10</xref>]). In order to overcome hazardous effects of abiotic conditions, plants have evolved different response mechanisms at molecular, physiological and biochemical levels (Zhou et al., 2010[<xref rid="R68" ref-type="bibr">68</xref>]). The stress response leads to a diverse set of gene expression regulated by specific transcription factors (TFs) (Bouaziz et al., 2015[<xref rid="R5" ref-type="bibr">5</xref>]). Analysis of the function of such TFs provides useful insights to understand molecular mechanisms that govern plant abiotic stress tolerance and elucidates development of genetic manipulation strategies to maintain crop productivity (Kalavacharla et al., 2011[<xref rid="R27" ref-type="bibr">27</xref>]).</p><p>Apetala2/ethylene-responsive element binding factor (AP2/ERF) family is among central plant specific transcription factors that have crucial roles in the regulation of stress-responsive gene expression upon exposure to abiotic stresses such as salinity, drought, temperature fluctuation, disease resistance, and under floral development (Yamaguchi-Shinozaki and Shinozaki, 2006[<xref rid="R65" ref-type="bibr">65</xref>]; Mizoi et al., 2012[<xref rid="R40" ref-type="bibr">40</xref>]). By the presence of conserved AP2-ERF DNA-binding domain composed of 57-70 amino acid residue, AP2-ERF binds to specific <italic>cis</italic>-acting elements located at promoter regions of related stress-responsive target genes. These <italic>cis</italic>-acting elements are named as GCC box and/or <italic>cis</italic>-acting dehydration responsive element/C-repeat element (DRE/CRT) (Wessler, 2005[<xref rid="R61" ref-type="bibr">61</xref>]; Zhou et al., 2010[<xref rid="R68" ref-type="bibr">68</xref>]). AP2-ERF family is divided into five subgroups according to the sequence similarities and the number of AP2 domains they possess: </p><p>(i) AP2 (APETALA2), </p><p>(ii) RAV (related to ABI3/VP1), </p><p>(iii) ERF, </p><p>(iv) DREB (dehydration-responsive element-binding protein) and </p><p>(v) other ones (Sakuma et al., 2002[<xref rid="R50" ref-type="bibr">50</xref>]). </p><p>AP2 protein contains two tandem AP2 domains (Nakano et al., 2006[<xref rid="R44" ref-type="bibr">44</xref>]) while RAV family includes a B3 domain in addition to a single AP2 domain (Hu and Liu, 2011[<xref rid="R24" ref-type="bibr">24</xref>]). Since ERF and DREB proteins contain only a single AP2, they are distinguished from each other by the presence of different amino acid residues. The conserved amino acids in positions 14 and 19 are alanine and aspartic acid for ERF, and valine and glutamine for DREB, respectively (Sharma et al., 2010[<xref rid="R52" ref-type="bibr">52</xref>]).</p><p>Up to now, several AP2/ERF-related proteins have been identified in different plant species; that of 147 in Arabidopsis (Sakuma et al., 2002[<xref rid="R50" ref-type="bibr">50</xref>]; Nakano et al., 2006[<xref rid="R44" ref-type="bibr">44</xref>]), 200 in poplar (Zhuang et al., 2008[<xref rid="R69" ref-type="bibr">69</xref>]), 117 in wheat (Zhuang et al., 2011[<xref rid="R70" ref-type="bibr">70</xref>]), 58 in apple (Zhuang et al., 2011[<xref rid="R71" ref-type="bibr">71</xref>]), 149 in grape (Licausi et al., 2010[<xref rid="R34" ref-type="bibr">34</xref>]), 119 in castor bean (Xu et al., 2013[<xref rid="R64" ref-type="bibr">64</xref>]), 210 in potato (Massa et al., 2011[<xref rid="R39" ref-type="bibr">39</xref>]) and 164 in rice (Riano-Pachon et al., 2007[<xref rid="R49" ref-type="bibr">49</xref>]). In <italic>P. vulgaris</italic>, AP2-ERF transcription factor (AP2-ERF TF) family has not been analyzed at the genome-wide scale. Thus, herein we report for the first time a comprehensive genome-wide analysis of AP2-ERF TFs in common bean under salt stress conditions. In addition, the characterization of genomic structures, chromosomal locations, promoter analyses, interactome analyses, sequence homologies of all common bean <italic>AP2-ERF</italic> TF genes were also undertaken in this study. The expression analyses of selected <italic>AP2-ERF</italic> genes were conducted using qRT-PCR and previously uploaded RNAseq data in root and leaf tissues exposed to salt stress.</p></sec><sec sec-type="materials|methods"><title>Materials and Methods</title><sec><title>Identification of AP2-ERF sequences and construction of the phylogeny</title><p>Comprehensive identification of AP2-ERF amino acid sequences was accomplished by using two approaches. In first step, AP2-ERF encoding amino acid sequences belonging to <italic>Arabidopsis thaliana, Brachypodium distachyon, Carica papaya, Cucumis sativus, Glycine max, Lotus japonicus, Medicago truncatula, Oryza sativa subsp. japonica, Physcomitrella patens, Populus trichocarpa, Sorghum bicolor, Vitis vinifera, and Zea mays </italic>were obtained from plant transcription factor database 3.0 <<ext-link ext-link-type="uri" xlink:href="http://planttfdb.cbi.pku.edu.cn">http://planttfdb.cbi.pku.edu.cn</ext-link>> (Jin et al., 2014[<xref rid="R26" ref-type="bibr">26</xref>]) in order to create local blast query sequences. A total of 2422 amino acid sequences was used for BLASTP search at PHYTOZOME v10.1 database <<ext-link ext-link-type="uri" xlink:href="www.phytozome.net">www.phytozome.net</ext-link>> with default parameters (Goodstein et al., 2012[<xref rid="R20" ref-type="bibr">20</xref>]) in order to identify genes encode homolog peptides from <italic>P. vulgaris</italic>. In addition to the Blast search, keyword search was also performed in PHYTOZOME v10.3 database <<ext-link ext-link-type="uri" xlink:href="www.phytozome.net">www.phytozome.net</ext-link>>. All the obtained sequences with expected values less than 1.0 were downloaded as FASTA files. Different decrease redundancy tools <<ext-link ext-link-type="uri" xlink:href="web.expasy.org/decrease_redundancy">web.expasy.org/decrease_redundancy</ext-link>> and elimdupes <<ext-link ext-link-type="uri" xlink:href="http://hcv.lanl.gov/content/sequence/elimdupes/elimdupes.html">http://hcv.lanl.gov/content/sequence/elimdupes/elimdupes.html</ext-link>> were utilized for removing of redundant sequences. All of non-redundant sequences were analyzed for the confirmation of conserved AP2-ERF domain by using InterProScan Sequence Search <ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/Tools/pfa/iprscan">http://www.ebi.ac.uk/Tools/pfa/iprscan</ext-link>. The miRNA locations on the MtARFs were searched using PMRD database <ext-link ext-link-type="uri" xlink:href="http://bioinformatics.cau.edu.cn/PMRD/">http://bioinformatics.cau.edu.cn/PMRD/</ext-link>. </p><p>The multiple alignments of the final amino acid sequences of PvAP2-ERF proteins were performed with Muscle by using CLC Genomics Workbench 8.0 software (CLC bio, Aarhus, Denmark) with default parameters. Furthermore, alignments of amino acid sequences of AP2-ERF domains from <italic>P. vulgaris and Arabidopsis thaliana </italic>were carried out in the same way. Then, the phylogenetic trees of aligned AP2-ERF proteins were constructed using CLC Genomics Workbench via the Neighbor-Joining (NJ) method with the following parameters: WAG protein substitution model, gamma distribution, and bootstrap (1,000). The constructed phylogenetic trees were visualized with ITOL (Letunic and Bork, 2007[<xref rid="R32" ref-type="bibr">32</xref>]). Amino acid composition of the AP2-ERF proteins was calculated by using MEGA 6.0.1. </p></sec><sec><title>Intron/Exon structure, genome distribution, and motif prediction</title><p>In order to illustrate the intron exon structures of <italic>AP2-ERF</italic> genes, DNA and cDNA sequences corresponding to each predicted gene from the <italic>P. vulgaris</italic> genome and the intron distribution pattern information of <italic>PvAP2</italic>-<italic>ERFs</italic> were downloaded from the <ext-link ext-link-type="uri" xlink:href="http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Pvulgaris">http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Pvulgaris</ext-link>. The gene schematic structure was drawn by the Gene Structure Display Server (GSDS) <<ext-link ext-link-type="uri" xlink:href="http://gsds.cbi.pku.edu.cn/index.php">http://gsds.cbi.pku.edu.cn/index.php</ext-link>> (Hu et al., 2015[<xref rid="R23" ref-type="bibr">23</xref>]). The nucleotide sequences of all <italic>PvAP2-ERF</italic> genes were used as query sequences for BLASTN search of the <italic>P. vulgaris</italic> sequences against the PHYTOZOME v10.1 database using default settings <ext-link ext-link-type="uri" xlink:href="www.phytozome.net">www.phytozome.net</ext-link> for determination of location of these genes on bean chromosomes. Genes were distributed onto bean chromosomes according to their order of physical position (bp), from the first chromosome to eleventh chromosome and finally visualized with a software called MapChart v2.2 <<ext-link ext-link-type="uri" xlink:href="www.wageningenur.nl/en/show/Mapchart.htm">www.wageningenur.nl/en/show/Mapchart.htm</ext-link>>. </p><p>Gene duplications were also studied based on Plant Genome Duplication Database (Tang et al., 2008[<xref rid="R57" ref-type="bibr">57</xref>]). <italic>PvAP2-ERF</italic> genes found within the same chromosome were characterized as tandem duplication (Shiu and Bleecker, 2003[<xref rid="R53" ref-type="bibr">53</xref>]; Du et al., 2014[<xref rid="R14" ref-type="bibr">14</xref>]). For segmental duplications, BLASTP search was performed against all identified peptide sequences of identified PvAP2-ERF in common bean. As potential anchors, top five matches with an e-value (≤ 1e-05) was evaluated and then, MCScan was utilized for the determination of collinear blocks. Finally, the alignment was performed and e-value with ≤ 1e-10 was selected as significant matches (Tang et al., 2008[<xref rid="R57" ref-type="bibr">57</xref>]; Du et al., 2014[<xref rid="R14" ref-type="bibr">14</xref>]).</p><p>Conserved motifs of AP2-ERF transcription factors were detected with web-based sequence analysis tool called as MEME (4.10.1) with the following parameters: optimum width 80-100 amino acids, any number of repetitions of a motif, and maximum number of motifs set at 10. The BLAST search for the resulting motifs in the NCBI and SMART databases was performed to determine their biological context (Sharma et al., 2010[<xref rid="R52" ref-type="bibr">52</xref>]).</p></sec><sec><title>Prediction of 3D protein homology, molecular and physicochemical parameters</title><p>The isoelectric point (pI), amino acid composition, molecular weight of common bean AP2-ERF deduced proteins and instability indexes were determined using the ProtParam tool <ext-link ext-link-type="uri" xlink:href="http://us.expasy.org/tools/protparam.html">http://us.expasy.org/tools/protparam.html</ext-link>. The sub-cellular localization was investigated using the mGOASVM (V2) <<ext-link ext-link-type="uri" xlink:href="http://bioinfo.eie.polyu.edu.hk/mGoaSvmServer2/mGOASVM_v2.html">http://bioinfo.eie.polyu.edu.hk/mGoaSvmServer2/mGOASVM_v2.html</ext-link>>. The PROSOII program <ext-link ext-link-type="uri" xlink:href="http://mips.helmholtz-muenchen.de/prosoII/prosoII.seam">http://mips.helmholtz-muenchen.de/prosoII/prosoII.seam</ext-link> was used to predict the sequence-based solubility of proteins (Smialowski et al., 2012[<xref rid="R54" ref-type="bibr">54</xref>]).</p><p>For prediction of 3D protein structures of PvAP2-ERF proteins, Phyre2 server (Protein Homology/Analogy Recognition Engine) (Kelley and Sternberg, 2009[<xref rid="R29" ref-type="bibr">29</xref>]) was used. Firstly, all PvAP2-ERF protein sequences were searched in the Protein Data Bank (PDB) (Berman et al., 2000[<xref rid="R3" ref-type="bibr">3</xref>]) with the default parameters. Then, the data was analyzed in Phyre2 server with 'intensive' mode for identification of the best template having similar sequence and known three-dimensional structure. Finally, predicted protein structures of bean PvAP2-ERF was evaluated in terms of confidence level (> 90 %) and percentage residue level (80 to 100).</p></sec><sec><title>Analyses of the putative PvAP2-ERF promoter region and miRNAs targeting</title><p>A total of 180 common bean <italic>AP2-ERF</italic> genes were analyzed in LegumeIP <<ext-link ext-link-type="uri" xlink:href="http://plantgrn.noble.org/LegumeIP/v2">http://plantgrn.noble.org/LegumeIP/v2</ext-link>> in order to obtain promoter sequences of identified genes. The 2000 bp fragment upstream of the transcriptional start site of <italic>PvAP2-ERFs</italic> was determined as promoter region to identify the <italic>cis</italic>-elements. The identified <italic>cis</italic>-elements of promoter sequences were analyzed by using the PLACE <ext-link ext-link-type="uri" xlink:href="http://www.dna.affrc.go.jp/PLACE/">http://www.dna.affrc.go.jp/PLACE/</ext-link> database. </p><p>Detection of miRNA target genes plays important role for understanding the functions of miRNAs. Bioinformatics and prediction analyses of miRNAs and their target <italic>PvAP2-ERF</italic> genes were performed in the web-based psRNA Target Server <<ext-link ext-link-type="uri" xlink:href="http://plantgrn.noble.org/psRNATarget">http://plantgrn.noble.org/psRNATarget</ext-link>> with default parameters. Alignment of identified genes with all known plant miRNAs was conducted based on Zhang (2005[<xref rid="R67" ref-type="bibr">67</xref>]). Furthermore, miRNA targets were also checked with BLASTX searches with ≤ 1e-10 against <italic>P. vulgaris</italic> EST sequences at NCBI database for confirmation of putative gene homologous.</p></sec><sec><title>Gene ontology (GO) and functional annotation</title><p>The functional characterization and annotation of <italic>AP2-ERF</italic> sequences were performed using Blast2GO, which is a sequence-based tool to assign GO terms and annotation for each BLAST hit (Conesa et al., 2005[<xref rid="R11" ref-type="bibr">11</xref>]). The GO terms for each of the three main categories (biological process-BP, molecular function-MF and cellular component-CC) were obtained from sequence similarity using the default parameters. Firstly, the common bean amino acid sequences were used as queries in a BLASTP search launched from CLC Genomics Workbench. The BLAST search was performed by using non-redundant (NR) database at NCBI with an e-value of 1xE-5 and top 100 alignments for each sequence was used for further analysis. The resulting Multi Blast data collection was then converted into a Blast2GO Project. GO annotation was carried out by applying the Blast2GO annotation rule, which computes an annotation score for each candidate GO term.</p></sec><sec><title>Prediction of protein-protein interaction network</title><p>Since there were no references for common bean interactome data, the protein-protein interaction data from Arabidopsis was used for predicting protein-protein interaction network of PvAP2-ERF members. First, PvAP2-ERFs sequences were used to search Arabidopsis homologous sequences in Inparanoid <<ext-link ext-link-type="uri" xlink:href="http://inparanoid.sbc.su.se/cgi-bin/index.cgi">http://inparanoid.sbc.su.se/cgi-bin/index.cgi</ext-link>> with default parameters. Secondly, the edge information file (querynw.sif) of Arabidopsis orthologous (<italic>AtAP2-ERFs</italic>) were created via AraNet <ext-link ext-link-type="uri" xlink:href="http://www.functionalnet.org/aranet/">http://www.functionalnet.org/aranet/</ext-link>, and placed to PvAP2-ERF data to create an edge information file of PvAP2-ERF members. Finally, the protein-protein interaction network of PvAP2-ERF was illustrated with Cytoscape_v3.2.1 (National Institute of General Medical Sciences, MD, USA).</p></sec><sec><title>In silico expression analysis of PvAP2-ERF genes </title><p>To obtain insight into the global expression pattern of common bean<italic> PvAP2-ERF </italic>genes in root and leaf tissues under high salt concentration, Illumina RNA-seq data that was reported previously by Hiz et al. (2014[<xref rid="R21" ref-type="bibr">21</xref>]) were utilized. Sequencing reads were obtained from Sequence Read Archive (SRA), following accession numbers of SRR957668 (salt-treated leaf), SRR957667 (control leaf), SRR958472 (salt-treated root) and SRR958469 (control root). The low-quality reads (Phred quality (Q) score < 20) determined by FastQC were trimmed with CLC Genomics Workbench 8.0. To evaluate the expression pattern of root and leaf tissues, high quality reads were mapped to <italic>P. vulgaris</italic> genome (v1.0), downloaded from PHYTOZOME V10.3 database (<<ext-link ext-link-type="uri" xlink:href="http://www.phytozome.net">http://www.phytozome.net</ext-link>>), by using CLC Genomics Workbench with default parameters. Normalization of the gene expression values were carried out by the reads per kilobase of exon model per million mapped reads (RPKM) algorithm (Mortazavi et al., 2008[<xref rid="R41" ref-type="bibr">41</xref>]). To identify differentially expressed <italic>PvAP2-ERF </italic>genes, a FDR-value ≤ 0.001, fold change (RPKM-tr/RPKM-cont) ≥ 2 and the absolute ratio of log2 (RPKM-tr/RPKM-cont) ≥ 1 were used as threshold values. Finally, the heat maps of hierarchical clustering were visualized with PermutMatrix (Caraux and Pinloche, 2005[<xref rid="R8" ref-type="bibr">8</xref>]).</p></sec><sec><title>Plant materials, growth conditions, and salt stress applications</title><p>The seeds of Ispir, a salt tolerant local common bean variety, were germinated in vermiculite containing plug trays. Seedlings were incubated in growth chamber at 24/ 20 °C cycle under a 16h/8h photoperiod with 350 μmol m<sup>−2</sup> s<sup>−1</sup> light intensity, and 50-60 % relative humidity (Dasgan and Koc, 2009[<xref rid="R13" ref-type="bibr">13</xref>]) . Hoagland`s solution (Hoagland and Arnon, 1950[<xref rid="R22" ref-type="bibr">22</xref>]) was applied to the seedlings in a growth chamber up to trifoliate leaf stage. Salt stress was applied with Hoagland`s solution including 150 mM NaCl for 9 days (Kavas et al., 2015[<xref rid="R28" ref-type="bibr">28</xref>]). After this period, root and leaf tissues were collected from salt treated and control plants for gene expression analysis with qRT-PCR. Three separate biological replicates were used.</p></sec><sec><title>RNA extraction and quantitative real-time PCR analysis</title><p>RNeasy Plant Mini Kit (Qiagen, Valencia, California, USA) was used to isolate total RNAs of leaf and root tissues collected after 150 mM salt treatment. Isolated total RNAs were quantified by using NanoDrop 2000 UV-VIS spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and quality-analyzed using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). The cDNA was synthesized from 1 µg of DNAse I treated total RNA in a 20 µl reaction volume with RevertAid™ First Strand cDNA Synthesis Kit (Thermo Scientific, USA). </p><p>Tissue-specific expression levels of <italic>PvAP2-ERF</italic> TF family genes that showed differentially upregulated expression pattern in RNA-seq analysis upon salt stress were evaluated with qRT-PCR. qRT-PCR amplifications were performed by BioRad CFX96 machine (BioRad, Hercules, CA) with default parameters. Primers for the genes of <italic>PvAP2-ERF100, PvAP2-ERF111, PvAP2-ERF119, PvAP2-ERF177, PvAP2-ERF69, PvAP2-ERF70, PvAP2-ERF72, PvAP2-ERF150 </italic>and<italic> PvAP2-ERF53</italic> genes were designed for both leaf and root tissues since they showed higher expression level in RNA-seq analysis. The Skip16 gene was used as an internal standard to calculate relative fold differences based on the comparative C<sub>T</sub> method (Borges et al., 2012[<xref rid="R4" ref-type="bibr">4</xref>]). The primer sequences are listed in Supplementary Table S1. PCR reactions were carried out in 96-well optical reaction plates by using SsoAdvance Universal SYBR Green Supermix (Biorad) according to the manufacturer's protocol. The reaction was set up using 20 ng of cDNA sample as a template. All reactions were repeated three times with triple biological replicates. The data were analyzed using the 2<sup>−ΔΔ</sup>C<sub>T</sub> method (Livak and Schmittgen, 2001[<xref rid="R37" ref-type="bibr">37</xref>]). </p></sec></sec><sec><title>Results and Discussion</title><sec><title>Identification and chromosomal distribution of PvAP2-ERF genes in P. vulgaris</title><p>Completed whole genome sequences of <italic>P. vulgaris</italic> provided an opportunity for the identification of <italic>AP2-ERF</italic> family member genes in common bean for the first time. AP2-ERF family protein sequences from different plant species including <italic>Arabidopsis thaliana, Cucumis sativus, Glycine max, Hordeum vulgare, Medicago truncatula, Nicotiana tabacum, Oryza sativa, Physcomitrella patens, Ricinus cummunis, Solanum lycopersicum, Sorghum bicolor, Triticum aestivum, Vigna radiate, Vitis vinifera </italic>and <italic>Zea mays</italic> were utilized as queries for performing BLAST searches in relevant databases. The putative proteins were examined for the validation of presence of AP2 domain (PF00847; E value < 0.001) using the Pfam database found in CLC Genomics Workbench 8.0. Sequences with insignificant matches were discarded from further analysis. As a result of this analysis, a total of 180 genes with AP2-ERF domain were identified in common bean (Table 1<xref ref-type="fig" rid="T1">(Tab. 1)</xref>, Supplementary Table S2). Accordingly, <italic>P. vulgaris</italic> was found to possess more AP2 and ERF domains as compared to <italic>Cucumis melo, Arabidopdsis thaliana, Glycine max</italic> and <italic>Solanum tuberosum</italic> thereby indicating a variation in number, function and structure among AP2-ERF members belonging to different plant species. <italic>AP2-ERF</italic> gene family members were named as <italic>PvAP2-ERF</italic> according to their order on the chromosomes. Only one gene located in scaffold_91 was called as<italic> PvAP2-ERF-180. </italic></p><p>The ORFs and gene lengths, protein MWs, pI values, stability index, solubility and subcellular localization of these putative genes were analyzed, and results are listed in Table S2. Gene lengths ranged from 363 (<italic>PvAP2</italic>-<italic>ERF155</italic>) to 7445 bp (<italic>PvAP2-ERF128</italic>), MWs from 13.33 (<italic>PvAP2-ERF155</italic>) to 75.70 kDa (<italic>PvAP2-ERF125</italic>) and pI values from 4.56 (PvAP2-ERF94) to 10.06 (PvAP2-ERF73). Cellular localization is often an important factor in determining the protein function (Thamilarasan et al., 2014[<xref rid="R58" ref-type="bibr">58</xref>]). Subcellular localization prediction made by mGOASVM suggested that 177 proteins were located in nucleus. It was suggested that TFs are located only in the nucleus in previous studies (Liu et al., 2013[<xref rid="R36" ref-type="bibr">36</xref>]). According to an instability index (II), most of the PvAP2-ERF proteins (95 %) were estimated as unstable in a test tube. Solubility of PvAP2-ERF proteins in <italic>Escherichia coli</italic> was evaluated according to their amino acid sequences. According to this evaluation, almost half of the PvAP2-ERF proteins were found as soluble. Based on the average amino acid composition of AP2-ERF proteins, the most abundant amino acid was Ser (S) with the value of 11.80. The average abundance of important salt responsive amino acids, Gly (G) and Pro (P) were found to be 6.28 and 6.00, respectively (Table S3).</p><p>It was reported that Glycine-rich proteins have important roles in plants under different abiotic and biotic stress conditions by regulating the gene expression post-transcriptionally (Mousavi and Hotta, 2005[<xref rid="R42" ref-type="bibr">42</xref>]).The average abundance of Trp and Cys amino acids in AP2-ERF proteins were 1.67 and 1.29, respectively.Except <italic>PvAP2/ERF-180</italic>, all other <italic>PvAP2-ERF </italic>genes were successfully mapped to eleven chromosomes. The exact position (in kp) of each <italic>PvAP2-ERF </italic>on bean chromosome is shown in Figure 1<xref ref-type="fig" rid="F1">(Fig. 1)</xref>. The highest number of <italic>AP2-ERF </italic>genes were found in chromosome 7 with 15 %. Following this, chromosome 2, 1 and 8 contained 23/180 (12.8 %), 22/180 (12.2 %) and 20/180 (11.1 %) <italic>PvAP2-ERF </italic>genes, respectively. Among all, the least gene distribution was observed in chromosome 4 and 11 with 4.4 % (Figure 1<xref ref-type="fig" rid="F1">(Fig. 1)</xref>). It was also realized that different distribution pattern of the <italic>PvAP2-ERF </italic>genes on chromosomes has occurred and gene clusters were accumulated on lower or upper end of the chromosome arms. For example, <italic>PvAP2-ERF </italic>genes located on chromosomes 1, 2, 7, 8 and 10 were distributed on both arms, whereas genes found on chromosomes 3, 5, 6 and 9 appear to be congregated at only lower end of the arm (Figure 1<xref ref-type="fig" rid="F1">(Fig. 1)</xref>).</p><p>The AP2-ERF transcription factor genes are one of the most identified gene family members in different plant genomes including 122 genes in <italic>Arabidopsis thaliana </italic>(Nakano et al., 2006[<xref rid="R44" ref-type="bibr">44</xref>]), 226 genes in <italic>Brassica oleracea</italic> (Thamilarasan et al., 2014[<xref rid="R58" ref-type="bibr">58</xref>]), 248 genes in <italic>Brassica rapa</italic> (Song et al., 2013[<xref rid="R56" ref-type="bibr">56</xref>]), 108 genes in <italic>Citrus sinensis</italic> (Ito et al., 2014[<xref rid="R25" ref-type="bibr">25</xref>]), 136 genes in <italic>Cucumis melo </italic>(Ma et al., 2015[<xref rid="R38" ref-type="bibr">38</xref>]), 103 genes in <italic>Cucumis sativus</italic> (Hu and Liu, 2011[<xref rid="R24" ref-type="bibr">24</xref>]), 267 genes in <italic>Daucus carota</italic> (Li et al., 2015[<xref rid="R33" ref-type="bibr">33</xref>]), 209 genes in <italic>Eucalyptus grandis</italic> (Cao et al., 2015[<xref rid="R7" ref-type="bibr">7</xref>]), 98 genes in <italic>Glycine max</italic> (Zhuang et al., 2008[<xref rid="R69" ref-type="bibr">69</xref>]), 209 genes in <italic>Malus domestica</italic> (Girardi et al., 2013[<xref rid="R19" ref-type="bibr">19</xref>]), 139 genes in <italic>Oryza sativa</italic> (Nakano et al., 2006[<xref rid="R44" ref-type="bibr">44</xref>]), 116 genes in <italic>Phyllostachys edulis</italic> (Wu et al., 2015[<xref rid="R63" ref-type="bibr">63</xref>]), 200 genes in <italic>Populus trichocarpa</italic> (Zhuang et al., 2008[<xref rid="R69" ref-type="bibr">69</xref>]), 114 genes in <italic>Ricinuscommunis</italic> (Xu et al., 2013[<xref rid="R64" ref-type="bibr">64</xref>]), 173 genes in <italic>Salix arbutifolia</italic> (Rao et al., 2015[<xref rid="R48" ref-type="bibr">48</xref>]), 171 genes in <italic>Setaria italica</italic> (Lata et al., 2014[<xref rid="R30" ref-type="bibr">30</xref>]), 112 genes in <italic>Solanum lypersicon</italic> (Sharma et al., 2010[<xref rid="R52" ref-type="bibr">52</xref>]), 155 genes in <italic>Solanum tuberosum</italic> (Charfeddine et al., 2015[<xref rid="R9" ref-type="bibr">9</xref>]), 117 genes in <italic>Triticum aestivum</italic> (Zhuang et al., 2011[<xref rid="R70" ref-type="bibr">70</xref>]), 132 genes in <italic>Vitis vinifera</italic> (Licausi et al., 2010[<xref rid="R34" ref-type="bibr">34</xref>]), 184 genes in <italic>Zea mays</italic> (Du et al., 2014[<xref rid="R14" ref-type="bibr">14</xref>]). The first discovery of these family genes at genomic level was accomplished in <italic>Arabidopsis </italic>and <italic>Oryza sativa </italic>in 2006 (Nakano et al., 2006[<xref rid="R44" ref-type="bibr">44</xref>]). From that time, characterization of <italic>AP2-ERF </italic>gene family members from different organisms has continued. The density of <italic>PvAP2-ERF </italic>is about 0.3066 which is higher than most of the analyzed plants. <italic>Arabidopsis thaliana</italic> (0.9037) and <italic>Triticum aestivum </italic>(0.0069) had the highest and lowest <italic>AP2-ERF </italic>gene density, respectively (Table S4). We also found similar gene numbers in <italic>P. vulgaris</italic> (180) with <italic>Zea mays</italic> (184) and <italic>Setaria italica</italic> (171). Advent of omics technologies and availability of draft genomes of organisms provide valuable sources for detection of new genes and determination of their function (Baloglu, 2014[<xref rid="R2" ref-type="bibr">2</xref>]). Although determination of <italic>AP2-ERF </italic>gene members at genome level are common for different plant species, there is a limited data for genome-wide identification and their characterizations in the common bean genome (Hiz et al., 2014[<xref rid="R21" ref-type="bibr">21</xref>]; Kavas et al., 2015[<xref rid="R28" ref-type="bibr">28</xref>]). Therefore, it can be concluded that we firstly found 180<italic> AP2-ERF </italic>genes in Phaseolus genome was found in this study for the first time on the basis of Pfam and SMART domain searches.</p></sec><sec><title>Phylogenetic analysis of the AP2-ERF family</title><p>The classification method of Sakuma et al. (2002[<xref rid="R50" ref-type="bibr">50</xref>]) used for AtAP2/ERFs was followed for further classification of PvAP2/ERFs. According to this classification, a total of 149 PvAP2/ERFs with only one domain was grouped into two subfamilies (ERF and DREB) based on the similarity of their amino acid sequences. Like other plants such as Arabidopsis, melon, sweet orange and potato, the ERF and DREB subfamilies are the most dominant form of AP2-ERF transcription factors in common bean. The ERF subfamily factors were divided into six subgroups: B1-B6. The DREB subfamily factors were also subdivided into six groups: A1-A6. A total of 27 factors carrying double AP2-ERF domains were grouped into the AP2 subfamily. Three factors that were identified with a single AP2-ERF domain and a B3 domain were clustered to the RAV subfamily. There was only one soloist gene namely <italic>PvAP2-ERF128</italic> which is ortholog of AT4G13040. Based on the multiple sequence alignment and motif analysis, unrooted tree with 180 PvAP2-ERF domain sequences was constructed (Figure 2<xref ref-type="fig" rid="F2">(Fig. 2)</xref>, Supplementary Figure S1). </p><p>Compared with <italic>Arabidopsis thaliana</italic> (122 members), <italic>Cucumis melo</italic> (136 members), <italic>Cucumis sativus</italic> (103 members), <italic>Solanum tuberosum</italic> (155 members), <italic>Solanum lypersicon</italic> (112 members) and <italic>Glycine max</italic> (98 members), the AP2-ERF family seems to have relatively higher number of members in common bean. It is expected result that the number of the AP2-ERF members varied among different species (Table 1<xref ref-type="fig" rid="T1">(Tab. 1)</xref> References in Table 1: Ma et al., 2015[<xref rid="R38" ref-type="bibr">38</xref>]; Sharma et al., 2010[<xref rid="R52" ref-type="bibr">52</xref>]; Zhang et al., 2008[<xref rid="R67" ref-type="bibr">67</xref>]; Nakano et al., 2006[<xref rid="R44" ref-type="bibr">44</xref>]). For instance, the number of members in the ERF subfamily ranges from 64 (in melon) to 95 (in common bean), and the number of DREB members ranges from 25 (in potato) to 54 (in common bean). </p></sec><sec><title>Gene structure and conserved motifs analysis of the AP2-ERF gene family</title><p>To gain further information of the structural diversity of common bean <italic>AP2-ERF</italic> genes, we analyzed exon/intron organization within PvAP2-ERF family members (Figure S2). A total of 42 intronless <italic>AP2-ERF</italic> genes were identified, which accounted for 23 % of total <italic>PvAP2-ERFs</italic>. Number of ERF subfamily genes (23 genes) without intron was higher than that of DREB subfamily genes (16). Intron organization and numbers of <italic>AP2-ERF</italic> genes in common bean showed different variation and distribution into different subgroups. AP2 subfamily members had 5-9 introns and almost half of the groups members had seven introns. In contrast to other members of AP2 subfamily, only <italic>PvAP2-ERF179</italic> had five introns (Figure S2). </p><p>The amino acid sequences of the AP2-ERF family members were aligned with multiple sequence alignment tools to determine the phylogenetic relationships between the genes in the common bean AP2-ERF family. A total of 20 consensus amino acids, 3G, 4V, 11G, 16E, 17I, 33R, 35W, 36L, 37G, 45A, 46A, 48A, 49Y, 50D, 51A, 52A, 57G, 60A, 63N and 64F were more than 80 % conserved among the 189 proteins in the PvAP2-ERF family (Figure S3). The alignment indicated that 95 of these genes were located in the ERF subfamily, 27 were in the AP2 subfamily, three were in the RAV subfamily and 54 were in the DREB subfamily. The differences within the subfamilies were further analyzed by examining the conserved motifs using MEME. The members in each subfamily had high sequence similarities (Figure S2). All members of the DREB subfamily and the ERF family contained a WLG motif; however, only a few ERF factors possessed WIG. Most of the members of AP2 subfamily contained YLG motif. In addition to these residues, most of members (more than 85 %) in common bean AP2-ERF family possessed the two featured conserved elements YRG and AYD elements within the AP2-ERF domain region.</p></sec><sec><title>Gene duplications rate of the PvAP2-ERF genes</title><p>Segmental and tandem gene duplications play important role for expansion and evolution of large gene families in plants (Baloglu et al., 2014[<xref rid="R2" ref-type="bibr">2</xref>]). We have also indicated gene duplication events of <italic>AP2-ERF </italic>genes in common bean. It was observed that segmental gene duplication mainly occurred in the Phaseolus genome rather than tandem duplication event (Table S5). Totally, 103 segmental duplicated <italic>AP2-ERF </italic>genes have been found which accounts for about 57 % (103/180) of total <italic>PvAP2-ERF </italic>genes. In contrast to segmental duplication rate, tandem duplication event has a limited contribution to the gene family expansion. A total of 14 (8 %) tandem duplicate <italic>PvAP2-ERF </italic>genes were detected. Similar results have been observed for in the sorghum, rice, Arabidopsis (Wang et al., 2011[<xref rid="R59" ref-type="bibr">59</xref>]), cucumber (Baloglu et al., 2014[<xref rid="R2" ref-type="bibr">2</xref>]) and common bean (Kavas et al., 2015[<xref rid="R28" ref-type="bibr">28</xref>]) genomes. Our observation might support the idea that segmental duplication of <italic>AP2-ERF </italic>genes in common bean has a major contribution to the expansion of this gene family in Phaseolus genome.</p></sec><sec><title>3D Protein Homology Modeling </title><p>Firstly, BLASTP search was conducted in the PDB for construction of 3D homology model for PvAP2-ERF proteins. Only three of PvAP2-ERF proteins (PvAP2/ERF-49-89-94) showed higher homology rate. Then, intensive mode of Phyre2 was used for enhancing higher accuracy. The alignment of hidden Markov models is used in this web-based software (Soding, 2005[<xref rid="R55" ref-type="bibr">55</xref>]). In addition, Poing which has a new folding simulation mode in Phyre2 has been improved for modelling of proteins regions with no significant homology for known structures. Finally, 3D protein homology modeling of PvAP2/ERF-49-89-94 proteins are predicted at above 90 % confidence and the percentage residue varied from 80 to 100 (Figure 3<xref ref-type="fig" rid="F3">(Fig. 3)</xref>). These results are consistent with the findings of the previous studies in which small number of predicted 3D homology of bHLH proteins (Kavas et al., 2015[<xref rid="R28" ref-type="bibr">28</xref>]) and bZIP ones (Baloglu et al., 2014[<xref rid="R2" ref-type="bibr">2</xref>]) were found.</p><p>The secondary structures were mainly composed of β strand and with small rate of α helices. Thus, all the predicted PvAP2-ERF proteins are considered highly reliable providing preliminary information for understanding the molecular function of AP2-ERF proteins in common bean, as well.</p></sec><sec><title>Identifying miRNAs for PvAP2-ERF gene targets</title><p>miRU database was used for identification of <italic>PvAP2-ERF </italic>gene targets with the consideration of two important parameters (Zhang, 2005[<xref rid="R67" ref-type="bibr">67</xref>]). The first one is the maximum expectation, which is the threshold of the score. The default cut-off threshold was adjusted to 3.0. If this score is greater than the threshold, a miRNA/target site pair has been omitted. UPE is the second one, which is defined as maximum energy to unpair the target site. Nearly all of <italic>PvAP2-ERF </italic>genes targeted by 44 different plant species` miRNAs were identified in this study. The most abundant target genes are <italic>PvAP2/ERF</italic>-20-25-62-78-113-173. Furthermore, miR156, miR172 and miR838 are the most important miRNAs found by targeting and BLAST analysis (Table S6).</p><p>MicroRNAs (abbreviated miRNA) are a small non-protein coding RNA molecule (aprox. 21 nucleotides) found in plants, animals, and some viruses, which regulate gene expression at post-transcriptional level (Eldem et al., 2013[<xref rid="R15" ref-type="bibr">15</xref>]). They play functional roles in plant development and stress response to biotic and abiotic environmental factors. Based on <italic>in silico</italic> analysis of <italic>PvAP2-ERF </italic>gene targets, miR172 appeared in all selected plant species miRNAs. The crucial role of miR172 has been described for soybean (Yan et al., 2013[<xref rid="R66" ref-type="bibr">66</xref>]), common bean-rhizobia symbiosis (Wang et al., 2014[<xref rid="R60" ref-type="bibr">60</xref>]) and common bean (Nova-Franco et al., 2015[<xref rid="R45" ref-type="bibr">45</xref>]). In common bean, miR172c indirectly regulates the expression of the transcription factors NF-YA1, NSP2 and CYCLOPS as well as the gene FLOT2, all of which are essential regulators of early stages of the symbiosis (Nova-Franco et al., 2015[<xref rid="R45" ref-type="bibr">45</xref>]). There is a close relationship between miR156 and miR172, which coordinated developmental timing in Arabidopsis. miR156 represses the expression of SPL transcription factors whereas miR172 acts downstream of miR156 to promote adult epidermal identity in Arabidopsis (Wu et al., 2009[<xref rid="R62" ref-type="bibr">62</xref>]). Additionally, miR156 is responsible for regulation of miR172 expression via SPL9 and SPL10, which immediately promotes the transcription of miR172b (Wu et al., 2009[<xref rid="R62" ref-type="bibr">62</xref>]). Therefore, identification of miRNAs and their <italic>PvAP2-ERF </italic>target genes might provide valuable information for determination of possible involvement of miRNAs in diverse physiological mechanisms. </p></sec><sec><title>The interaction network of AP2/ERF genes in common bean</title><p>Plant growth is a developmental process that multiple genes and their interaction genes are involved in. The Arabidopsis Interactions Viewer is a database that provides complex biomolecular and pathway information of thousands of interactions between proteins. In order to further understand the interactions between <italic>AP2/ERFs</italic> and other genes in common bean, an interaction network was constructed according to the orthologs in Arabidopsis (Figure 4<xref ref-type="fig" rid="F4">(Fig. 4)</xref>). There were 32 <italic>AP2/ERF</italic> genes that showed interactions with other genes in common genome. A total of 71 gene pairs with the value of Pearson correlation coefficient (PCC) over than zero were positive correlations, whereas 33 gene pairs with the value of PCC less than zero were negative correlations. Moreover, 27 gene pairs could not be calculated. The transcription factor PvAP2-ERF78, an ortholog of At2G28550, was potentially interacted with at least 15 proteins, indicating that it has very important role in transcriptional level regulation (Figure 4<xref ref-type="fig" rid="F4">(Fig. 4)</xref>). However, twelve AP2-ERF factors were regulated by a common bean protein Phvul.003G059500, an important protein for response to osmotic and oxidative stress. </p></sec><sec><title>Analysis of the putative promoter regions and GO terms of the AP2-ERF gene subfamily </title><p>DNA sequences located at upstream of genes in the promoter region and served as transcription factor (TF)-binding sites are called as <italic>cis</italic>-regulatory elements. It was reported that they have important roles in controlling tissue-specific and stress-responsive gene expression (Le et al., 2012[<xref rid="R31" ref-type="bibr">31</xref>]). There are many studies showing that multi-stimulated genes are closely correlated with <italic>cis</italic>-regulatory elements in their promoter sequences (Fang et al., 2008[<xref rid="R16" ref-type="bibr">16</xref>]). To increase knowledge about the transcriptional control and potential roles of <italic>AP2-ERFs</italic>, cis-elements in their promoter sequences were predicted using plant promoter database (PLACE). By searching the <italic>PvAP2-ERF</italic> promoter sequences in the plant promoter PLACE database, a number of potential regulatory sequences corresponding to <italic>cis</italic>-acting elements related to tissue specific gene expression, abiotic and biotic stress responses and hormone response were predicted. According to this putative promoter analysis, promoter region of AP2-ERFs was found to contain MYB, MYC, WBOX, and WRKY binding elements (Table S7). These interesting results reveal that MYB, MYC and WRKY transcription factors can regulate the expression of <italic>AP2-ERF</italic> genes. The fact that many cis-elements related to various developmental process suggests that these transcription factors are controlled by different signaling pathways involved in response to several stress conditions. In addition to these elements, many abiotic stress related cis-elements such as S000176, S000028, S000144, S000408 and S000415 for drought stress, S000453 for salt stress, S00030 for heat stress, S000407 for cold stress and S000457 for wound stress were found widely in the promoter regions of <italic>AP2-ERFS</italic> in common bean. In this context, <italic>PvAP2-ERF1</italic> had up to 23 light-responsive and tissue-specific activation of phenylpropanoid biosynthesis genes elements (S000144). This clearly showed that AP2-ERFS superfamily transcription factors might respond to abiotic stress and have potential functions in enhancing abiotic stress resistance. </p><p>The GO terms of the <italic>PvAP2-ERF</italic> genes were annotated according to their biological processes (BP), molecular functions (MF) or involvement as cellular components (CC). The <italic>PvAP2-ERF</italic> genes belonged to different biological processes, cellular components and molecular functions were shown in Figure 5<xref ref-type="fig" rid="F5">(Fig. 5)</xref>.</p><p>The maximum numbers of <italic>PvAP2-ERF</italic> genes were involved in biological processes, including nitrogen compound metabolic process, cellular metabolic processes and biosynthetic process. In the context of biological process, most of the <italic>PvAP2-ERF</italic> genes showed both organic cyclic and heterocyclic compound binding activity. </p></sec><sec><title>AP2-ERF gene expression profiling</title><p>In silico expression analysis <italic>AP2-ERF</italic> genes was carried out with two different tissue samples of common bean. According to RNA-seq analysis results , expression of 12 <italic>AP2-ERF</italic> genes (<italic>PvAP2-ERF117, PvAP2-ERF13, PvAP2-ERF152, PvAP2-ERF154, PvAP2-ERF155, PvAP2-ERF159, PvAP2-ERF160, PvAP2-ERF17, PvAP2-ERF38, PvAP2-ERF71, PvAP2-ERF85, PvAP2-ERF99</italic>) were not detected in reads belong to either root and leaf tissues based on normalized RPKM values. A total of 78 <italic>PvAP2-ERF </italic>genes were differentially expressed in at least one tissue. Among the 180 <italic>PvAP2-ERFs</italic>, 35 <italic>PvAP2-ERF</italic>s including <italic>PvAP2-ERF27, PvAP2-ERF1, PvAP2-ERF119, PvAP2-ERF126, PvAP2-ERF69, PvAP2-ERF111 and PvAP2-ERF3 </italic>were differentially upregulated in leaf tissue. In root tissue, a total of 10 <italic>PvAP2-ERFs </italic>including <italic>PvAP2-ERF150, PvAP2-ERF72, PvAP2-ERF119, PvAP2-ERF96, PvAP2-ERF53 </italic>showed higher expression pattern. Interestingly, six of total <italic>PvAP2-ERF</italic>s (<italic>PvAP2-ERF</italic>69, <italic>PvAP2-ERF</italic>119, <italic>PvAP2-ERF</italic>100, <italic>PvAP2-ERF</italic>53, <italic>PvAP2-ERF</italic>70 and <italic>PvAP2-ERF</italic>177) were highly expressed both in leaf and root tissues. Genome-wide expression analysis also showed that there were a total of 68 up-regulated <italic>PvAP2-ERF</italic>s and 56 down-regulated <italic>PvAP2-ERF</italic>s in leaf tissues after salt stress (Table S8). Likewise, there were 51 up-regulated <italic>PvAP2-ERF</italic>s genes and 84 down-regulated <italic>PvAP2-ERF</italic>s genes in root tissues. An expression profile of all identified <italic>PvAP2-ERF</italic>s genes was shown as heat map in Figure 6<xref ref-type="fig" rid="F6">(Fig. 6)</xref>.</p></sec><sec><title>Gene expression levels of salt responsive AP2-ERFs transcription factor family genes</title><p>Expression levels of 9 PvAP2-ERFs family members (PvAP2-ERF100, PvAP2-ERF111, PvAP2-ERF119, PvAP2-ERF177, PvAP2-ERF69, PvAP2-ERF70, PvAP2-ERF72, PvAP2-ERF150, PvAP2-ERF53) in salt-stressed leaf and root tissues were determined. qRT-PCR results revealed that seven of the nine selected genes were up-regulated in common bean leaf tissues after salt treatment (Figure 7<xref ref-type="fig" rid="F7">(Fig. 7)</xref>). Among them, PvAP2-ERF111, PvAP2-ERF119, PvAP2-ERF72 and PvAP2-ERF150 showed relatively higher expression level when compared to control sample. Therefore, we validated 7 PvAP2-ERFs in leaf tissue by using qRT-PCR. Likewise, the expression of most of genes selected after RNA-seq analysis were also validated with qRT-PCR in root tissue. According to these results, PvAP2-ERF111, PvAP2-ERF119, PvAP2-ERF72 and PvAP2-ERF150 showed two fold change in expression pattern when compared to expression level of the control tissue. Three of the selected PvAP2-ERFs (PvAP2-ERF100, PvAP2-ERF69 and PvAP2-ERF177) showed down-regulated gene expression pattern after salt treatment in root tissues. These results indicated that PvAP2-ERF genes were generally affected by salt stress, indicating, that they are involved in salt stress signal transduction by a positive regulation pathway. </p></sec></sec><sec sec-type="conclusions"><title>Conclusion</title><p>The AP2-ERF TFs have crucial roles in regulation of different plant processes such as growth, development and stress responses. Due to the theirs important functions, they have been subjected to comprehensive analysis in different plants. The present study is the first report related with identification and characterization of the AP2-ERF transcription factors in common bean. A total of 180 putative common bean genes belonging to AP2-ERF superfamily were identified by using bioinformatics tools. Additionally, the characterization of genomic structures, chromosomal locations, promoter analysis, protein interaction, sequence homologies of all common bean <italic>AP2-ERF</italic> TF genes were also undertaken. The expression analysis of selected <italic>AP2-ERF</italic> genes was conducted using qRT-PCR and previously uploaded RNAseq data in root and leaf tissues exposed to salt stress. </p><p>Results of the present extensive study would assist to understanding of roles of AP2-ERF family members in salt tolerant common bean cultivar and may also provide functional gene resources for genetic engineering approaches.</p></sec><sec><title>Acknowledgements</title><p>This research was supported by a Research Fund of Ondokuz Mayıs University (PYO.ZRT.1902.13.001). The authors would also like to thank Dr. Yıldız Daşgan for providing the seed of salt resistant common bean cultivar.</p></sec><sec><title>Declaration of interest</title><p>The authors report no conflicts of interest.</p></sec><sec sec-type="supplementary-material"><title>Supplementary Material</title><supplementary-material content-type="local-data" id="SD1"><caption><title>Supplementary material</title></caption><media mimetype="application" mime-subtype="application/pdf" xlink:href="EXCLI-14-1187-s-001.pdf" xlink:type="simple" id="d36e1229" position="anchor"></media></supplementary-material></sec></body><back><ref-list><ref id="R1"><label>1</label><element-citation publication-type="journal"><person-group><name><surname>Baloglu</surname><given-names>MC</given-names></name></person-group><article-title>Genome-wide in silico identification and comparison of Growth Regulating Factor (GRF) genes in Cucurbitaceae family</article-title><source>Plant Omics</source><year>2014</year><volume>7</volume><fpage>260</fpage><lpage>270</lpage></element-citation></ref><ref id="R2"><label>2</label><element-citation publication-type="journal"><person-group><name><surname>Baloglu</surname><given-names>MC</given-names></name><name><surname>Eldem</surname><given-names>V</given-names></name><name><surname>Hajyzadeh</surname><given-names>M</given-names></name><name><surname>Unver</surname><given-names>T</given-names></name></person-group><article-title>Genome-wide analysis of the bzip transcription factors in cucumber</article-title><source>Plos One</source><year>2014</year><volume>9</volume><fpage>e96014</fpage><pub-id pub-id-type="pmid">24760072</pub-id></element-citation></ref><ref id="R3"><label>3</label><element-citation publication-type="journal"><person-group><name><surname>Berman</surname><given-names>HM</given-names></name><name><surname>Westbrook</surname><given-names>J</given-names></name><name><surname>Feng</surname><given-names>Z</given-names></name><name><surname>Gilliland</surname><given-names>G</given-names></name><name><surname>Bhat</surname><given-names>TN</given-names></name><name><surname>Weissig</surname><given-names>H</given-names></name><etal></etal></person-group><article-title>The Protein Data Bank</article-title><source>Nucleic Acids Res</source><year>2000</year><volume>28</volume><fpage>235</fpage><lpage>242</lpage><pub-id pub-id-type="pmid">10592235</pub-id></element-citation></ref><ref id="R4"><label>4</label><element-citation publication-type="journal"><person-group><name><surname>Borges</surname><given-names>A</given-names></name><name><surname>Tsai</surname><given-names>SM</given-names></name><name><surname>Caldas</surname><given-names>DGG</given-names></name></person-group><article-title>Validation of reference genes for RT-qPCR normalization in common bean during biotic and abiotic stresses</article-title><source>Plant Cell Reports</source><year>2012</year><volume>31</volume><fpage>827</fpage><lpage>838</lpage><pub-id pub-id-type="pmid">22193338</pub-id></element-citation></ref><ref id="R5"><label>5</label><element-citation publication-type="journal"><person-group><name><surname>Bouaziz</surname><given-names>D</given-names></name><name><surname>Charfeddine</surname><given-names>M</given-names></name><name><surname>Jbir</surname><given-names>R</given-names></name><name><surname>Saidi</surname><given-names>M</given-names></name><name><surname>Pirrello</surname><given-names>J</given-names></name><name><surname>Charfeddine</surname><given-names>S</given-names></name><etal></etal></person-group><article-title>Identification and functional characterization of ten AP2/ERF genes in potato</article-title><source>Plant Cell Tiss Organ Cult</source><year>2015</year><fpage>1</fpage><lpage>18</lpage></element-citation></ref><ref id="R6"><label>6</label><element-citation publication-type="journal"><person-group><name><surname>Broughton</surname><given-names>WJ</given-names></name><name><surname>Hernandez</surname><given-names>G</given-names></name><name><surname>Blair</surname><given-names>M</given-names></name><name><surname>Beebe</surname><given-names>S</given-names></name><name><surname>Gepts</surname><given-names>P</given-names></name><name><surname>Vanderleyden</surname><given-names>J</given-names></name></person-group><article-title>Beans (Phaseolus spp.) - model food legumes</article-title><source>Plant Soil</source><year>2003</year><volume>252</volume><fpage>55</fpage><lpage>128</lpage></element-citation></ref><ref id="R7"><label>7</label><element-citation publication-type="journal"><person-group><name><surname>Cao</surname><given-names>PB</given-names></name><name><surname>Azar</surname><given-names>S</given-names></name><name><surname>SanClemente</surname><given-names>H</given-names></name><name><surname>Mounet</surname><given-names>F</given-names></name><name><surname>Dunand</surname><given-names>C</given-names></name><name><surname>Marque</surname><given-names>G</given-names></name><etal></etal></person-group><article-title>Genome-wide analysis of the AP2/ERF family in Eucalyptus grandis: an intriguing over-representation of stress-responsive DREB1/CBF Genes</article-title><source>Plos One</source><year>2015</year><volume>10</volume><fpage>e0121041</fpage><pub-id pub-id-type="pmid">25849589</pub-id></element-citation></ref><ref id="R8"><label>8</label><element-citation publication-type="journal"><person-group><name><surname>Caraux</surname><given-names>G</given-names></name><name><surname>Pinloche</surname><given-names>S</given-names></name></person-group><article-title>PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order</article-title><source>Bioinformatics</source><year>2005</year><volume>21</volume><fpage>1280</fpage><lpage>1281</lpage><pub-id pub-id-type="pmid">15546938</pub-id></element-citation></ref><ref id="R9"><label>9</label><element-citation publication-type="journal"><person-group><name><surname>Charfeddine</surname><given-names>M</given-names></name><name><surname>Saïdi</surname><given-names>M</given-names></name><name><surname>Charfeddine</surname><given-names>S</given-names></name><name><surname>Hammami</surname><given-names>A</given-names></name><name><surname>Gargouri Bouzid</surname><given-names>R</given-names></name></person-group><article-title>Genome-wide analysis and expression profiling of the ERF transcription factor family in potato (Solanum tuberosum L.)</article-title><source>Mol Biotechnol</source><year>2015</year><volume>57</volume><fpage>348</fpage><lpage>358</lpage><pub-id pub-id-type="pmid">25491236</pub-id></element-citation></ref><ref id="R10"><label>10</label><element-citation publication-type="journal"><person-group><name><surname>Chinnusamy</surname><given-names>V</given-names></name><name><surname>Jagendorf</surname><given-names>A</given-names></name><name><surname>Zhu</surname><given-names>JK</given-names></name></person-group><article-title>Understanding and improving salt tolerance in plants</article-title><source>Crop Sci</source><year>2005</year><volume>45</volume><fpage>437</fpage><lpage>448</lpage></element-citation></ref><ref id="R11"><label>11</label><element-citation publication-type="journal"><person-group><name><surname>Conesa</surname><given-names>A</given-names></name><name><surname>Götz</surname><given-names>S</given-names></name><name><surname>García-Gómez</surname><given-names>JM</given-names></name><name><surname>Terol</surname><given-names>J</given-names></name><name><surname>Talón</surname><given-names>M</given-names></name><name><surname>Robles</surname><given-names>M</given-names></name></person-group><article-title>Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research</article-title><source>Bioinformatics</source><year>2005</year><volume>21</volume><fpage>3674</fpage><lpage>3676</lpage><pub-id pub-id-type="pmid">16081474</pub-id></element-citation></ref><ref id="R12"><label>12</label><element-citation publication-type="journal"><person-group><name><surname>Contreras-Cubas</surname><given-names>C</given-names></name><name><surname>Rabanal</surname><given-names>F</given-names></name><name><surname>Arenas-Huertero</surname><given-names>C</given-names></name><name><surname>Ortiz</surname><given-names>M</given-names></name><name><surname>Covarrubias</surname><given-names>A</given-names></name><name><surname>Reyes</surname><given-names>J</given-names></name></person-group><article-title>The Phaseolus vulgaris miR159a precursor encodes a second differentially expressed microRNA</article-title><source>Plant Mol Biol</source><year>2012</year><volume>80</volume><fpage>103</fpage><lpage>115</lpage><pub-id pub-id-type="pmid">22083131</pub-id></element-citation></ref><ref id="R13"><label>13</label><element-citation publication-type="journal"><person-group><name><surname>Dasgan</surname><given-names>HY</given-names></name><name><surname>Koc</surname><given-names>S</given-names></name></person-group><article-title>Evaluation of salt tolerance in common bean genotypes by ion regulation and searching for screening parameters</article-title><source>J Food Agric Environ</source><year>2009</year><volume>7</volume><fpage>363</fpage><lpage>372</lpage></element-citation></ref><ref id="R14"><label>14</label><element-citation publication-type="journal"><person-group><name><surname>Du</surname><given-names>H</given-names></name><name><surname>Huang</surname><given-names>M</given-names></name><name><surname>Zhang</surname><given-names>Z</given-names></name><name><surname>Cheng</surname><given-names>S</given-names></name></person-group><article-title>Genome-wide analysis of the AP2/ERF gene family in maize waterlogging stress response</article-title><source>Euphytica</source><year>2014</year><volume>198</volume><fpage>115</fpage><lpage>126</lpage></element-citation></ref><ref id="R15"><label>15</label><element-citation publication-type="journal"><person-group><name><surname>Eldem</surname><given-names>V</given-names></name><name><surname>Okay</surname><given-names>S</given-names></name><name><surname>Unver</surname><given-names>T</given-names></name></person-group><article-title>Plant microRNAs: new players in functional genomics</article-title><source>Turk J Agric For</source><year>2013</year><volume>37</volume><fpage>1</fpage><lpage>21</lpage></element-citation></ref><ref id="R16"><label>16</label><element-citation publication-type="journal"><person-group><name><surname>Fang</surname><given-names>Y</given-names></name><name><surname>You</surname><given-names>J</given-names></name><name><surname>Xie</surname><given-names>K</given-names></name><name><surname>Xie</surname><given-names>W</given-names></name><name><surname>Xiong</surname><given-names>L</given-names></name></person-group><article-title>Systematic sequence analysis and identification of tissue-specific or stress-responsive genes of NAC transcription factor family in rice</article-title><source>Mol Genet Genomics</source><year>2008</year><volume>280</volume><fpage>547</fpage><lpage>563</lpage><pub-id pub-id-type="pmid">18813954</pub-id></element-citation></ref><ref id="R17"><label>17</label><element-citation publication-type="confproc"><collab>FAO, Food and Agriculture Organization of the United Nations</collab><article-title>FAOstat, Statistical Databases, last updated 15 Aug 2014</article-title><year>2014</year><conf-name>www.fao.org</conf-name></element-citation></ref><ref id="R18"><label>18</label><element-citation publication-type="journal"><person-group><name><surname>Formey</surname><given-names>D</given-names></name><name><surname>Iniguez</surname><given-names>L</given-names></name><name><surname>Pelaez</surname><given-names>P</given-names></name><name><surname>Li</surname><given-names>Y-F</given-names></name><name><surname>Sunkar</surname><given-names>R</given-names></name><name><surname>Sanchez</surname><given-names>F</given-names></name><etal></etal></person-group><article-title>Genome-wide identification of the Phaseolus vulgaris sRNAome using small RNA and degradome sequencing</article-title><source>BMC Genomics</source><year>2015</year><volume>16</volume><fpage>423</fpage><pub-id pub-id-type="pmid">26059339</pub-id></element-citation></ref><ref id="R19"><label>19</label><element-citation publication-type="journal"><person-group><name><surname>Girardi</surname><given-names>CL</given-names></name><name><surname>Rombaldi</surname><given-names>CV</given-names></name><name><surname>Dal Cero</surname><given-names>J</given-names></name><name><surname>Nobile</surname><given-names>PM</given-names></name><name><surname>Laurens</surname><given-names>F</given-names></name><name><surname>Bouzayen</surname><given-names>M</given-names></name><etal></etal></person-group><article-title>Genome-wide analysis of the AP2/ERF superfamily in apple and transcriptional evidence of ERF involvement in scab pathogenesis</article-title><source>Scientia Horticulturae</source><year>2013</year><volume>151</volume><fpage>112</fpage><lpage>121</lpage></element-citation></ref><ref id="R20"><label>20</label><element-citation publication-type="journal"><person-group><name><surname>Goodstein</surname><given-names>DM</given-names></name><name><surname>Shu</surname><given-names>S</given-names></name><name><surname>Howson</surname><given-names>R</given-names></name><name><surname>Neupane</surname><given-names>R</given-names></name><name><surname>Hayes</surname><given-names>RD</given-names></name><name><surname>Fazo</surname><given-names>J</given-names></name><etal></etal></person-group><article-title>Phytozome: a comparative platform for green plant genomics</article-title><source>Nucleic Acids Res</source><year>2012</year><volume>40</volume><fpage>D1178</fpage><lpage>D1186</lpage><pub-id pub-id-type="pmid">22110026</pub-id></element-citation></ref><ref id="R21"><label>21</label><element-citation publication-type="journal"><person-group><name><surname>Hiz</surname><given-names>MC</given-names></name><name><surname>Canher</surname><given-names>B</given-names></name><name><surname>Niron</surname><given-names>H</given-names></name><name><surname>Turet</surname><given-names>M</given-names></name></person-group><article-title>Transcriptome analysis of salt tolerant common bean (phaseolus vulgaris l.) under saline conditions</article-title><source>PloS One</source><year>2014</year><volume>9</volume><fpage>e92598</fpage><pub-id pub-id-type="pmid">24651267</pub-id></element-citation></ref><ref id="R22"><label>22</label><element-citation publication-type="journal"><person-group><name><surname>Hoagland</surname><given-names>DR</given-names></name><name><surname>Arnon</surname><given-names>DI</given-names></name></person-group><article-title>The water-culture method for growing plants without soil</article-title><source>Circular California Agricultural Experiment Station</source><year>1950</year><volume>347</volume><fpage>1</fpage><lpage>32</lpage></element-citation></ref><ref id="R23"><label>23</label><element-citation publication-type="journal"><person-group><name><surname>Hu</surname><given-names>B</given-names></name><name><surname>Jin</surname><given-names>J</given-names></name><name><surname>Guo</surname><given-names>A-Y</given-names></name><name><surname>Zhang</surname><given-names>H</given-names></name><name><surname>Luo</surname><given-names>J</given-names></name><name><surname>Gao</surname><given-names>G</given-names></name></person-group><article-title>GSDS 2.0: an upgraded gene feature visualization server</article-title><source>Bioinformatics</source><year>2015</year><volume>31</volume><fpage>1296</fpage><lpage>1297</lpage><pub-id pub-id-type="pmid">25504850</pub-id></element-citation></ref><ref id="R24"><label>24</label><element-citation publication-type="journal"><person-group><name><surname>Hu</surname><given-names>L</given-names></name><name><surname>Liu</surname><given-names>S</given-names></name></person-group><article-title>Genome-wide identification and phylogenetic analysis of the ERF gene family in cucumbers</article-title><source>Genet Mol Biol</source><year>2011</year><volume>34</volume><fpage>624</fpage><lpage>633</lpage><pub-id pub-id-type="pmid">22215967</pub-id></element-citation></ref><ref id="R25"><label>25</label><element-citation publication-type="journal"><person-group><name><surname>Ito</surname><given-names>TM</given-names></name><name><surname>Polido</surname><given-names>PB</given-names></name><name><surname>Rampim</surname><given-names>MC</given-names></name><name><surname>Kaschuk</surname><given-names>G</given-names></name><name><surname>Souza</surname><given-names>SG</given-names></name></person-group><article-title>Genome-wide identification and phylogenetic analysis of the AP2/ERF gene superfamily in sweet orange (Citrus sinensis)</article-title><source>Genet Mol Res</source><year>2014</year><volume>13</volume><fpage>7839</fpage><lpage>7851</lpage><pub-id pub-id-type="pmid">25299098</pub-id></element-citation></ref><ref id="R26"><label>26</label><element-citation publication-type="journal"><person-group><name><surname>Jin</surname><given-names>J</given-names></name><name><surname>Zhang</surname><given-names>H</given-names></name><name><surname>Kong</surname><given-names>L</given-names></name><name><surname>Gao</surname><given-names>G</given-names></name><name><surname>Luo</surname><given-names>J</given-names></name></person-group><article-title>PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors</article-title><source>Nucleic Acids Res</source><year>2014</year><volume>42</volume><fpage>D1182</fpage><lpage>D1187</lpage><pub-id pub-id-type="pmid">24174544</pub-id></element-citation></ref><ref id="R27"><label>27</label><element-citation publication-type="journal"><person-group><name><surname>Kalavacharla</surname><given-names>V</given-names></name><name><surname>Liu</surname><given-names>Z</given-names></name><name><surname>Meyers</surname><given-names>B</given-names></name><name><surname>Thimmapuram</surname><given-names>J</given-names></name><name><surname>Melmaiee</surname><given-names>K</given-names></name></person-group><article-title>Identification and analysis of common bean (Phaseolus vulgaris L.) transcriptomes by massively parallel pyrosequencing</article-title><source>BMC Plant Biol</source><year>2011</year><volume>11</volume><fpage>135</fpage><pub-id pub-id-type="pmid">21985325</pub-id></element-citation></ref><ref id="R28"><label>28</label><element-citation publication-type="journal"><person-group><name><surname>Kavas</surname><given-names>M</given-names></name><name><surname>Baloğlu</surname><given-names>M</given-names></name><name><surname>Atabay</surname><given-names>E</given-names></name><name><surname>Ziplar</surname><given-names>U</given-names></name><name><surname>Daşgan</surname><given-names>H</given-names></name><name><surname>Ünver</surname><given-names>T</given-names></name></person-group><article-title>Genome-wide characterization and expression analysis of common bean bHLH transcription factors in response to excess salt concentration. Mol Genet Genomics. 2015</article-title><source>Mol Genet Genomics</source><volume>2015</volume><fpage>Epub ahead of print</fpage></element-citation></ref><ref id="R29"><label>29</label><element-citation publication-type="journal"><person-group><name><surname>Kelley</surname><given-names>LA</given-names></name><name><surname>Sternberg</surname><given-names>MJE</given-names></name></person-group><article-title>Protein structure prediction on the Web: a case study using the Phyre server</article-title><source>Nat Protocols</source><year>2009</year><volume>4</volume><fpage>363</fpage><lpage>371</lpage><pub-id pub-id-type="pmid">19247286</pub-id></element-citation></ref><ref id="R30"><label>30</label><element-citation publication-type="journal"><person-group><name><surname>Lata</surname><given-names>C</given-names></name><name><surname>Mishra</surname><given-names>AK</given-names></name><name><surname>Muthamilarasan</surname><given-names>M</given-names></name><name><surname>Bonthala</surname><given-names>VS</given-names></name><name><surname>Khan</surname><given-names>Y</given-names></name><name><surname>Prasad</surname><given-names>M</given-names></name></person-group><article-title>Genome-wide investigation and expression profiling of AP2/ERF transcription factor superfamily in Foxtail Millet (Setaria italica L.)</article-title><source>PLoS ONE</source><year>2014</year><volume>9</volume><issue>11</issue><fpage>e113092</fpage><pub-id pub-id-type="pmid">25409524</pub-id></element-citation></ref><ref id="R31"><label>31</label><element-citation publication-type="journal"><person-group><name><surname>Le</surname><given-names>DT</given-names></name><name><surname>Nishiyama</surname><given-names>R</given-names></name><name><surname>Watanabe</surname><given-names>Y</given-names></name><name><surname>Vankova</surname><given-names>R</given-names></name><name><surname>Tanaka</surname><given-names>M</given-names></name><name><surname>Seki</surname><given-names>M</given-names></name><etal></etal></person-group><article-title>Identification and expression analysis of cytokinin metabolic genes in soybean under normal and drought conditions in relation to cytokinin levels</article-title><source>PLoS ONE</source><year>2012</year><volume>7</volume><issue>8</issue><fpage>e42411</fpage><pub-id pub-id-type="pmid">22900018</pub-id></element-citation></ref><ref id="R32"><label>32</label><element-citation publication-type="journal"><person-group><name><surname>Letunic</surname><given-names>I</given-names></name><name><surname>Bork</surname><given-names>P</given-names></name></person-group><article-title>Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation</article-title><source>Bioinformatics</source><year>2007</year><volume>23</volume><fpage>127</fpage><lpage>128</lpage><pub-id pub-id-type="pmid">17050570</pub-id></element-citation></ref><ref id="R33"><label>33</label><element-citation publication-type="journal"><person-group><name><surname>Li</surname><given-names>M-Y</given-names></name><name><surname>Xu</surname><given-names>Z-S</given-names></name><name><surname>Huang</surname><given-names>Y</given-names></name><name><surname>Tian</surname><given-names>C</given-names></name><name><surname>Wang</surname><given-names>F</given-names></name><name><surname>Xiong</surname><given-names>A-S</given-names></name></person-group><article-title>Genome-wide analysis of AP2/ERF transcription factors in carrot (Daucus carota L.) reveals evolution and expression profiles under abiotic stress</article-title><source>Mol Genet Genomics</source><year>2015</year><volume>290</volume><fpage>2049</fpage><lpage>2061</lpage><pub-id pub-id-type="pmid">25971861</pub-id></element-citation></ref><ref id="R34"><label>34</label><element-citation publication-type="journal"><person-group><name><surname>Licausi</surname><given-names>F</given-names></name><name><surname>Giorgi</surname><given-names>FM</given-names></name><name><surname>Zenoni</surname><given-names>S</given-names></name><name><surname>Osti</surname><given-names>F</given-names></name><name><surname>Pezzotti</surname><given-names>M</given-names></name><name><surname>Perata</surname><given-names>P</given-names></name></person-group><article-title>Genomic and transcriptomic analysis of the AP2/ERF superfamily in Vitis vinifera</article-title><source>BMC Genomics</source><year>2010</year><volume>11</volume><fpage>719</fpage><pub-id pub-id-type="pmid">21171999</pub-id></element-citation></ref><ref id="R35"><label>35</label><element-citation publication-type="journal"><person-group><name><surname>Liu</surname><given-names>Z</given-names></name><name><surname>Crampton</surname><given-names>M</given-names></name><name><surname>Todd</surname><given-names>A</given-names></name><name><surname>Kalavacharla</surname><given-names>V</given-names></name></person-group><article-title>Identification of expressed resistance gene-like sequences by data mining in 454-derived transcriptomic sequences of common bean (Phaseolus vulgaris L.)</article-title><source>BMC Plant Biol</source><year>2012</year><volume>12</volume><fpage>42</fpage><pub-id pub-id-type="pmid">22443214</pub-id></element-citation></ref><ref id="R36"><label>36</label><element-citation publication-type="journal"><person-group><name><surname>Liu</surname><given-names>Z</given-names></name><name><surname>Kong</surname><given-names>L</given-names></name><name><surname>Zhang</surname><given-names>M</given-names></name><name><surname>Lv</surname><given-names>Y</given-names></name><name><surname>Liu</surname><given-names>Y</given-names></name><name><surname>Zou</surname><given-names>M</given-names></name><etal></etal></person-group><article-title>Genome-wide identification, phylogeny, evolution and expression patterns of AP2/ERF Genes and cytokinin response factors in Brassica rapa ssp. pekinensis</article-title><source>PLoS ONE</source><year>2013</year><volume>8</volume><issue>12</issue><fpage>e83444</fpage><pub-id pub-id-type="pmid">24386201</pub-id></element-citation></ref><ref id="R37"><label>37</label><element-citation publication-type="journal"><person-group><name><surname>Livak</surname><given-names>KJ</given-names></name><name><surname>Schmittgen</surname><given-names>TD</given-names></name></person-group><article-title>Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method</article-title><source>Methods</source><year>2001</year><volume>25</volume><fpage>402</fpage><lpage>408</lpage><pub-id pub-id-type="pmid">11846609</pub-id></element-citation></ref><ref id="R38"><label>38</label><element-citation publication-type="journal"><person-group><name><surname>Ma</surname><given-names>Y</given-names></name><name><surname>Zhang</surname><given-names>F</given-names></name><name><surname>Bade</surname><given-names>R</given-names></name><name><surname>Daxibater</surname><given-names>A</given-names></name><name><surname>Men</surname><given-names>Z</given-names></name><name><surname>Hasi</surname><given-names>A</given-names></name></person-group><article-title>Genome-wide identification and phylogenetic analysis of the ERF gene family in melon</article-title><source>J Plant Growth Regul</source><year>2015</year><volume>34</volume><fpage>66</fpage><lpage>77</lpage></element-citation></ref><ref id="R39"><label>39</label><element-citation publication-type="journal"><person-group><name><surname>Massa</surname><given-names>AN</given-names></name><name><surname>Childs</surname><given-names>KL</given-names></name><name><surname>Lin</surname><given-names>HN</given-names></name><name><surname>Bryan</surname><given-names>GJ</given-names></name><name><surname>Giuliano</surname><given-names>G</given-names></name><name><surname>Buell</surname><given-names>CR</given-names></name></person-group><article-title>The transcriptome of the reference potato genome solanum tuberosum group Phureja Clone DM1-3 516R44</article-title><source>Plos ONE</source><year>2011</year><volume>6</volume><issue>10</issue><fpage>e26801</fpage><pub-id pub-id-type="pmid">22046362</pub-id></element-citation></ref><ref id="R40"><label>40</label><element-citation publication-type="journal"><person-group><name><surname>Mizoi</surname><given-names>J</given-names></name><name><surname>Shinozaki</surname><given-names>K</given-names></name><name><surname>Yamaguchi-Shinozaki</surname><given-names>K</given-names></name></person-group><article-title>AP2/ERF family transcription factors in plant abiotic stress responses</article-title><source>Biochim Biophys Acta</source><year>2012</year><volume>1819</volume><fpage>86</fpage><lpage>96</lpage><pub-id pub-id-type="pmid">21867785</pub-id></element-citation></ref><ref id="R41"><label>41</label><element-citation publication-type="journal"><person-group><name><surname>Mortazavi</surname><given-names>A</given-names></name><name><surname>Williams</surname><given-names>BA</given-names></name><name><surname>McCue</surname><given-names>K</given-names></name><name><surname>Schaeffer</surname><given-names>L</given-names></name><name><surname>Wold</surname><given-names>B</given-names></name></person-group><article-title>Mapping and quantifying mammalian transcriptomes by RNA-Seq</article-title><source>Nat Meth</source><year>2008</year><volume>5</volume><fpage>621</fpage><lpage>628</lpage></element-citation></ref><ref id="R42"><label>42</label><element-citation publication-type="journal"><person-group><name><surname>Mousavi</surname><given-names>A</given-names></name><name><surname>Hotta</surname><given-names>Y</given-names></name></person-group><article-title>Glycine-rich proteins</article-title><source>Appl Biochem Biotechnol</source><year>2005</year><volume>120</volume><fpage>169</fpage><lpage>174</lpage><pub-id pub-id-type="pmid">15767691</pub-id></element-citation></ref><ref id="R43"><label>43</label><element-citation publication-type="journal"><person-group><name><surname>Munns</surname><given-names>R</given-names></name></person-group><article-title>Comparative physiology of salt and water stress</article-title><source>Plant Cell Environ</source><year>2002</year><volume>25</volume><fpage>239</fpage><lpage>250</lpage><pub-id pub-id-type="pmid">11841667</pub-id></element-citation></ref><ref id="R44"><label>44</label><element-citation publication-type="journal"><person-group><name><surname>Nakano</surname><given-names>T</given-names></name><name><surname>Suzuki</surname><given-names>K</given-names></name><name><surname>Fujimura</surname><given-names>T</given-names></name><name><surname>Shinshi</surname><given-names>H</given-names></name></person-group><article-title>Genome-wide analysis of the ERF gene family in Arabidopsis and rice</article-title><source>Plant Physiol</source><year>2006</year><volume>140</volume><fpage>411</fpage><lpage>432</lpage><pub-id pub-id-type="pmid">16407444</pub-id></element-citation></ref><ref id="R45"><label>45</label><element-citation publication-type="journal"><person-group><name><surname>Nova-Franco</surname><given-names>B</given-names></name><name><surname>Íñiguez</surname><given-names>LP</given-names></name><name><surname>Valdés-López</surname><given-names>O</given-names></name><name><surname>Alvarado-Affantranger</surname><given-names>X</given-names></name><name><surname>Leija</surname><given-names>A</given-names></name><name><surname>Fuentes</surname><given-names>SI</given-names></name><etal></etal></person-group><article-title>The miR172c-AP2-1 Node as a key regulator of the common bean - Rhizobia Nitrogen fixation symbiosis</article-title><source>Plant Physiol</source><year>2015</year><volume>168</volume><fpage>273</fpage><lpage>291</lpage><pub-id pub-id-type="pmid">25739700</pub-id></element-citation></ref><ref id="R46"><label>46</label><element-citation publication-type="journal"><person-group><name><surname>Parida</surname><given-names>AK</given-names></name><name><surname>Das</surname><given-names>AB</given-names></name></person-group><article-title>Salt tolerance and salinity effects on plants: a review</article-title><source>Ecotox Environ Safe</source><year>2005</year><volume>60</volume><fpage>324</fpage><lpage>349</lpage></element-citation></ref><ref id="R47"><label>47</label><element-citation publication-type="journal"><person-group><name><surname>Qin</surname><given-names>F</given-names></name><name><surname>Shinozaki</surname><given-names>K</given-names></name><name><surname>Yamaguchi-Shinozaki</surname><given-names>K</given-names></name></person-group><article-title>Achievements and challenges in understanding plant abiotic stress responses and tolerance</article-title><source>Plant Cell Physiol</source><year>2011</year><volume>52</volume><fpage>1569</fpage><lpage>1582</lpage><pub-id pub-id-type="pmid">21828105</pub-id></element-citation></ref><ref id="R48"><label>48</label><element-citation publication-type="journal"><person-group><name><surname>Rao</surname><given-names>G</given-names></name><name><surname>Sui</surname><given-names>J</given-names></name><name><surname>Zeng</surname><given-names>Y</given-names></name><name><surname>He</surname><given-names>C</given-names></name><name><surname>Zhang</surname><given-names>J</given-names></name></person-group><article-title>Genome-wide analysis of the AP2/ERF gene family in Salix arbutifolia</article-title><source>FEBS Open Bio</source><year>2015</year><volume>5</volume><fpage>132</fpage><lpage>137</lpage></element-citation></ref><ref id="R49"><label>49</label><element-citation publication-type="journal"><person-group><name><surname>Riano-Pachón</surname><given-names>DM</given-names></name><name><surname>Ruzicic</surname><given-names>S</given-names></name><name><surname>Dreyer</surname><given-names>I</given-names></name><name><surname>Mueller-Roeber</surname><given-names>B</given-names></name></person-group><article-title>PlnTFDB: an integrative plant transcription factor database</article-title><source>BMC Bioinformatics</source><year>2007</year><volume>8</volume><fpage>42</fpage><pub-id pub-id-type="pmid">17286856</pub-id></element-citation></ref><ref id="R50"><label>50</label><element-citation publication-type="journal"><person-group><name><surname>Sakuma</surname><given-names>Y</given-names></name><name><surname>Liu</surname><given-names>Q</given-names></name><name><surname>Dubouzet</surname><given-names>JG</given-names></name><name><surname>Abe</surname><given-names>H</given-names></name><name><surname>Shinozaki</surname><given-names>K</given-names></name><name><surname>Yamaguchi-Shinozaki</surname><given-names>K</given-names></name></person-group><article-title>DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration- and cold-inducible gene expression</article-title><source>Biochem Biophys Res Commun</source><year>2002</year><volume>290</volume><fpage>998</fpage><lpage>1009</lpage><pub-id pub-id-type="pmid">11798174</pub-id></element-citation></ref><ref id="R51"><label>51</label><element-citation publication-type="journal"><person-group><name><surname>Schmutz</surname><given-names>J</given-names></name><name><surname>McClean</surname><given-names>PE</given-names></name><name><surname>Mamidi</surname><given-names>S</given-names></name><name><surname>Wu</surname><given-names>GA</given-names></name><name><surname>Cannon</surname><given-names>SB</given-names></name><name><surname>Grimwood</surname><given-names>J</given-names></name><etal></etal></person-group><article-title>A reference genome for common bean and genome-wide analysis of dual domestications</article-title><source>Nat Genet</source><year>2014</year><volume>46</volume><fpage>707</fpage><lpage>713</lpage><pub-id pub-id-type="pmid">24908249</pub-id></element-citation></ref><ref id="R52"><label>52</label><element-citation publication-type="journal"><person-group><name><surname>Sharma</surname><given-names>MK</given-names></name><name><surname>Kumar</surname><given-names>R</given-names></name><name><surname>Solanke</surname><given-names>AU</given-names></name><name><surname>Sharma</surname><given-names>R</given-names></name><name><surname>Tyagi</surname><given-names>AK</given-names></name><name><surname>Sharma</surname><given-names>AK</given-names></name></person-group><article-title>Identification, phylogeny, and transcript profiling of ERF family genes during development and abiotic stress treatments in tomato</article-title><source>Mol Genet Genomics</source><year>2010</year><volume>284</volume><fpage>455</fpage><lpage>475</lpage><pub-id pub-id-type="pmid">20922546</pub-id></element-citation></ref><ref id="R53"><label>53</label><element-citation publication-type="journal"><person-group><name><surname>Shiu</surname><given-names>SH</given-names></name><name><surname>Bleecker</surname><given-names>AB</given-names></name></person-group><article-title>Expansion of the receptor-like kinase/Pelle gene family and receptor-like proteins in Arabidopsis</article-title><source>Plant Physiol</source><year>2003</year><volume>132</volume><fpage>530</fpage><lpage>543</lpage><pub-id pub-id-type="pmid">12805585</pub-id></element-citation></ref><ref id="R54"><label>54</label><element-citation publication-type="journal"><person-group><name><surname>Smialowski</surname><given-names>P</given-names></name><name><surname>Doose</surname><given-names>G</given-names></name><name><surname>Torkler</surname><given-names>P</given-names></name><name><surname>Kaufmann</surname><given-names>S</given-names></name><name><surname>Frishman</surname><given-names>D</given-names></name></person-group><article-title>PROSO II – a new method for protein solubility prediction</article-title><source>FEBS J</source><year>2012</year><volume>279</volume><fpage>2192</fpage><lpage>2200</lpage><pub-id pub-id-type="pmid">22536855</pub-id></element-citation></ref><ref id="R55"><label>55</label><element-citation publication-type="journal"><person-group><name><surname>Soding</surname><given-names>J</given-names></name></person-group><article-title>Protein homology detection by HMM-HMM comparison</article-title><source>Bioinformatics</source><year>2005</year><volume>21</volume><fpage>951</fpage><lpage>960</lpage><pub-id pub-id-type="pmid">15531603</pub-id></element-citation></ref><ref id="R56"><label>56</label><element-citation publication-type="journal"><person-group><name><surname>Song</surname><given-names>XM</given-names></name><name><surname>Li</surname><given-names>Y</given-names></name><name><surname>Hou</surname><given-names>XL</given-names></name></person-group><article-title>Genome-wide analysis of the AP2/ERF transcription factor superfamily in Chinese cabbage (Brassica rapa ssp pekinensis)</article-title><source>BMC Genomics</source><year>2013</year><volume>14</volume><fpage>573</fpage><pub-id pub-id-type="pmid">23972083</pub-id></element-citation></ref><ref id="R57"><label>57</label><element-citation publication-type="journal"><person-group><name><surname>Tang</surname><given-names>HB</given-names></name><name><surname>Bowers</surname><given-names>JE</given-names></name><name><surname>Wang</surname><given-names>XY</given-names></name><name><surname>Ming</surname><given-names>R</given-names></name><name><surname>Alam</surname><given-names>M</given-names></name><name><surname>Paterson</surname><given-names>AH</given-names></name></person-group><article-title>Perspective - Synteny and collinearity in plant genomes</article-title><source>Science</source><year>2008</year><volume>320</volume><fpage>486</fpage><lpage>488</lpage><pub-id pub-id-type="pmid">18436778</pub-id></element-citation></ref><ref id="R58"><label>58</label><element-citation publication-type="journal"><person-group><name><surname>Thamilarasan</surname><given-names>SK</given-names></name><name><surname>Park</surname><given-names>JI</given-names></name><name><surname>Jung</surname><given-names>HJ</given-names></name><name><surname>Nou</surname><given-names>IS</given-names></name></person-group><article-title>Genome-wide analysis of the distribution of AP2/ERF transcription factors reveals duplication and CBFs genes elucidate their potential function in Brassica oleracea</article-title><source>BMC Genomics</source><year>2014</year><volume>15</volume><fpage>422</fpage><pub-id pub-id-type="pmid">24888752</pub-id></element-citation></ref><ref id="R59"><label>59</label><element-citation publication-type="journal"><person-group><name><surname>Wang</surname><given-names>JZ</given-names></name><name><surname>Zhou</surname><given-names>JX</given-names></name><name><surname>Zhang</surname><given-names>BL</given-names></name><name><surname>Vanitha</surname><given-names>J</given-names></name><name><surname>Ramachandran</surname><given-names>S</given-names></name><name><surname>Jiang</surname><given-names>SY</given-names></name></person-group><article-title>Genome-wide expansion and expression divergence of the basic leucine zipper transcription factors in higher plants with an emphasis on Sorghum</article-title><source>J Integr Plant Biol</source><year>2011</year><volume>53</volume><fpage>212</fpage><lpage>231</lpage><pub-id pub-id-type="pmid">21205183</pub-id></element-citation></ref><ref id="R60"><label>60</label><element-citation publication-type="journal"><person-group><name><surname>Wang</surname><given-names>YN</given-names></name><name><surname>Wang</surname><given-names>LX</given-names></name><name><surname>Zou</surname><given-names>YM</given-names></name><name><surname>Chen</surname><given-names>L</given-names></name><name><surname>Cai</surname><given-names>ZM</given-names></name><name><surname>Zhang</surname><given-names>SL</given-names></name><etal></etal></person-group><article-title>Soybean miR172c targets the repressive AP2 transcription factor NNC1 to activate ENOD40 expression and regulate nodule initiation</article-title><source>Plant Cell</source><year>2014</year><volume>26</volume><fpage>4782</fpage><lpage>4801</lpage><pub-id pub-id-type="pmid">25549672</pub-id></element-citation></ref><ref id="R61"><label>61</label><element-citation publication-type="journal"><person-group><name><surname>Wessler</surname><given-names>SR</given-names></name></person-group><article-title>Homing into the origin of the AP2 DNA binding domain</article-title><source>Trends Plant Sci</source><year>2005</year><volume>10</volume><fpage>54</fpage><lpage>56</lpage><pub-id pub-id-type="pmid">15708341</pub-id></element-citation></ref><ref id="R62"><label>62</label><element-citation publication-type="journal"><person-group><name><surname>Wu</surname><given-names>G</given-names></name><name><surname>Park</surname><given-names>MY</given-names></name><name><surname>Conway</surname><given-names>SR</given-names></name><name><surname>Wang</surname><given-names>J-W</given-names></name><name><surname>Weigel</surname><given-names>D</given-names></name><name><surname>Poethig</surname><given-names>RS</given-names></name></person-group><article-title>The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis</article-title><source>Cell</source><year>2009</year><volume>138</volume><fpage>750</fpage><lpage>759</lpage><pub-id pub-id-type="pmid">19703400</pub-id></element-citation></ref><ref id="R63"><label>63</label><element-citation publication-type="journal"><person-group><name><surname>Wu</surname><given-names>HL</given-names></name><name><surname>Lv</surname><given-names>H</given-names></name><name><surname>Li</surname><given-names>L</given-names></name><name><surname>Liu</surname><given-names>J</given-names></name><name><surname>Mu</surname><given-names>SH</given-names></name><name><surname>Li</surname><given-names>XP</given-names></name><etal></etal></person-group><article-title>Genome-wide analysis of the AP2/ERF transcription factors family and the expression patterns of DREB genes in Moso Bamboo (Phyllostachys edulis)</article-title><source>PloS One</source><year>2015</year><volume>10</volume><issue>5</issue><fpage>e0126657</fpage><pub-id pub-id-type="pmid">25985202</pub-id></element-citation></ref><ref id="R64"><label>64</label><element-citation publication-type="journal"><person-group><name><surname>Xu</surname><given-names>W</given-names></name><name><surname>Li</surname><given-names>F</given-names></name><name><surname>Ling</surname><given-names>LZ</given-names></name><name><surname>Liu</surname><given-names>AZ</given-names></name></person-group><article-title>Genome-wide survey and expression profiles of the AP2/ERF family in castor bean (Ricinus communis L.)</article-title><source>BMC Genomics</source><year>2013</year><volume>14</volume><fpage>785</fpage><pub-id pub-id-type="pmid">24225250</pub-id></element-citation></ref><ref id="R65"><label>65</label><element-citation publication-type="journal"><person-group><name><surname>Yamaguchi-Shinozaki</surname><given-names>K</given-names></name><name><surname>Shinozaki</surname><given-names>K</given-names></name></person-group><article-title>Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses</article-title><source>Annu Rev Plant Biol</source><year>2006</year><volume>57</volume><fpage>781</fpage><lpage>803</lpage><pub-id pub-id-type="pmid">16669782</pub-id></element-citation></ref><ref id="R66"><label>66</label><element-citation publication-type="journal"><person-group><name><surname>Yan</surname><given-names>Z</given-names></name><name><surname>Hossein</surname><given-names>MS</given-names></name><name><surname>Wang</surname><given-names>J</given-names></name><name><surname>Valdes-Lopez</surname><given-names>O</given-names></name><name><surname>Liang</surname><given-names>Y</given-names></name><name><surname>Libault</surname><given-names>M</given-names></name><etal></etal></person-group><article-title>miR172 regulates soybean nodulation</article-title><source>Mol Plant Microbe In</source><year>2013</year><volume>26</volume><fpage>1371</fpage><lpage>1377</lpage></element-citation></ref><ref id="R67"><label>67</label><element-citation publication-type="journal"><person-group><name><surname>Zhang</surname><given-names>Y</given-names></name></person-group><article-title>miRU: an automated plant miRNA target prediction server</article-title><source>Nucleic Acids Res</source><year>2005</year><volume>33</volume><fpage>W701</fpage><lpage>W704</lpage><pub-id pub-id-type="pmid">15980567</pub-id></element-citation></ref><ref id="R68"><label>68</label><element-citation publication-type="journal"><person-group><name><surname>Zhou</surname><given-names>ML</given-names></name><name><surname>Ma</surname><given-names>JT</given-names></name><name><surname>Pang</surname><given-names>JF</given-names></name><name><surname>Zhang</surname><given-names>ZL</given-names></name><name><surname>Tang</surname><given-names>YX</given-names></name><name><surname>Wu</surname><given-names>YM</given-names></name></person-group><article-title>Regulation of plant stress response by dehydration responsive element binding (DREB) transcription factors</article-title><source>Afr J Biotechnol</source><year>2010</year><volume>9</volume><fpage>9255</fpage><lpage>9259</lpage></element-citation></ref><ref id="R69"><label>69</label><element-citation publication-type="journal"><person-group><name><surname>Zhuang</surname><given-names>J</given-names></name><name><surname>Cai</surname><given-names>B</given-names></name><name><surname>Peng</surname><given-names>RH</given-names></name><name><surname>Zhu</surname><given-names>B</given-names></name><name><surname>Jin</surname><given-names>XF</given-names></name><name><surname>Xue</surname><given-names>Y</given-names></name><etal></etal></person-group><article-title>Genome-wide analysis of the AP2/ERF gene family in Populus trichocarpa</article-title><source>Biochem Biophys Res Commun</source><year>2008</year><volume>371</volume><fpage>468</fpage><lpage>474</lpage><pub-id pub-id-type="pmid">18442469</pub-id></element-citation></ref><ref id="R70"><label>70</label><element-citation publication-type="journal"><person-group><name><surname>Zhuang</surname><given-names>J</given-names></name><name><surname>Chen</surname><given-names>JM</given-names></name><name><surname>Yao</surname><given-names>QH</given-names></name><name><surname>Xiong</surname><given-names>F</given-names></name><name><surname>Sun</surname><given-names>CC</given-names></name><name><surname>Zhou</surname><given-names>XR</given-names></name><etal></etal></person-group><article-title>Discovery and expression profile analysis of AP2/ERF family genes from Triticum aestivum</article-title><source>Mol Biol Rep</source><year>2011</year><volume>38</volume><fpage>745</fpage><lpage>753</lpage><pub-id pub-id-type="pmid">20407836</pub-id></element-citation></ref><ref id="R71"><label>71</label><element-citation publication-type="journal"><person-group><name><surname>Zhuang</surname><given-names>J</given-names></name><name><surname>Yao</surname><given-names>QH</given-names></name><name><surname>Xiong</surname><given-names>AS</given-names></name><name><surname>Zhang</surname><given-names>JA</given-names></name></person-group><article-title>Isolation, phylogeny and expression patterns of AP2-like genes in apple (Malus x domestica Borkh)</article-title><source>Plant Mol Biol Rep</source><year>2011</year><volume>29</volume><fpage>209</fpage><lpage>216</lpage></element-citation></ref></ref-list></back><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></record>Pour manipuler ce document sous Unix (Dilib)
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