Genome-wide identification and expression profiles of AP2/ERF transcription factor family in mung bean (Vigna radiata L.)

Journal of Applied Genetics - Tập 63 Số 2 - Trang 223-236 - 2022
Chen, Honglin1, Hu, Liangliang1, Wang, Lixia1, Wang, Suhua1, Cheng, Xuzhen1
1Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China

Tóm tắt

Mung bean (Vigna radiata L. Wilczek) is an economically important grain legume crop in Asia, with high nutritional quality and potential in other parts of the world particularly arid and semiarid regions. Considering the potential adverse effects of drought, high salt, and other abiotic stresses on crop yield, significant efforts have been made to understand the underlying molecular mechanisms of tolerance to these abiotic stresses in legumes. In this study, a total of 186 putative AP2/ERF genes were identified, which were named VrERF1-186. These VrERF genes were classified into four main subfamilies according to the number of AP2 domains and sequence similarity, including 24 AP2 gene members, 81 ERF gene members, 79 DREB gene members, and 2 RAV members. VrERF genes are scattered across all 11 chromosomes and form small gene clusters on chromosomes due to segmental or tandem duplication. Promoter analysis revealed various cis-acting elements related to light, hormones, and stress responsiveness processes. The expression profiles of the VrERF genes in tissues during development and in response to abiotic stresses were assessed by transcriptome sequencing, and the selected reference genes were validated by qRT-PCR. A total of 174 VrERF genes were expressed in at least one of five tissues, while others showed distinct expression patterns in different tissues or under specific abiotic stress treatments, which indicates that VrERF genes are involved in developmental and environmental stress responses in V. radiata. In conclusion, the genome localization, genome-wide characterization, gene duplication, phylogenetic relationships, and expression pattern of VrERF genes in V. radiata were analyzed, and these results will lay the foundation for further functional analysis of these genes and improve stress tolerance to adverse conditions in plants.

Tài liệu tham khảo

citation_journal_title=Plant Cell; citation_title=Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes; citation_author=MJ Aukerman, H Sakai; citation_volume=15; citation_publication_date=2003; citation_pages=2730-2741; citation_doi=10.1105/tpc.016238; citation_id=CR1 citation_journal_title=Plant Biotechnol J; citation_title=Genome-wide dissection of AP2/ERF and HSP90 gene families in five legumes and expression profiles in chickpea and pigeonpea; citation_author=G Agarwal, V Garg, H Kudapa, D Doddaman, LT Pazhamala, AW Khan, M Thudi, SH Lee, RK Varshney; citation_volume=14; citation_publication_date=2016; citation_pages=1563-1577; citation_doi=10.1111/pbi.12520; citation_id=CR2 citation_journal_title=Nucleic Acids Res; citation_title=MEME SUITE: tools for motif discovery and searching; citation_author=TL Bailey, M Boden, FA Buske, M Frith, CE Grant, L Clementi, JY Ren, WW Li, WS Noble; citation_volume=37; citation_publication_date=2009; citation_pages=202-208; citation_doi=10.1093/nar/gkp335; citation_id=CR3 Cao D, Lin Z, Huang L, Damaris RN, Yang P (2021) Genome-wide analysis of AP2/ERF superfamily in lotus (Nelumbo nucifera) and the association between NnADAP and rhizome morphology. BMC Genomics 22:171 citation_journal_title=Plant Physiol; citation_title=Regulating the regulators: the future prospects for transcription-factor-based agricultural biotechnology products; citation_author=K Century, TL Reuber, OJ Ratcliffe; citation_volume=147; citation_publication_date=2008; citation_pages=20-29; citation_doi=10.1104/pp.108.117887; citation_id=CR5 Chankaew S, Somta P, Sorajjapinun W, Srinives P (2011) Quantitative trait loci mapping of Cercospora leaf spot resistance in mungbean, Vigna radiata (L.) Wilczek. Mol Breed 28:255–264 citation_journal_title=Mol Plant; citation_title=TBtools: an integrative toolkit developed for interactive analyses of big biological data; citation_author=C Chen, H Chen, Y Zhang, HR Thomas, MH Frank, YH He, R Xia; citation_volume=13; citation_publication_date=2020; citation_pages=1194-1202; citation_doi=10.1016/j.molp.2020.06.009; citation_id=CR7 citation_journal_title=J Integr Plant Biol; citation_title=A proximal promoter region of Arabidopsis DREB2C confers tissue-specific expression under heat stress; citation_author=H Chen, J Je, C Song, JE Hwang, CO Lim; citation_volume=54; citation_publication_date=2012; citation_pages=640-651; citation_doi=10.1111/j.1744-7909.2012.01137.x; citation_id=CR8 citation_journal_title=PLoS One; citation_title=Transcriptome sequencing of mung bean (Vigna radiate L) genes and the identification of EST-SSR markers; citation_author=H Chen, L Wang, S Wang, C Liu, MW Blair, X Cheng; citation_volume=10; citation_publication_date=2015; citation_pages=e0120273; citation_doi=10.1371/journal.pone.0120273; citation_id=CR9 citation_journal_title=J Plant Res; citation_title=VrDREB2A, a DREB-binding transcription factor from Vigna radiata, increased drought and high-salt tolerance in transgenic Arabidopsis thaliana; citation_author=H Chen, L Liu, L Wang, S Wang, X Cheng; citation_volume=129; citation_publication_date=2016; citation_pages=263-273; citation_doi=10.1007/s10265-015-0773-0; citation_id=CR10 citation_journal_title=New Phytol; citation_title=ORA47 (octadecanoid-responsive AP2/ERF-domain transcription factor 47) regulates jasmonic acid and abscisic acid biosynthesis and signaling through binding to a novel cis-element; citation_author=HY Chen, EJ Hsieh, MC Cheng, CY Chen, SY Hwang, TP Lin; citation_volume=211; citation_publication_date=2016; citation_pages=599-613; citation_doi=10.1111/nph.13914; citation_id=CR11 citation_journal_title=Front Plant Sci; citation_title=Over-expression of ERF38 gene enhances salt and osmotic tolerance in transgenic Poplar; citation_author=Z Cheng, X Zhang, K Zhao, W Yao, R Li, B Zhou, T Jiang; citation_volume=10; citation_publication_date=2019; citation_pages=1375; citation_doi=10.3389/fpls.2019.01375; citation_id=CR12 Cui LC, Feng KW, Wang MX, Wang M, Deng PC, Song WN, Nie XJ (2016) Genome-wide identification, phylogeny and expression analysis of AP2/ERF transcription factors family in Brachypodium distachyon. BMC Genomics 17 Dossa K, Wei X, Li DH, Fonceka D, Zhang YX, Wang LH, Yu JY, Liao SB, Diouf D, Cisse N, Zhang XR (2016) Insight into the AP2/ERF transcription factor superfamily in sesame and expression profiling of DREB subfamily under drought stress. BMC Plant Biol 16 citation_journal_title=Front Plant Sci; citation_title=The AP2/ERF transcription factor DRNL modulates gynoecium development and affects its response to cytokinin; citation_author=Y Duran-Medina, J Serwatowska, JI Reyes-Olalde, S Folter, N Marsch-Martinez; citation_volume=8; citation_publication_date=2017; citation_pages=1841; citation_doi=10.3389/fpls.2017.01841; citation_id=CR15 Eddy SR (2011) Accelerated profile HMM searches. PLoS Computer Biology 7 citation_journal_title=Plant Cell; citation_title=DREB duo defines distinct drought and cold response pathways; citation_author=NA Eckardt; citation_volume=31; citation_publication_date=2019; citation_pages=1196-1197; citation_doi=10.1105/tpc.19.00331; citation_id=CR17 Fan W, Hai MR, Guo YL, Ding ZH, Tie WW, Ding XP, Yan Y, Wei Y, Liu Y. Wu C, Shi H, Li K, Hu W (2016) The ERF transcription factor family in cassava: genome-wide characterization and expression analyses against drought stress. Sci Rep 6 citation_journal_title=Plant Mol Biol Rep; citation_title=A buckwheat (Fagopyrum esculentum) DRE-binding transcription factor gene, FeDREB1, enhances freezing and drought tolerance of transgenic Arabidopsis; citation_author=ZW Fang, XH Zhang, JF Gao, PK Wang, XY Xu, ZX Liu, SH Shen, BL Feng; citation_volume=33; citation_publication_date=2015; citation_pages=1510-1525; citation_doi=10.1007/s11105-015-0851-4; citation_id=CR19 Feng K, Hou XL, Xing GM, Liu JX, Duan AQ, Xu ZS, Li MY, Zhuang J, Xiong AS (2020) Advances in AP2/ERF super-family transcription factors in plant. Crit Rev Biotechnol 40:750-776 Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A (2008) The Pfam protein families database. Nucleic Acids Res 36:281–288 citation_journal_title=Plant Cell; citation_title=Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression; citation_author=SY Fujimoto, M Ohta, A Usui, H Shinshi, M Ohme-Takagi; citation_volume=12; citation_publication_date=2000; citation_pages=393-404; citation_id=CR22 Guo BJ, Wei YF, Xu RB, Lin S, Luan HY, Lv C, Zhang X, Song X, Xu R (2016) Genome-wide analysis of APETALA2/ethylene-responsive factor (AP2/ERF) gene family in barley (Hordeum vulgare L.). PLoS One 11 citation_journal_title=Bioinformatics; citation_title=GSDS 2.0: an upgraded gene feature visualization server; citation_author=B Hu, J Jin, AY Guo, H Zhang, J Luo, G Gao; citation_volume=31; citation_publication_date=2015; citation_pages=1296-1297; citation_doi=10.1093/bioinformatics/btu817; citation_id=CR24 citation_journal_title=Mol Biol Rep; citation_title=Signal transduction during cold, salt, and drought stresses in plants; citation_author=GT Huang, SL Ma, LP Bai, L Zhang, H Ma, P Jia, J Liu, M Zhong, ZF Guo; citation_volume=39; citation_publication_date=2012; citation_pages=969-987; citation_doi=10.1007/s11033-011-0823-1; citation_id=CR25 citation_journal_title=Plant Mol Biol; citation_title=Over-expression of AtDREB1A in chrysanthemum enhances tolerance to heat stress; citation_author=B Hong, C Ma, Y Yang, T Wang, K Yamaguchi-Shinozaki, J Gao; citation_volume=70; citation_publication_date=2009; citation_pages=231-240; citation_doi=10.1007/s11103-009-9468-z; citation_id=CR26 citation_journal_title=Plant Cell Physiol; citation_title=Functional analysis of rice DREB1/CBF-type transcription factors involved in cold-responsive gene expression in transgenic rice; citation_author=Y Ito, K Katsura, K Maruyama, T Taji, M Kobayashi, M Seki, K Shinozaki, K Yamaguchi-Shinozaki; citation_volume=47; citation_publication_date=2006; citation_pages=141-153; citation_doi=10.1093/pcp/pci230; citation_id=CR27 citation_journal_title=Science; citation_title=Arabidopsis CBF1 overexpression induces COR genes and enhances freezing tolerance; citation_author=KR Jaglo-Ottosen, SJ Gilmour, DG Zarka, O Schabenberger, MF Thomashow; citation_volume=280; citation_publication_date=1998; citation_pages=104-106; citation_doi=10.1126/science.280.5360.104; citation_id=CR28 citation_journal_title=DNA Cell Biol; citation_title=Genome-Wide identification and expression profiling of the ERF gene family in Medicago sativa L. under various abiotic stresses; citation_author=X Jin, X Yin, B Ndayambaza, Z Zhang, X Min, X Lin, Y Wang, W Liu; citation_volume=38; citation_publication_date=2019; citation_pages=1056-1068; citation_doi=10.1089/dna.2019.4881; citation_id=CR29 citation_journal_title=Proc Natl Acad Sci U S A; citation_title=Control of seed mass and seed yield by the floral homeotic gene APETALA2; citation_author=KD Jofuku, PK Omidyar, Z Gee, JK Okamuro; citation_volume=102; citation_publication_date=2005; citation_pages=3117-3122; citation_doi=10.1073/pnas.0409893102; citation_id=CR30 citation_journal_title=Nat Commun; citation_title=Genome sequence of mungbean and insights into evolution within Vigna species; citation_author=YJ Kang, SK Kim, MY Kim, P Lestari, KH Kim, BK Ha, TH Jun, WJ Hwang, T Lee, J Lee, S Shim, MY Yoon, YE Jang, KS Han, P Taeprayoon, N Yoon, P Somta, P Tanya, KS Kim, JG Gwag, JK Moon, YH Lee, BS Park, A Bombarely, JJ Doyle, SA Jackson, R Schafleitner, P Srinives, RK Varshney, SH Lee; citation_volume=5; citation_publication_date=2014; citation_pages=5443; citation_doi=10.1038/ncomms6443; citation_id=CR31 Kim NY, Jang YJ, Park OK (2018) AP2/ERF Family Transcription Factors ORA59 and RAP2.3 Interact in the Nucleus and Function Together in Ethylene Responses. Front Plant Sci 9:1675 Lee JG, Yi G, Seo J, Kang BC, Choi JH, Lee EJ (2020) Jasmonic acid and ERF family genes are involved in chilling sensitivity and seed browning of pepper fruit after harvest. Sci Rep 10:17949 V LescotDe´hais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouze´ P, Rombauts S, 2002 PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences Nucleic Acids Res 30 325 327 Li A, Zhou YA, Jin C, Song WQ, Chen CB, Wang CG (2013) LaAP2L1, a heterosis-associated AP2/EREBP transcription factor of larix, increases organ size and final biomass by affecting cell proliferation in Arabidopsis. Plant Cell Physiol 54:1822–1836 citation_journal_title=Front Plant Sci; citation_title=Genome-wide identification of AP2/ERF transcription factors in Cauliflower and expression profiling of the ERF family under salt and drought stresses; citation_author=H Li, Y Wang, M Wu, LH Li, C Li, ZP Han, JY Yuan, CB Chen, WQ Song, CG Wang; citation_volume=8; citation_publication_date=2017; citation_pages=946; citation_doi=10.3389/fpls.2017.00946; citation_id=CR36 Ma R, Xiao Y, Lv Z, Tan H, Chen R, Li Q, Chen J, Wang Y, Yin J, Zhang L, Chen W (2017) AP2/ERF Transcription Factor, Ii049, Positively Regulates Lignan Biosynthesis in Isatis indigotica through Activating Salicylic Acid Signaling and Lignan/Lignin Pathway Genes. Front Plant Sci 8:1361 (MAPKKK) gene family in bread wheat (Triticum aestivum L.). BMC Genomics 17: 668 Mittal A, Jiang YW, Ritchie GL, Burke JJ, Rock CD (2015) AtRAV1 and AtRAV2 overexpression in cotton increases fiber length differentially under drought stress and delays flowering. Plant Sci 241:78–95 citation_journal_title=Plant Physiol; citation_title=Genome-wide analysis of the ERF gene family in Arabidopsis and rice; citation_author=T Nakano, K Suzuki, T Fujimura, H Shinshi; citation_volume=140; citation_publication_date=2006; citation_pages=411-432; citation_doi=10.1104/pp.105.073783; citation_id=CR40 citation_journal_title=Plant Physiol; citation_title=Identification of Arabidopsis ethylene-responsive element binding factors with distinct induction kinetics after pathogen infection; citation_author=L Onate-Sanchez, KB Singh; citation_volume=128; citation_publication_date=2002; citation_pages=1313-1322; citation_doi=10.1104/pp.010862; citation_id=CR41 citation_journal_title=Plant Cell Rep; citation_title=Improved drought and salt tolerance of Arabidopsis thaliana by transgenic expression of a novel DREB gene from Leymus chinensis; citation_author=XJ Peng, XY Ma, WH Fan, M Su, LQ Cheng, A Iftekhar, HL Byung, DM Qi, SSH Liu, null GS, ; citation_volume=30; citation_publication_date=2011; citation_pages=1493-1502; citation_doi=10.1007/s00299-011-1058-2; citation_id=CR42 citation_journal_title=Plant J; citation_title=Regulation and functional analysis of ZmDREB2A in response to drought and heat stresses in Zea mays L; citation_author=F Qin, M Kakimoto, Y Sakuma, K Maruyama, Y Osakabe, LSP Tran, K Shinozaki, K Yamaguchi-Shinozaki; citation_volume=50; citation_publication_date=2007; citation_pages=54-69; citation_doi=10.1111/j.1365-313X.2007.03034.x; citation_id=CR43 citation_journal_title=Mol Biol Evol; citation_title=DnaSP 6: DNA sequence polymorphism analysis of large data sets; citation_author=J Rozas, MA Ferrer, JC Sánchez-DelBarrio, S GuiraoRico, P Librado, SE Ramos-Onsins, A Sánchez-Gracia; citation_volume=34; citation_publication_date=2017; citation_pages=3299-3302; citation_doi=10.1093/molbev/msx248; citation_id=CR44 citation_journal_title=Biochem Bioph Res Co; citation_title=DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration- and cold-inducible gene expression; citation_author=Y Sakuma, Q Liu, JG Dubouzet, H Abe, K Shinozaki, K Yamaguchi-Shinozaki; citation_volume=290; citation_publication_date=2002; citation_pages=998-1009; citation_doi=10.1006/bbrc.2001.6299; citation_id=CR45 citation_journal_title=Mol Cells; citation_title=Overexpression of the ethylene-responsive factor gene BrERF4 from Brassica rapa increases tolerance to salt and drought in Arabidopsis plants; citation_author=YJ Seo, JB Park, YJ Cho, C Jung, HS Seo, SK Park, BH Nahm, JT Song; citation_volume=30; citation_publication_date=2010; citation_pages=271-277; citation_doi=10.1007/s10059-010-0114-z; citation_id=CR46 citation_journal_title=Mol Biol Evol; citation_title=MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods; citation_author=K Tamura, D Peterson, N Peterson, G Stecher, M Nei, S Kumar; citation_volume=28; citation_publication_date=2011; citation_pages=2731-2739; citation_doi=10.1093/molbev/msr121; citation_id=CR47 citation_journal_title=Nucleic Acids Res; citation_title=The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools; citation_author=JD Thompson, TJ Gibson, F Plewniak, F Jeanmougin, DG Higgins; citation_volume=25; citation_publication_date=1997; citation_pages=4876-4882; citation_doi=10.1093/nar/25.24.4876; citation_id=CR48 citation_journal_title=Trends Plant Sci; citation_title=Homing into the origin of the AP2 DNA binding domain; citation_author=SR Wessler; citation_volume=10; citation_publication_date=2005; citation_pages=54-56; citation_doi=10.1016/j.tplants.2004.12.007; citation_id=CR49 Wang M, Yue H, Feng KW, Deng PC, Song WN, Nie XJ (2016) Genome-wide identification, phylogeny and expressional profiles of mitogen activated protein kinase kinase kinase citation_journal_title=Nucleic Acids Res; citation_title=MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity; citation_author=Y Wang, H Tang, JD Debarry, X Tan, J Li, X Wang, TH Lee, H Jin, B Marler, H Guo, JC Kissinger, AH Paterson; citation_volume=40; citation_publication_date=2012; citation_pages=e49; citation_doi=10.1093/nar/gkr1293; citation_id=CR51 citation_journal_title=J Exp Bot; citation_title=Phylogeny, gene structures, and expression patterns of the ERF gene family in soybean (Glycine max L.); citation_author=GY Zhang, M Chen, XP Chen, ZS Xu, S Guan, LC Li, A Li, J Guo, L Mao, Y Ma; citation_volume=59; citation_publication_date=2008; citation_pages=4095-4107; citation_doi=10.1093/jxb/ern248; citation_id=CR52 citation_journal_title=BMC Genomics; citation_title=Genome-wide identification, molecular evolution, and expression analysis provide new insights into the APETALA2/ethylene responsive factor (AP2/ERF) superfamily in Dimocarpus longan Lour; citation_author=S Zhang, C Zhu, Y Lyu, Y Chen, Z Zhang, Z Lai, Y Lin; citation_volume=21; citation_publication_date=2020; citation_pages=62; citation_doi=10.1186/s12864-020-6469-4; citation_id=CR53 citation_journal_title=BMC Plant Biol; citation_title=The ABA-induced soybean ERF transcription factor gene GmERF75 plays a role in enhancing osmotic stress tolerance in Arabidopsis and soybean; citation_author=MJ Zhao, LJ Yin, Y Liu, J Ma, JC Zheng, JH Lan, JD Fu, M Chen, ZS Xu, YZ Ma; citation_volume=19; citation_publication_date=2019; citation_pages=506; citation_doi=10.1186/s12870-019-2066-6; citation_id=CR54 citation_journal_title=Annu Rev Plant Biol; citation_title=Salt and drought stress signal transduction in plants; citation_author=JK Zhu; citation_volume=53; citation_publication_date=2002; citation_pages=247-273; citation_doi=10.1146/annurev.arplant.53.091401.143329; citation_id=CR55 citation_journal_title=Cell; citation_title=Abiotic stress signaling and responses in plants; citation_author=JK Zhu; citation_volume=167; citation_publication_date=2016; citation_pages=313-324; citation_doi=10.1016/j.cell.2016.08.029; citation_id=CR56