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中国农学通报 ›› 2016, Vol. 32 ›› Issue (21): 106-116.doi: 10.11924/j.issn.1000-6850.casb16040091

所属专题: 生物技术 园艺

• 生物技术科学 • 上一篇    下一篇

番茄GRAS转录因子家族的生物信息学分析

牛义岭,姜秀明,许向阳   

  1. 东北农业大学园艺学院,东北农业大学园艺学院,东北农业大学园艺学院
  • 收稿日期:2016-04-14 修回日期:2016-06-27 接受日期:2016-05-25 出版日期:2016-07-15 发布日期:2016-07-15
  • 通讯作者: 许向阳
  • 基金资助:
    现代农业产业技术体系专项资金“国家大宗蔬菜产业技术体系岗位专家”(CARS-25-A-15);国家自然科学基金“抗叶霉病基因Cf19 的克隆功能验证及防御信号传导途径的研究”(31272171);黑龙江省杰出青年科学基金“抗叶霉病基因Cf11 的克隆功能验证及防御信号传导途径的研究”(JC201204);黑龙江省大宗蔬菜新品种选育“黑龙江省大宗蔬菜新品种选育”(GA15B103-1)。

Bioinformatic Analysis of GRAS Transcription Factors in Tomato

  • Received:2016-04-14 Revised:2016-06-27 Accepted:2016-05-25 Online:2016-07-15 Published:2016-07-15

摘要: 笔者旨在为进一步了解番茄GRAS基因家族的结构特征和进化信息,也为GRAS转录因子的后续相关研究提供一定的理论基础。利用HMMER 3.0软件,通过从Pfam蛋白数据库中下载的GRAS保守域(PF03514),来鉴定番茄GRAS 基因。采用MEGA5.2、Web Logo 3、DNAMAN 5.0、Map Inspect和MEME等软件对其蛋白序列进行生物信息学分析。采用RT-PCR技术检测番茄GRAS基因在番茄根、茎、叶、花和果实中的表达情况。番茄基因组共挖掘出53条GRAS转录子基因,划分为I、II、III、IV、V、VI、VII、VIII 8个亚族。系统进化树结果显示V和VI组中GRAS家族成员最多,且拟南芥的GRAS基因家族中基因功能类似的基因聚类的在一起,则可能同组内番茄GRAS基因家族成员也具有类似功能;染色体定位分析显示GRAS基因在12条染色体中呈不均匀分布;根据WebLogo 3.0对GRAS基因家族的结构域蛋白分析,结果显示GRAS基因家族的蛋白序列并不都是高度保守的;保守元件分析表明番茄GRAS基因家族成员是部分高度保守的。番茄GRAS基因家族大部分成员结构是高度保守,可能参与调控番茄生长和发育等过程。

关键词: 地中海仙客来, 地中海仙客来, 叶纹变异, 基因模式

Abstract: The paper aims to know the structural feature and evolutional information of GRAS gene family in tomato, and provide theoretical basis for further study on GRAS transcription factors. GRAS DNA-binding domain (PF03514) was downloaded from Pfam protein database, and was employed to identify GRAS genes from tomato genome using HMMER 3.0. The obtained amino acid sequences were analyzed with the bioinformatics software, including MEGA 5.2, Weblogo 3, DNAMAN 5.0, Map Inspect and MEME. RT-PCR was used to detect GRAS genes expression in the tissue of roots, stems, leaves, flowers and fruit in tomato. All together 53 tomato GRAS transcription factors were identified and classified into 8 groups, including I, II, III, IV, V, VI, VII, VIII. The phylogenetic tree of GRAS genes among tomato and Arabidopsis demonstrated that the group V and VI encompassed the largest number of GRAS genes, genes with similar function in Arabidopsis thaliana clustered together, so the tomato GRAS genes had similar function within the same group. Chromosome mapping analysis showed that tomato GRAS genes were distributed with different densities on 12 chromosomes. According to the result of the GRAS domain sequence analysis with WebLogo3.0, not all GRAS genes were highly conserved in tomato. Conserved motifs analysis indicated that the part of GRAS genes family was highly conserved. These results suggested that the most of GRAS genes were highly and structurally conserved, and might be involved in the regulation of growth and development processes in tomato.

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