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ZHAO Bingxue, NIE Gongping, ZHANG Xiaohui, HUANG Qingjun. Bioinformatics Identification and Analysis of AP2/ERF Gene Family in Sesame[J]. Journal of Technology, 2022, 22(4): 399-412. DOI: 10.3969/j.issn.2096-3424.2022.04.018
Citation: ZHAO Bingxue, NIE Gongping, ZHANG Xiaohui, HUANG Qingjun. Bioinformatics Identification and Analysis of AP2/ERF Gene Family in Sesame[J]. Journal of Technology, 2022, 22(4): 399-412. DOI: 10.3969/j.issn.2096-3424.2022.04.018
shu

Bioinformatics Identification and Analysis of AP2/ERF Gene Family in Sesame

  • 1.

    School of Ecological Technology and Engineering, Shanghai Institute of Technology, Shanghai 201418, China

  • 2.

    College of Horticulture and Gardening, Yangtz University, Jingzhou 434023, Hubei, China

  • Received Date: September 12, 2021
    Graphical Abstract
    • Abstract
  • AP2/ERF (APETALA2/ethylene responsive factor) is one of families of transcription factors unique to plants, which plays an important role in controlling plant growth and development, participating in secondary metabolism and resisting abiotic stress. Based on the reported AP2/ERF genes in Arabidopsis thaliana, 142 AP2/ERF genes were identified in the newly published sesame (Sesamum indicum L.) reference sequences by bioinformatics. The physicochemical properties, phylogeny, domains, conserved motifs, chromosome localization, species collinearity, expression specificity in different tissues and gene expression response to stress were analyzed. According to the analysis of physicochemical properties, the AP2/ERF gene family of sesame encodes 121-697 amino acids, the relative molecular weight of the protein is 13428.04-76020.09 KD, and the theoretical isoelectric point is between 4.50 and 10.24. According to the analysis of domain and phylogenetic analysis, the AP2/ERF protein in sesame can be divided into four subfamilies: AP2 contains 26 members, ERF contains 116 members, soloist contains 2 members and Rav contains 3 members. 136 members are unevenly distributed on 16 chromosomes, and are clustered in homologous groups of chromosomes 1-4 and 6-12. According to the collinearity analysis, there are 32 and 49 AP2/ERF genes on Sesame chromosome, which are collinear with barley and maize respectively. In the evolution process, the conservation of AP2/ERF gene with maize is higher than that with barley, and the variability with barley is higher than that with maize. The LOC105157874 gene in subgroup VII was up-regulated in both sesame varieties, which may be involved in the regulation of sesame response to flooding stress and needs further experimental verification.This study provides a scientific basis for further study on the biological function of AP2/ERF transcription factor family and the improvement of sesame stress resistance.
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  • [1]
    AGARWAL P K, AGARWAL P, REDDY M K, et al Role of DREB transcription factors in abiotic and biotic stress tolerance in plants[J]. Plant Cell Reports, 2006, 25（3）: 1263-1274.
    [2]
    AKHTAR M,JAISWAL A,TAJ G,et al. DREB1/CBF transcription factors:Their structure,function and role in abiotic stress tolerance in plants[J]. Journal of Genetics,2012,91(3): 385-395. DOI: 10.1007/s12041-012-0201-3
    [3]
    LATA C,PRASAD M. Role of DREBs in regulation of abiotic stress responses in plants[J]. Journal of Experimental Botany,2011,62(14): 4731-4748. DOI: 10.1093/jxb/err210
    [4]
    OHMETAKAGI M,SHINSHI H. Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive elemen[J]. Plant Cell,1995,7(2): 173-182.
    [5]
    NAKANO T,SUZUKI K,FUJIMURA T,et al. Genome-wide analysis of the ERF gene family in arabidopsis and rice[J]. Plant Physiology,2006,140(2): 411-432. DOI: 10.1104/pp.105.073783
    [6]
    RIECHMANN J L,MEYEROWITZ E M. The AP2/EREBP family of plant transcription factors[J]. Biological chemistry,1998,379(6): 633-646. DOI: 10.1515/bchm.1998.379.6.633
    [7]
    LICAUSI F,GIORGI F M,ZENONI S,et al. Genomic and transcriptomic analysis of the AP2/ERF uperfamily in Vitis vinifera[J]. BMC Genomics,2010(11): 0719. DOI: 10.1186/1471-2164-11-719
    [8]
    MOOSE S P,SISCO P H. Glossy15,an APETALA2-like gene from maize that regulates leaf epidermal cell identity[J]. Genes Dev,1996,10(23): 3018-3027. DOI: 10.1101/gad.10.23.3018
    [9]
    AUKERMAN M J,SAKAI H. Regulation of flowering time and floral organ identity by a micro RNA and its APETALA2-like target genes[J]. Plant Cell,2003(15): 2730-2741. DOI: 10.1105/tpc.016238
    [10]
    DINH T T,GIRKE T,LIU X,et al. The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element[J]. Development,2012,139(11): 1978-1986. DOI: 10.1242/dev.077073
    [11]
    CHUCK G,MEELEY R B,HAKE S. The control of maize spikelet meristem fate by the APETALA2-like gene indeterminate spikelet1[J]. Genes & Development,1998,12(8): 1145-1154.
    [12]
    JOFUKU K D,OMIDYAR P K,GEE Z,et al. Control of seed mass and seed yield by the floral homeotic gene APETALA2[J]. Proceedings of the National Academy of Sciences of the United States of America,2005,102(8): 3117-3122. DOI: 10.1073/pnas.0409893102
    [13]
    OHTO M A,FLOYD S K,FISCHER R L,et al. Effects of APETALA2 onembryo,endosperm,and seed coat development determine seed size in Arabidopsis[J]. Sexual Plant Reproduction,2009,22(4): 277-289. DOI: 10.1007/s00497-009-0116-1
    [14]
    HU L,LIU S. Genome-wide identification and phylogenetic analysis of the ERF genefamily in cucumbers[J]. Genetics and Molecular Biology,2011,34(4): 624-633. DOI: 10.1590/S1415-47572011005000054
    [15]
    ALONSO J M,STEPANOVA A N,LEISSE T J,et al. Genome-wide insertional mutagenesis of Arabidopsis thaliana[J]. Science,2003,301(5633): 653-657. DOI: 10.1126/science.1086391
    [16]
    HU Y X, WANG Y X, LIU X F, et al. Arabidopsis RAV1 is down-regulated by brassinosteroid and may act as anegative regulator during plant development[J]. Cell Research, 2004(14): 8-15.
    [17]
    LI C W,SU R C,CHENG C P,et al. Tomato RAV transcription factor is a pivotal modulator involved in the AP2/EREBP-mediated defense pathway[J]. Plant Physiology,2011,156(1): 213-227. DOI: 10.1104/pp.111.174268
    [18]
    RAMEGOWDA V,BASU S,KRISHNAN A,et al. Rice growth under drought kinase is required for drought tolerance and grain yield under normal and drought stress conditions[J]. Plant physiology,2014,166(3): 248203.
    [19]
    DOSSA K,WEI X,LI D,et al. Insight into the AP2/ERF transcription factor superfamily in sesame and expression profiling of DREB subfamily under drought stress[J]. BMC plant biology,2016,16(1): 0171. DOI: 10.1186/s12870-016-0859-4
    [20]
    HAO D Y,OHME-TAKAGI M,SARAI A. Unique mode of GCC box recognition by the DNA-binding domain of ethylene responsive element-binding factor(ERF domain) in plants[J]. Journal of Biological Chemistry,1998(273): 26857-26861. DOI: 10.1074/jbc.273.41.26857
    [21]
    LIANG C L,LI Y N,ZHANG X P,et al. Immunotoxicologic assessment of genetically modified drought-resistant wheat T349 with GmDREB1[J]. Chinese Journal of Preventive Medicine,2012(46): 556-560.
    [22]
    JAGLO-OTTOSEN K R,GILMOUR S J,ZARKA D G,et al. Arabidopsis CBF1 overexpression induces COR genes and enhances freezing tolerance[J]. Science,1998,280(5360): 104-106. DOI: 10.1126/science.280.5360.104
    [23]
    HONG J P,KIM W T. Isolation and functional characterization of the Ca-DREBLP1 gene encoding adehydration-responsive element binding-factor-like protein1 in hot pepper(Capsicumannuum Lcv Pukang)[J]. Planta,2005,220(6): 875-888. DOI: 10.1007/s00425-004-1412-5
    [24]
    HONG B,MA C,YANG Y,et al. Over-expression of AtDREB1A in chrysanthemum enhances tolerance to heat stress[J]. Plant Molecular Biology,2009,70(3): 231-240. DOI: 10.1007/s11103-009-9468-z
    [25]
    WANG X M,CHEN X F,LIU Y,et al. CkDREB gene in Caragana korshinskii is involved in the regulation of stress response to multiple abiotic stresses as an AP2/EREBP transcription factor[J]. Molecular Biology Reports,2011,38(4): 2801-2811. DOI: 10.1007/s11033-010-0425-3
    [26]
    QIN F,KAKIMOTO M,SAKUMA Y,et al. Regulation and functional analysis of ZmDREB2A in response to drought and heat stresses in Zea mays L.[J]. The Plant Journal,2007,50(1): 54-69. DOI: 10.1111/j.1365-313X.2007.03034.x
    [27]
    LU S N,WANG J Y,FARIDEH C,et al. CDD/SPARCLE:The conserved domain database in 2020[J]. Nucleic Acids Research,2019,48(1): 265-268.
    [28]
    TIMOTHY L B, MIKAEL B, FABIAN A B, et al. MEME Suite: Tools for motif discovery and searching[J]. Nucleic Acids Research, 2009, 37（1）: 202-208.
    [29]
    CHEN C,CHEN H,ZHANG Y,et al. TBtools:An integrative toolkit developed for interactive analyses of big biological data[J]. Molecular Plant,2020,13(8): 1194-1202. DOI: 10.1016/j.molp.2020.06.009
    [30]
    WANG Y P,TANG H B,DEBARRY J D,et al. MCScanX:A toolkit for detection and evolutionary analysis of gene synteny and collinearity[J]. Nucleic Acids Research,2012,40(7): e49. DOI: 10.1093/nar/gkr1293
    [31]
    赵金玲,姚文静,王升级,等. 杨树AP2/ERF转录因子家族生物信息学分析[J]. 东北林业大学学报,2015,43(10): 21-29. DOI: 10.3969/j.issn.1000-5382.2015.10.005
    [32]
    孙滨,占小登,曹立勇,等. 水稻AP2/ERF转录因子的研究进展[J]. 农业生物技术学报,2017,25(11): 1860-1869.
    [33]
    DOSSA K,YOU J,WANG L,et al. Transcriptomic profiling of sesame during waterlogging and recovery[J]. Scientific Data,2019,6(1): 0226. DOI: 10.1038/s41597-019-0230-3
    [34]
    SUN J,ZHANG X,ZHANG Y,et al. Effects of waterlogging on leaf protective enzyme activities and seed yield of sesame at different growth stages[J]. Chinese Journal of Applied & Environmental Biology,2009(15): 790-795.
    [35]
    HATTORI Y,NAGAI K,FURUKAWA S,et al. The ethylene response factors SNORKEL1 and SNORKEL2 allows rice to adapt to deep water[J]. Nature,2009,460(7258): 1026-1030. DOI: 10.1038/nature08258
    [36]
    KREUZWIESER J,HAUBERG J,HOWELL K A,et al. Differential response of Gray Poplar leaves and roots underpins stress adaptation during hypoxia[J]. Plant Physiology,2009,149(1): 461-473. DOI: 10.1104/pp.108.125989
    [37]
    HINZ M,WILSON I W,YANG J,et al. Arabidopsis RAP22:An ethylene response transcription factor that is important for hypoxia survival[J]. Plant Physiology,2010,153(2): 757-772. DOI: 10.1104/pp.110.155077
    [38]
    YANG C Y,HSU F C,LI J P,et al. The AP2/ERF transcription factor AtERF73/HRE1 modulates ethylene responses during hypoxia in Aarabidopsis[J]. Plant Physiology,2011,156(1): 202-212. DOI: 10.1104/pp.111.172486
    [39]
    HESS N,KLODE M,ANDERS M,et al. The hypoxia responsive transcription factor genes ERF71/HRE2 and ERF73/HRE1 of Arabidopsis are differentially regulated by ethylene[J]. Physiologia plantarum,2011,143(1): 41-49. DOI: 10.1111/j.1399-3054.2011.01486.x
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