中国农业科学 ›› 2014, Vol. 47 ›› Issue (13): 2602-2612.doi: 10.3864/j.issn.0578-1752.2014.13.012

• 园艺 • 上一篇    下一篇

苹果LysM基因家族的生物信息学及表达分析

 周喆, 张彩霞, 张利义, 王强, 李武兴, 田义, 丛佩华   

  1. 中国农业科学院果树研究所/农业部园艺作物种质资源利用重点实验室/国家苹果育种中心,辽宁兴城 125100
  • 收稿日期:2014-01-13 出版日期:2014-07-01 发布日期:2014-03-04
  • 通讯作者: 田义,Tel:0429-3598272;E-mail:taiyangheizi_129@163.com;丛佩华,Tel:0429-3598103;E-mail:congph@163.com
  • 作者简介:周喆,Tel:0429-3598272;E-mail:zz_jer@163.com。张彩霞,Tel:0429-3598135;E-mail:cxzhang-bj@163.com。周喆与张彩霞为同等贡献作者
  • 基金资助:

    国家自然科学基金(31201602)、农业部现代农业产业技术体系建设专项资金(CARS-28)、国家科技支撑计划(2013BAD02B01)

Bioinformatics and Expression Analysis of the LysM Gene Family in Apple

 ZHOU  Zhe, ZHANG  Cai-Xia, ZHANG  Li-Yi, WANG  Qiang, LI  Wu-Xing, TIAN  Yi, CONG  Pei-Hua   

  1. Institute of Pomology, Chinese Academy of Agricultural Sciences/Key Laboratory of Fruit Germplasm Resources Utilization, Ministry of Agriculture/National Apple Breeding Center, Xingcheng 125100, Liaoning
  • Received:2014-01-13 Online:2014-07-01 Published:2014-03-04

摘要: 【目的】在苹果全基因组中鉴定LysM,通过基因聚类分析、染色体定位、结构分析以及组织表达分析,为苹果LysM的功能研究和利用奠定基础。【方法】利用已公布的苹果基因组数据库GDR和FEM-IASMA,鉴定苹果LysM基因家族成员,并对其进行编号。MdLysM蛋白氨基酸序列的基本信息通过ExPASy Proteomics Server进行预测,亚细胞定位的预测利用WoLF PSORT进行。采用MEGA5软件构建了进化树。应用Plaza程序绘制基因结构,染色体定位信息取自GMDO,鉴定出的39个基因的染色体定位作图使用MapInspector完成;另外,通过实时荧光定量RT-PCR对各基因的组织表达特性进行分析,差异显著性分析通过SPSS完成。【结果】系统地鉴定了39个苹果LysM家族成员。这39个MdLysM蛋白包含241至1 119个不等的氨基酸残基,等电点分布在4.70—9.60范围内。亚细胞定位结果表明,苹果LysM蛋白在细胞核、细胞质、叶绿体、液泡、胞外基质中均有分布。根据聚类分析可将这些基因分为A、B和C 3组,且A组又可进一步被分为Ⅰ、Ⅱ 和 Ⅲ 3个亚族,说明它们的功能可能已经发生了分化。MdLysM蛋白结构域的预测结果及基因结构分析结果均与进化树聚类结果吻合。染色体定位表明,MdLysM分布在苹果17条染色体中的13条上,且此家族的基因在13条染色体上的分布为非均匀的,其中以4号染色体上分布最多,达到了9个,而1、5、7和8号染色体上则未见分布。在苹果LysM家族中鉴定出了10对和1组旁系同源基因,MdLysM基因间存在串联重复和片段重复,它们是苹果LysM家族扩张的主要动力。对39个基因在根、茎、叶、花、果5个组织器官中的实时荧光定量RT-PCR结果显示,5个器官中均能检测到MdLysM的表达,这些基因的组织表达模式具有多样性,表明它们在不同组织中可能扮演不同的角色。【结论】苹果LysM基因家族拥有39个成员,进化上可分为3组,基因结构的复杂程度与进化树聚类存在联系。39个基因分布于13条染色体上,存在重复事件。这些信息为今后苹果LysM基因家族的功能研究奠定了基础。

关键词: 苹果 , LysM基因家族 , 系统发育分析 , 表达分析

Abstract: 【Objective】 The objective of this study is to lay a basis for the further functional identification and application of LysM genes by bioinformatics and expression analysis. 【Method】 Based on apple genome database GDR and FEM-IASMA, the sequences of LysM family genes were identified and numbered in apple. Basic information of the MdLysM amino acid sequence was predicted by ExPASy Proteomics Server, the prediction of the sublocation was finished by the WoLF PSORT. A phylogenetic tree was constructed using the MEGA5 software. The plaza was used to draw the structure of the genes. Information about the chromosome location was obtained from the GMDO. Finally, the map of the chromosome location of the 39 MdLysM genes was accomplished through MapInspector. In addition, real-time qRT-PCR was used to determine the expression pattern of these genes, and the significance of difference was analyzed by SPSS. 【Result】A sum of 39 LysM genes were identified systematically in apple. The number of amino acid of the 39 MdLysM proteins ranges from 241 to 1 119. The isoelectric point distributed from 4.70 to 9.60. Sublocation results indicated that the LysM proteins in apple exist in the nucleus, cytoplasm, chloroplast, vacuole and extracellular matrix. They were classified into three groups (group A, B and C), of which group A was divided into three subgroups according to the phylogeny relationship and gene structures, this implies that function differentiation may have happened. The predicted results of the protein domains were congruent with the clustering in phylogenetic tree. The results of chromosomes location indicated that among apple’s all 17 chromosomes, 13 chromosomes have LysM genes located on and the distribution of these genes was not homogeneous. Compared to other chromosomes, chromosome No. 4 contains more genes with a number of 9, while none of the identified genes localized on chromosomes No.1, No.5, No.7 and No.8. Ten pairs and 1 group of paralogs were identified in apple LysM gene family. Tandem and segmental duplication exist among them, and they are the main power for the expansion of apple LysM gene family. The expression patterns of the 39 MdLysM genes in roots, stems, leaves, flowers and fruits were determined by quantitative real-time PCR, and the result shows that their expression can be detected in all of the five organs. Their expression patterns are diverse which indicate that they may play different roles in different organs.【Conclusion】Thirty-nine LysM gene family in apple were identified in genome-wide scan. These genes were classified into three groups and distributed on 13 chromosomes with different tissues expression patterns. These results were significant to forecast the functions of LysM gene family in apple.

Key words: apple , LysM gene family , phylogenetic analysis , expression analysis