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园艺学报 ›› 2019, Vol. 46 ›› Issue (11): 2082-2098.doi: 10.16420/j.issn.0513-353x.2019-0046

• 研究论文 • 上一篇    下一篇

苹果Trihelix转录因子家族生物信息学鉴定与基因表达分析

王 萍,卢世雄,梁国平,马宗桓,李文芳,毛 娟,陈佰鸿*   

  1. 甘肃农业大学园艺学院,兰州 730070
  • 出版日期:2019-11-25 发布日期:2019-11-25
  • 基金资助:
    甘肃省科技重大专项(18ZD2NA006);国家自然科学基金项目(31860530)

Bioinformatics Identification and Expression Analysis of Trihelix Transcription Factor Family in Apple

WANG Ping,LU Shixiong,LIANG Guoping,MA Zonghuan,LI Wenfang,MAO Juan,and CHEN Baihong*   

  1. College of Horticulture,Gansu Agricultural University,Lanzhou 730070,China
  • Online:2019-11-25 Published:2019-11-25

摘要: 利用生物信息学方法在苹果全基因组中鉴定了Trihelix转录因子基因,对基因结构、染色体的定位,以及其对应蛋白的理化性质、保守基序和进化关系等进行了分析;同时基于基因芯片表达数据和qRT-PCR分析,明确了苹果Trihelix在不同组织和逆境胁迫下的差异表达情况。通过分析,共鉴定得到了39个苹果Trihelix转录因子,其蛋白质的大小介于227 ~ 917 aa,分子量介于25.751 ~ 101.294 kD,等电点介于4.78 ~ 9.80。根据进化关系将其分为5个亚族,分别为GT-1、GT-2、GTγ、SIP1和SH4,亚族内部分成员的基因结构相似。基于MEME程序分析苹果Trihelix 转录因子家族的保守基序与聚类分析结果具有较高的一致性。启动子上游1 kb区域顺式作用元件分析表明MdTrihelix1、MdTrihelix19在CGTCA-motif上,MdTrihelix6、MdTrihelix13在ABRE上,MdTrihelix2、MdTrihelix7、MdTrihelix14和MdTrihelix16在GT1-motif上的响应均较高。基因芯片表达发现,Trihelix38、Trihelix14、Trihelix9和Trihelix11在花、果实、叶、茎、根、种子和幼苗中几乎不表达,其余35个基因在多种组织中均存在一定水平的表达,对花和果实表达上调的基因中除Trihelix36属于GT-1亚家族外,其余都属于GT-2亚家族和SIP1亚家族成员。通过qRT-PCR分析,检测到33个MdTrihelix在响应逆境胁迫应答方面表现出多样性。

关键词: 苹果, 外源基因, 花粉, 育性, 绒毡层, 苹果, Trihelix, 转录因子家族, 生物信息学, 表达分析

Abstract: In this paper,the members of Trihelix were identified in the whole genome of apple by bioinformatics method,gene structure,chromosome location,and physical and chemical properties,conservative motifs,evolutionary relationships of Trihelix transcription factor were analyzed. At the same time,based on microarray expression data and qRT-PCR analysis,the differential expression of apple Trihelix in different tissues and stresses was identified. A total of 39 Trihelix transcription factors were identified,with protein sizes ranging from 227 to 917 aa,their molecular weights ranging from 25.751 to 101.294 kD,and their isoelectric points ranging from 4.78 to 9.80. According to the evolutionary relationship,it was divided into five subfamilies,namely GT-1,GT-2,GTγ,SIP1 and SH4. The genetic structure of some subfamily members are similar. Based on the MEME program,the conserved motifs of the apple Trihelix transcription factor family were highly consistent with the results of cluster analysis. The cis-acting element analysis of the 1 kb upstream to the promoter showed that the response of MdTrihelix1,MdTrihelix19 on CGTCA-motif,MdTrihelix6,MdTrihelix13 on ABRE-motif,MdTrihelix2,MdTrihelix7,MdTrihelix14 and MdTrihelix16 on GT1-motif were higher. Gene chip expression found that Trihelix 38,Trihelix 14,Trihelix 9 and Trihelix 11 were hardly expressed in flowers,fruits,leaves,stems,roots,seeds and seedlings,and the remaining 35 genes were expressed at a certain level in various tissues. Among those genes whose expression is up-regulatd in flowers and fruits,except for Trihelix36 belonging to the GT-1 subfamily,the others belong to the members of GT-2 and SIP1 subfamily. Through qRT-PCR analysis,33 MdTrihelix genes showed diversity in response to stress.

Key words: apple, exogenous gene, pollen, viability, tapetum, apple, Trihelix, transcription factor family, bioinformatics, expression analysis

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