水稻WRKY转录因子家族的生物信息学分析
|
摘要
[目的]对水稻WRKY转录因子家族成员进行生物信息学分析,为进一步研究水稻WRKY转录因子的功能提供依据。[方法]从NCBI网站下载水稻全基因组序列,利用CDD、Blast、MEME、MEGA、ProtParam等在线工具或本地软件筛选WRKY家族成员,对所得WRKY家族成员的理化性质、系统进化亲缘关系、保守元件等项目进行生物信息学分析。[结果]共从水稻基因组中鉴定筛选出65个WRKY家族成员,每一个成员中都具有WRKYGQK的保守元件,除此之外还有一个保守锌指结构的元件存在。利用MEGA对所得WRKY家族成员进行聚类发现,65个WRKY家族成员可以分为A、B、C、D、E 5类,其中A、B、C、D 4类的亲缘关系较近,可以聚为一类;而A类相对亲缘关系较远,认为A类成员可能是长期进化过程中被保留下来的较为原始的一类。[结论]该研究较系统地鉴定了水稻WRKY家族,为进一步研究水稻WRKY转录因子功能和互作关系提供参考。
[Objective]Bioinformatics analysis of WRKY transcription factor family members in rice was carried out to provide basis for further study on the function of WRKY transcription factor family in rice.[Method]The whole genome sequence of rice was downloaded from NCBI website.The WRKY family members were screened by CDD,Blast,MEME,MEGA,ProtParam and other online tools or local software.The physical and chemical properties,phylogenetic relationships and conservative elements of the WRKY family members were analyzed by bioinformatics.[Results]A total of 65 WRKY family members were identified from the rice genome,each of which had a conserved element of WRKYGQK,in addition to a conserved zinc finger structure.Using MEGA to cluster the obtained WRKY family members,65 WRKY family members can be divided into A,B,C,D,E 5 categories,among which A,B,C,D 4 are closely related and can be clustered into one group;while class A is relatively distantly related,and it is considered that class A members may be a relatively primitive class that has been preserved during long-term evolution.[Conclusion]This study systematically identified the WRKY family of rice,and provided a reference for further study on the function and interaction of WRKY transcription factors in rice.
[Objective]Bioinformatics analysis of WRKY transcription factor family members in rice was carried out to provide basis for further study on the function of WRKY transcription factor family in rice.[Method]The whole genome sequence of rice was downloaded from NCBI website.The WRKY family members were screened by CDD,Blast,MEME,MEGA,ProtParam and other online tools or local software.The physical and chemical properties,phylogenetic relationships and conservative elements of the WRKY family members were analyzed by bioinformatics.[Results]A total of 65 WRKY family members were identified from the rice genome,each of which had a conserved element of WRKYGQK,in addition to a conserved zinc finger structure.Using MEGA to cluster the obtained WRKY family members,65 WRKY family members can be divided into A,B,C,D,E 5 categories,among which A,B,C,D 4 are closely related and can be clustered into one group;while class A is relatively distantly related,and it is considered that class A members may be a relatively primitive class that has been preserved during long-term evolution.[Conclusion]This study systematically identified the WRKY family of rice,and provided a reference for further study on the function and interaction of WRKY transcription factors in rice.
引文
[1] ZHU D W,QIAN Z H,WEI H Y,et al.The effects of field pre-harvest sprouting on the morphological structure and physicochemical properties of rice (Oryza sativa L.) starch[J].Food chemistry,2019,278:10-16.
[2] YADAV S,GILL S S,PASSRICHA N,et al.Genome-wide analysis and transcriptional expression pattern-assessment of superoxide dismutase (SOD) in rice and Arabidopsis under abiotic stresses[J].Plant gene,2019,17:1-9.
[3] 朱景福,李芳,鹿保鑫.基于聚类改进的Fisher与KNN判别分类算法对比研究[J].安徽农业科学,2019,47(1):250-252,257.
[4] 谷彦冰,冀志蕊,迟福梅,等.苹果WRKY基因家族生物信息学及表达分析[J].中国农业科学,2015,48(16):3221-3238.
[5] 赵楠楠,刘立峰.植物WRKY转录因子及其生物学功能[J/OL].分子植物育种.[2018-12-25].http://kns.cnki.net/kcms/detail/46.1068.S.20181218.1113.004.html.
[6] ISHIGURO S,NAKAMURA K.Characterization of a cDNA encoding a novel DNA-binding protein,SPF1,that recognizes SP8 sequences in the 5' upstream regions of genes coding for sporamin and beta-amylase from sweet potato[J].Molecular and general genetics,1994,244(6):563-571.
[7] ZHANG Y J,WANG L J.The WRKY transcription factor superfamily:Its origin in eukaryotes and expansion in plants[J].BMC Evolution Biology,2005,5(1):1-12.
[8] 刘梦佳,李海峰.水稻WRKY转录因子家族研究进展[J].河南农业科学,2016,45(3):1-8.
[9] 肖俊.水稻WRKY13通过选择性结合不同顺式作用元件调控非生物和生物胁迫信号路径间的互作[D].武汉:华中农业大学,2013.
[10] 周丽霞,曹红星.低温胁迫下油棕WRKY转录因子基因的表达特性分析[J].南方农业学报,2018,49(8):1490-1497.
[11] 万永青,毛铭铢,万东莉,等.中间锦鸡儿WRKY75基因对拟南芥耐受盐和ABA能力的影响[J].西北植物学报,2018,38(1):17-25.
[12] 梁滨,董冬.植物WRKY转录因子的研究进展[J].生物学通报,2018,53(6):5-8.
[13] 刘洋,郑洋洋,宫超,等.番茄AS2基因家族的系统进化分析[J].基因组学与应用生物学,2018,37(9):3958-3965.
[14] SAITOU N,NEI M.The neighbor-joining method:A new method for reconstructing phylogenetic trees[J].Molecular biology and evolution,1987,4(4):406-425.
[15] 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.
[16] 向贵生,王开锦,晏慧君,等.蔷薇科植物MLO蛋白家族的生物信息学分析[J].基因组学与应用生物学,2018,37(5):2043-2059.
[17] ROSS C A,LIU Y,SHEN Q J.The WRKY gene family in rice (Oryza sativa)[J].J Integr Plant Biol,2007,49(6):827-842.
[2] YADAV S,GILL S S,PASSRICHA N,et al.Genome-wide analysis and transcriptional expression pattern-assessment of superoxide dismutase (SOD) in rice and Arabidopsis under abiotic stresses[J].Plant gene,2019,17:1-9.
[3] 朱景福,李芳,鹿保鑫.基于聚类改进的Fisher与KNN判别分类算法对比研究[J].安徽农业科学,2019,47(1):250-252,257.
[4] 谷彦冰,冀志蕊,迟福梅,等.苹果WRKY基因家族生物信息学及表达分析[J].中国农业科学,2015,48(16):3221-3238.
[5] 赵楠楠,刘立峰.植物WRKY转录因子及其生物学功能[J/OL].分子植物育种.[2018-12-25].http://kns.cnki.net/kcms/detail/46.1068.S.20181218.1113.004.html.
[6] ISHIGURO S,NAKAMURA K.Characterization of a cDNA encoding a novel DNA-binding protein,SPF1,that recognizes SP8 sequences in the 5' upstream regions of genes coding for sporamin and beta-amylase from sweet potato[J].Molecular and general genetics,1994,244(6):563-571.
[7] ZHANG Y J,WANG L J.The WRKY transcription factor superfamily:Its origin in eukaryotes and expansion in plants[J].BMC Evolution Biology,2005,5(1):1-12.
[8] 刘梦佳,李海峰.水稻WRKY转录因子家族研究进展[J].河南农业科学,2016,45(3):1-8.
[9] 肖俊.水稻WRKY13通过选择性结合不同顺式作用元件调控非生物和生物胁迫信号路径间的互作[D].武汉:华中农业大学,2013.
[10] 周丽霞,曹红星.低温胁迫下油棕WRKY转录因子基因的表达特性分析[J].南方农业学报,2018,49(8):1490-1497.
[11] 万永青,毛铭铢,万东莉,等.中间锦鸡儿WRKY75基因对拟南芥耐受盐和ABA能力的影响[J].西北植物学报,2018,38(1):17-25.
[12] 梁滨,董冬.植物WRKY转录因子的研究进展[J].生物学通报,2018,53(6):5-8.
[13] 刘洋,郑洋洋,宫超,等.番茄AS2基因家族的系统进化分析[J].基因组学与应用生物学,2018,37(9):3958-3965.
[14] SAITOU N,NEI M.The neighbor-joining method:A new method for reconstructing phylogenetic trees[J].Molecular biology and evolution,1987,4(4):406-425.
[15] 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.
[16] 向贵生,王开锦,晏慧君,等.蔷薇科植物MLO蛋白家族的生物信息学分析[J].基因组学与应用生物学,2018,37(5):2043-2059.
[17] ROSS C A,LIU Y,SHEN Q J.The WRKY gene family in rice (Oryza sativa)[J].J Integr Plant Biol,2007,49(6):827-842.