丁香假单胞菌基因组内简单重复序列的比较分析  

Comparative Analysis of SSR in Pseudomonas syringae Genomes

作　　者：连玲丽[1,2] 洪旭鸿[1] 郑璐平[2] 黄碧芳[1] 谢荔岩[2] 林奇英[2] 

机构地区：[1]福建农林大学生命科学学院,福州350002 [2]生物农药与化学生物学教育部重点实验室,福州350002

出　　处：《四川农业大学学报》2012年第2期150-155,共6页Journal of Sichuan Agricultural University

基　　金：福建省青年人才项目(No.2008F3011)

摘　　要：【目的】分析丁香假单胞菌3个致病变种基因组内简单重复序列(simple sequence repeats,SSR),为病菌SSR标记开发和遗传多样性研究提供有用信息。【方法】基于公共的基因组数据库资源,对3个菌株的完全重复SSR和不完全重复SSR的丰度和组成类型等进行分析。【结果】3个菌株完全重复SSR的分布规律较为相似,其中单碱基的短重复SSR均占绝对优势,多碱基和长重复SSR则较少;菌株B728a、1448A和DC3000的不完全重复SSR总数也较相近,分别为562、529和567,其中数量最多的均为六碱基重复。但3个菌株以四、五和六碱基为基序的SSR在基序组成和数量上则表现出较高的变异性,完全重复SSR中,除AGCC、ACCTGC等基序在两个菌株中同时出现,绝大多数基序仅在单个菌株基因组内出现;不完全重复SSR中,部分基序如CCCTG、ACGCA等的出现频率在不同菌株间存在明显差异。【结论】3个菌株的不完全重复SSR在数量和结构类型上均具有较大的相似性,而菌株间的完全重复SSR在数量和组成上则存在一定差异。[Objective] The objective of this study is to analyze the abundance and composition of simple sequence repeat （SSR） in three pathovars of Pseudomonas syringae and to provide useful information for the development of SSR markers of Pseudomonas syringae and related research on genetic diversity. [Method] Based on the complete genome sequence in the genome database, the perfect and imperfect SSRs of three pathovars of Pseudornonas syringae were examined. [Re- sults] The distribution of perfect SSRs was similar among three pathovars. The mononueleotide repeats were predominant but polynucleotide and long SSRs were relatively few in three genomes. Similar to perfect SSRs, the total number of SSRs in strain B728a, 1448A and DC3000 were 562, 529 and 567 respectively in imperfect SSRs. The most abundant imperfect SSRs in each genome was hexanucleotide repeats. However, three pathovars of perfect and imperfect SSRs with motifs of 4--6 nucleotides exhibited great variations in the composition or abundance. In perfect SSRs, most of the motifs, except for AGCC and ACCTGC, were detected in single strain. In imperfect SSRs, the frequency of occurrence in some motifs, such as CCCTG and ACGCA, were different among strains. [Conclusion] There was large similarity in the abundance and structure of imper- fect SSRs among the three strains. Nevertheless, the opposite was true for perfect SSRs.

关 键 词：丁香假单胞菌 简单重复序列 基因组 

分 类 号：S435.111.49[农业科学—农业昆虫与害虫防治]