苹果MADS-box转录因子的生物信息学及其在不同组织中的表达

doi:10.3864/j.issn.0578-1752.2014.06.011

摘要/Abstract

摘要： 【目的】分析已知苹果（Malus×domestica）MADS-box基因基本信息，研究其在不同组织中表达情况。【方法】利用NCBI数据库查询并获得苹果MADS-box基因，采用CLC Combined Workbench version 6、WebLogo 3、MEGA4.1、MapInspect和MEME等软件对其蛋白序列进行生物信息学分析。采用RT-PCR技术研究MdMADS基因在不同组织中的表达情况。【结果】共得到26个苹果MADS-box基因。MADS-box结构域分析显示，氨基酸10（I）、16-19（RQVT）、22-23（KR）、29-31（KKA）、33（E）、37-39（LCD）、42（V）和48（S）是保守不变的。保守元件分析表明，苹果MADS-box基因包含4个保守元件：元件1、3为MADS盒；元件2、4为K盒。所有苹果MADS-box蛋白都包含有MADS盒（除MdMADS9）和K盒。进化树分析结果显示，苹果MADS基因共分为5个亚组。MdMADS1、3、4、6、7、8、11、18属于SEP亚组；MdMADS2、5、12属于AP1亚组；MdMADS10、14、15、19、22和MdAGL属于AG亚组；MdMADS16、17、21、MdSOC1、MdSOC1a和MdSOC1c属于SOC1亚组；MdMADS13、23和MdPI属于AP3亚组；MdMADS20属于SVP亚组。染色体定位分析显示，MdMADS在8号染色体上分布最多，共有4个；其次是染色体2、14和17，均分布3个；染色体1、5、6、7、11和16均分布1个；染色体3、4、12和15则没有分布。RT-PCR结果分析显示，SEP和AGL亚组表达模式较为一致，主要在花和果实中表达；AP1亚组除在花和果实中表达外，在其它组织器官中也有表达。【结论】苹果MADS-box基因结构高度保守，多数成员参与调控花和果实发育过程。

关键词: 苹果 , MADS-box , 转录因子 , 生物信息学 , 表达分析

Abstract: 【Objective】The study aimed to analyze the basic information of MADS-box genes of apple (Malus × domestica), and study their expression levels in different apple tissues.【Method】Apple MADS-box genes were obtained by the NCBI database query, and the amino acid sequences were analyzed with CLC Combined Workbench version 6, WebLogo 3, MEGA4.1, MapInspect and MEME bioinformatics software, their expression levels in different tissues were further studied with RT-PCR.【Result】Totally 26 apple MADS-box genes were found in NCBI database. The results of domain analysis indicated that amino acid 10(I), 16-19 (RQVT), 22-23 (KR), 29-31 (KKA), 33 (E), 37, 39 (LCD), 42 (V) and 48 (S) of apple MADS-box domain were conserved. Conserved motif analysis showed that the conserved motifs 1 and 3, which specify the MADS domain and motifs 2 and 4, which specify the K domain, were observed in all apple MADS-box proteins (except for MdMADS9). The result of phylogenetic analysis revealed that apple MADS-box genes were divided into 5 subclasses. MdMADS1, 3, 4, 6, 7, 8, 11 and 18 belong to SEP subclass. MdMADS2, 5 and 12 are AP1 subclass. MdMADS10, 14, 15, 19, 22 and MdAGL belong to AG subclass. MdMADS16, 17, 21, MdSOC1, MdSOC1a and MdSOC1c are SOC1 subclass. MdMADS13, 23 and MdPI belong to AP3 subclass. MdMADS20 belong to SVP subclass. Chromosome mapping analysis showed that the largest number of apple MADS-box genes were found on chromosome 08 (four genes), followed by chromosomes 02, 14 and 17 (three genes each). Only one gene is located on chromosomes 01, 05, 06, 07, 11 and 16, respectively. No gene is located on chromosomes 03, 04, 12 and 15. RT-PCR results indicated that MdMADS genes were highly expressed in flowers and mature fruits. Similar expression patterns were observed within the SEP and AGL subclasses. AP1 subclass was not only expressed in flowers and mature fruits, but also expressed in other tissues. 【Conclusion】 MdMADS genes are highly and structurally conserved and involved in regulation of apple flower and fruit development processes.

Key words: apple , MADS-box , transcription factor , bioinformatics , expression analysis

董庆龙, 冀志蕊, 迟福梅, 田义, 安秀红, 徐成楠, 周宗山. 苹果MADS-box转录因子的生物信息学及其在不同组织中的表达[J]. 中国农业科学, 2014, 47(6): 1151-1161.

DONG Qing-Long, JI Zhi-Rui, CHI Fu-Mei, TIAN Yi, AN Xiu-Hong, XU Cheng-Nan, ZHOU Zong-Shan. Bioinformatics of the MADS-Box Transcription Factor and Their Expression in Different Apple Tissues[J]. Scientia Agricultura Sinica, 2014, 47(6): 1151-1161.

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