WANG Yan-wei,WANG Min,WANG Jiang,et al.Genome-wide Identification and Expression Analysis of Soybean OPR GeneFamily[J].Soybean Science,2022,41(02):129-139.[doi:10.11861/j.issn.1000-9841.2022.02.0129]
大豆OPR基因家族全基因组鉴定与表达分析
- Title:
- Genome-wide Identification and Expression Analysis of Soybean OPR GeneFamily
- 文献标志码:
- A
- 摘要:
- 为了揭示大豆12-氧-植物二烯酸还原酶（12-oxo-phytodienoic acid reductase，OPR）家族成员GmOPRs在大豆生长发育中和非生物胁迫下发挥的作用，本研究运用生物信息学方法进行大豆OPR基因家族全基因组鉴定及表达分析。结果显示：大豆基因组中共有12个OPR家族基因成员，分布在8条不同染色体上。系统发育进化分析、基因结构分析和保守基序分析结果显示，GmOPRs可分为两个亚组，含有外显子4~5个，内含子3~5个，GmOPR蛋白之间保守基序分布相似。共线性分析鉴定表明共有4对基因存在共线关系，均为片段复制。GmOPRs启动子区域含有响应厌氧、干旱和低温等非生物胁迫以及JA、ABA等多种激素的顺式作用元件。不同的大豆品种及不同的组织中，GmOPRs的表达模式有差异。GmOPR1、GmOPR4和GmOPR9受干旱胁迫影响后表达量下降，GmOPR7、GmOPR8、GmOPR11和GmOPR12随着盐胁迫影响时间的增长表达量增加，表明GmOPRs基因通过多种表达模式响应干旱和盐胁迫。GmOPRs在系统发育进化和基因结构上比较保守，基因家族数量的扩增主要归因于片段重复。GmOPRs受干旱、盐胁迫等非生物胁迫的影响，表现出不同的表达模式，表明GmOPR基因家族可能在响应非生物胁迫中发挥重要作用。
- Abstract:
- In order to reveal the role of GmOPRs, a member of soybean 12-oxo-phytodienoic acid reductase (OPR) family in soybean growth and development under abiotic stress, we identified and analyzed the whole genome of soybean OPR gene family with bioinformatics method. The results showed that there were twelve OPR genes distributed on 8 chromosomes in soybean genome. The phylogenetic analysis, gene structure analysis and conserved motifs analysis showed that GmOPRs could be divided into two subgroups, containing 4-5 exons and 3-5 introns respectively. The conserved motifs of GmOPR proteins were similar in distribution. Colinear analysis identified colinear relationship among four pairs of genes, all of which were fragment replication. The promoter region of GmOPRs contained cis-acting elements responding to abiotic stress such as anaerobic, drought and low temperature, JA, ABA and other hormones. The expression patterns of GmOPRs were different in different soybean varieties and tissues. The expression of GmOPR1, GmOPR4 and GmOPR9 decreased under drought stress, while the expression of GmOPR7, GmOPR8, GmOPR11 and GmOPR12 increased over time under salt stress, suggesting that the GmOPRs responded to drought and salt stress through multiple expression patterns. GmOPRs were conserved in phylogenetic evolution and gene structure, and the amplification of the gene families was mainly attributed to fragment repetition. GmOPRs were affected by abiotic stresses such as drought and salt stress, and showed different expression patterns. The results suggest that GmOPR gene family may play an important role in abiotic stress responding.
参考文献/References:
［1］蒋科技,皮妍,侯嵘,等.植物内源茉莉酸类物质的生物合成途径及其生物学意义[J].植物学报,2010, 45(2):137-148. (JIANG K J, PI Y, HOU R, et al. Jasmonate biosynthetic pathway: Its physiological role and potential application in plant secondary metabolic engineering[J]. Chinese Bulletin of Botany, 2010, 45(2): 137-148.[2]宋云, 李林宣, 卓凤萍, 等. 茉莉酸信号传导在植物抗逆性方面研究进展[J]. 中国农业科技导报, 2015, 17(2): 17-24. (SONG Y, LI L X, ZHUO F P, et al. Progress on jasmonic acid signaling in plant stress resistant[J] . Journal of Agricultural Science and Technology, 2015, 17(2): 17-24.[3]LI C, WILLIAMS M M, LOH Y T, et al. Resistance of cultivated tomato to cell content-feeding herbivores is regulated by the octadecanoid-signaling pathway[J]. Plant Physiology, 2002, 130(1): 494-503.[4]孙清鹏, 王小菁. 植物伤反应中的茉莉酸类信号[J]. 植物学报通报, 2003, 20(4):481-488. (SUN Q P, WANG X J. Jasmonates in plant wound signaling[J]. Chinese Bulletin of Botany, 2003, 20(4): 481-488.[5]HOWE G A. Jasmonates as signals in the wound response[J].Journal of Plant Growth Regulation, 2004, 23(3): 223-237.[6]WASTERNACK C, STENZEL I, HAUSE B, et al. The wound response in tomato-role of jasmonic acid[J]. Journal of Plant Physiology, 2006, 163(3): 297-306.[7]WASTERNACK C, HAUSE B. A bypass injasmonate biosynthesis the OPR3-independent formation [J]. Trends in Plant Science, 2018, 23(4): 276-279.[8]TURNER J G, ELLIS C, DEVOTO A. The jasmonate signal pathway[J]. The Plant Cell, 2002, 14(1): S153-S164.[9]LI W, LIU B, YU L, et al. Phylogenetic analysis, structural evo-lution and functional divergence of the 12-oxo-phytodienoate acid reductase gene family in plants[J]. BMC Evolutionary Biology, 2009, 9(1): 1-19.[10]BEYNON E R, SYMONS Z C, JACKSON R G, et al. The role of oxophytodienoate reductases in the detoxification of the explosive 2, 4, 6-trinitrotoluene by Arabidopsis[J]. Plant Physiology, 2009, 151(1): 253-261.[11]SCHALLER F, WEILER E W. Molecular cloning and characte-rization of 12-oxophytodienoatereductase, an enzyme of the octadecanoid signaling pathway from Arabidopsis thaliana: Structural and functional relationship to yeast old yellow enzyme[J]. Journal of Biological Chemistry, 1997, 272(44): 28066-28072.[12]LAUDERT D, HENNIG P, STELMACH B A, et al. Analysis of 12-oxo-phytodienoic acid enantiomers in biological samples by capillary gas chromatography-mass spectrometry using cyclodextrin stationary phases[J]. Analytical Biochemistry, 1997, 246(2): 211-217.[13]STINTZI A. The Arabidopsis male-sterile mutant, opr3, lacks the 12-oxophytodienoic acid reductase required for jasmonate synthesis[J]. Proceedings of the National Academy of Sciences, 2000, 97(19): 10625-10630.[14]SCHALLER F, HENNIG P, WEILER E W. 12-Oxophytodienoate-10, 11-reductase:Occurrence of two isoenzymes of different specificity against stereoisomers of 12-oxophytodienoic acid[J]. Plant Physiology, 1998, 118(4): 1345-1351.[15]SCHALLER F, BIESGEN C, MSSIG C, et al. 12-oxophyto-dienoatereductase 3 (OPR3) is the isoenzyme involved in jasmonate biosynthesis[J]. Planta, 2000, 210(6): 979-984.[16]BIESGEN C, WEILER E W. Structure and regulation of OPR1 and OPR2, two closely related genes encoding 12-oxophytodienoic acid-10, 11-reductases from Arabidopsis thaliana[J]. Planta, 1999, 208(2): 155-165.[17]ZHANG J, SIMMONS C, YALPANI N, et al. Genomic analysis of the 12-oxo-phytodienoic acidreductase gene family of Zea mays[J]. Plant Molecular Biology, 2005, 59(2): 323-343.[18]BREITHAUPT C, KURZBAUER R, LILIE H, et al. Crystal structure of 12-oxophytodienoatereductase 3 from tomato: Self-inhibition by dimerization[J]. Proceedings of the National Academy of Sciences, 2006, 103(39): 14337-14342.[19]LI W, ZHOU F, LIU B, et al. Comparative characterization, expression pattern and function analysis of the 12-oxo-phytodienoic acidreductase gene family in rice[J]. Plant Cell Reports, 2011, 30(6): 981-995. [20]MOU Y, LIU Y, TIAN S, et al. Genome-wide identification and characterization of the OPR gene family in wheat (Triticum aestivum L.)[J]. International Journal of Molecular Sciences, 2019, 20(8): 1-18.[21]MATSUI H, NAKAMURA G, ISHIGA Y, et al. Structure and expression of 12-oxophytodienoatereductase (subgroup I) genes in pea, and characterization of the oxidoreductase activities of their recombinant products[J]. Molecular Genetics and Genomics, 2004, 271(1): 1-10.[22]PAK H, WANG H, KIM Y, et al. Creation of male-sterile lines that can be restored to fertility by exogenous methyl jasmonate for the establishment of a two-line system for the hybrid production of rice (Oryza sativa L.)[J]. Plant Biotechnology Journal, 2021, 19(2): 365-374.[23]TANI T, SOBAJIMA H, OKADA K, et al. Identification of the OsOPR7 gene encoding 12-oxophytodienoate reductase involved in the biosynthesis of jasmonic acid in rice[J]. Planta, 2008, 227(3): 517-526.[24]夏凡, 代婷婷, 姚新转, 等. 水稻OPR基因的克隆及其在烟草中抗镉性分析[J]. 种子, 2020, 39(5): 53-58. (XIA F, DAI T T, YAO X C, et al. Cloning of Oryza sativa OPR gene and its cadmium resistance in tobacco[J]. Seed, 2020, 39(5):53-58.[25]PIGOLEV A V, MIROSHNICHENKO D N, PUSHIN A S, et al. Overexpression of Arabidopsis OPR3 in hexaploid wheat (Triticum aestivum L.) alters plant development and freezing tolerance[J]. International Journal of Molecular Sciences, 2018, 19(12): 1-17.[26]DONG W, WANG M, XU F, et al. Wheat oxophytodienoate reductase gene TaOPR1 confers salinity tolerance via enhancement of abscisic acid signaling and reactive oxygen species scavenging[J]. Plant Physiology, 2013, 161(3): 1217-1228.[27]WANG Y, YUAN G, YUAN S, et al.TaOPR2 encodes a 12-oxo-phytodienoic acid reductase involved in the biosynthesis of jasmonic acid in wheat (Triticum aestivum L.)[J]. Biochemical and Biophysical Research Communications, 2016, 470(1): 233-238.[28]YAN Y, CHRISTENSEN S, ISAKEIT T, et al. Disruption of OPR7 and OPR8 reveals the versatile functions of jasmonic acid in maize development and defense[J]. The Plant Cell, 2012, 24(4): 1420-1436.[29]林延慧, 唐力琼, 徐靖, 等. 大豆响应涝害bZIP基因Glyma04g04170的生物信息学分析及互作蛋白预测[J]. 大豆科学, 2020, 39(5): 727-733. (LIN Y H, TANG L Q, XU J, et al. Bioinformatics analysis and interacting protein prediction of soybean bZIP gene Glyma04g04170 in response to submergence stress[J]. Soybean Science, 2020, 39(5): 727-733.[30]EL-GEBALI S, MISTRY J, BATEMAN A, et al. The Pfam protein families database in 2019[J]. Nucleic Acids Research, 2019, 47(D1): D427-D432.[31]FINN R D, CLEMENTS J, EDDY S R. HMMER web server: Interactive sequence similarity searching[J]. Nucleic Acids Research, 2011, 39(suppl_2): W29-W37.[32]KUMAR S, STECHER G, LI M, et al. MEGA X:Molecular evolutionary genetics analysis across computing platforms[J]. Molecular Biology and Evolution, 2018, 35(6): 1547-1549.[33]CHEN N 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.[34]HU B, JIN J, GUO A Y, et al. GSDS 2.0: An upgraded gene feature visualization server[J]. Bioinformatics, 2015, 31(8): 1296-1297.[35]BAILEY T L, BODEN M, BUSKE F A, et al. MEME SUITE: Tools for motif discovery and searching[J]. Nucleic Acids Research, 2009, 37(suppl_2): W202-W208.[36]TAMANG B G, LI S, RAJASUNDARAM D, et al. Overlapping and stress-specific transcriptomic and hormonal responses to flooding and drought in soybean[J]. The Plant Journal, 2021, 107(1): 100-117.[37]BELAMKAR V, WEEKS N T, BHARTI A K, et al. Compre-hensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress[J]. BMC Genomics, 2014, 15(1): 1-25.[38]WANG M, CHEN B, ZHOU W, et al. Genome-wide identification and expression analysis of the AT-hook Motif Nuclear Localized gene family in soybean[J]. BMC Genomics, 2021, 22(1): 1-26.[39]WANG T Y, LIU Q,REN Y, et al. A pan-cancer transcriptome analysis of exitron splicing identifies novel cancer driver genes and neoepitopes[J]. Molecular Cell, 2021, 81(10): 2246-2260.[40]GUANG Y, LUO S, AHAMMED G J, et al. The OPR gene family in watermelon: Genome-wide identification and expression profiling under hormone treatments and root-knot nematode infection[J]. Plant Biology, 2021, 23(1): 80-88.[41]GUPTA A, RICO-MEDINA A, CAO-DELGADOA I. The physi-ology of plant responses to drought[J]. Science, 2020, 368(6488): 266-269.
相似文献/References:
[1]刘章雄,李卫东,孙石,等.1983～2010年北京大豆育成品种的亲本地理来源及其遗传贡献[J].大豆科学,2013,32(01):1.[doi:10.3969/j.issn.1000-9841.2013.01.002]
LIU Zhang-xiong,LI Wei-dong,SUN Shi,et al.Geographical Sources of Germplasm and Their Nuclear Contribution to Soybean Cultivars Released during 1983 to 2010 in Beijing[J].Soybean Science,2013,32(02):1.[doi:10.3969/j.issn.1000-9841.2013.01.002]
[2]李彩云,余永亮,杨红旗,等.大豆脂质转运蛋白基因GmLTP3的特征分析[J].大豆科学,2013,32(01):8.[doi:10.3969/j.issn.1000-9841.2013.01.003]
LI Cai-yun,YU Yong-liang,YANG Hong-qi,et al.Characteristics of a Lipid-transfer Protein Gene GmLTP3 in Glycine max[J].Soybean Science,2013,32(02):8.[doi:10.3969/j.issn.1000-9841.2013.01.003]
[3]王明霞,崔晓霞,薛晨晨,等.大豆耐盐基因GmHAL3a的克隆及RNAi载体的构建[J].大豆科学,2013,32(01):12.[doi:10.3969/j.issn.1000-9841.2013.01.004]
WANG Ming-xia,CUI Xiao-xia,XUE Chen-chen,et al.Cloning of Halotolerance 3 Gene and Construction of Its RNAi Vector in Soybean (Glycine max)[J].Soybean Science,2013,32(02):12.[doi:10.3969/j.issn.1000-9841.2013.01.004]
[4]张春宝,李玉秋,彭宝,等.线粒体ISSR与SCAR标记鉴定大豆细胞质雄性不育系与保持系[J].大豆科学,2013,32(01):19.[doi:10.3969/j.issn.1000-9841.2013.01.005]
ZHANG Chun-bao,LI Yu-qiu,PENG Bao,et al.Identification of Soybean Cytoplasmic Male Sterile Line and Maintainer Line with Mitochondrial ISSR and SCAR Markers[J].Soybean Science,2013,32(02):19.[doi:10.3969/j.issn.1000-9841.2013.01.005]
[5]卢清瑶,赵琳,李冬梅,等.RAV基因对拟南芥和大豆不定芽再生的影响[J].大豆科学,2013,32(01):23.[doi:10.3969/j.issn.1000-9841.2013.01.006]
LU Qing-yao,ZHAO Lin,LI Dong-mei,et al.Effects of RAV gene on Shoot Regeneration of Arabidopsis and Soybean[J].Soybean Science,2013,32(02):23.[doi:10.3969/j.issn.1000-9841.2013.01.006]
[6]杜景红,刘丽君.大豆fad3c基因沉默载体的构建[J].大豆科学,2013,32(01):28.[doi:10.3969/j.issn.1000-9841.2013.01.007]
DU Jing-hong,LIU Li-jun.Construction of fad3c Gene Silencing Vector in Soybean[J].Soybean Science,2013,32(02):28.[doi:10.3969/j.issn.1000-9841.2013.01.007]
[7]张力伟,樊颖伦,牛腾飞,等.大豆“冀黄13”突变体筛选及突变体库的建立[J].大豆科学,2013,32(01):33.[doi:10.3969/j.issn.1000-9841.2013.01.008]
ZHANG Li-wei,FAN Ying-lun,NIU Teng-fei?,et al.Screening of Mutants and Construction of Mutant Population for Soybean Cultivar "Jihuang13”[J].Soybean Science,2013,32(02):33.[doi:10.3969/j.issn.1000-9841.2013.01.008]
[8]盖江南,张彬彬,吴瑶,等.大豆不定胚悬浮培养基因型筛选及基因枪遗传转化的研究[J].大豆科学,2013,32(01):38.[doi:10.3969/j.issn.1000-9841.2013.01.009]
GAI Jiang-nan,ZHANG Bin-bin,WU Yao,et al.Screening of Soybean Genotypes Suitable for Suspension Culture with Adventitious Embryos and Genetic Transformation by Particle Bombardment[J].Soybean Science,2013,32(02):38.[doi:10.3969/j.issn.1000-9841.2013.01.009]
[9]王鹏飞,刘丽君,唐晓飞,等.适于体细胞胚发生的大豆基因型筛选[J].大豆科学,2013,32(01):43.[doi:10.3969/j.issn.1000-9841.2013.01.010]
WANG Peng-fei,LIU Li-jun,TANG Xiao-fei,et al.Screening of Soybean Genotypes Suitable for Somatic Embryogenesis[J].Soybean Science,2013,32(02):43.[doi:10.3969/j.issn.1000-9841.2013.01.010]
[10]刘德兴,年海,杨存义,等.耐酸铝大豆品种资源的筛选与鉴定[J].大豆科学,2013,32(01):46.[doi:10.3969/j.issn.1000-9841.2013.01.011]
LIU De-xing,NIAN Hai,YANG Cun-yi,et al.Screening and Identifying Soybean Germplasm Tolerant to Acid Aluminum[J].Soybean Science,2013,32(02):46.[doi:10.3969/j.issn.1000-9841.2013.01.011]
备注/Memo
收稿日期：2021-10-04