引起芭蕉芋细菌性软腐病的玉米迪基氏菌(Dickeya zeae) CE1的全基因组序列及比较基因组学分析

Comparative genomics analysis of Dickeya zeae CE1 causing bacterial soft rot of Canna edulis

摘要:

【背景】玉米迪基氏菌(Dickeya zeae)可引起香蕉、水稻等重要作物的细菌性软腐病，并造成巨大的损失。芭蕉芋抗性较好且与病虫害相关的报道很少，本研究团队首次报道了由D. zeae CE1引起的芭蕉芋细菌性软腐病。【目的】揭示CE1菌株的全基因组序列，并与同样来源于广东香蕉和水稻的D. zeae菌株作比较基因组学分析，初步探讨D. zeae种内不同病原细菌在与寄主互作过程中可能存在的遗传分化机制。【方法】采用三代测序结合二代测序对CE1菌株进行完整基因组测序，利用比较基因组学方法分析该菌株与香蕉和水稻菌株的进化关系和基因组特征差异。【结果】细菌基因组测序表明，CE1菌株的完整基因组大小为4 714 731 bp，注释预测到4 052个编码基因。与芭蕉芋和香蕉两个寄主亲缘关系类似，基因组比较分析发现来自芭蕉芋和香蕉的病菌菌株亲缘关系较近，它们在遗传进化上明显不同于水稻菌株。基因家族分析表明，编码重要致病因子如细菌分泌系统、鞭毛蛋白、胞外多糖、规律间隔成簇短回文重复序列(clustered regularly interspaced short palindromic repeats，CRISPR)等的基因簇在不同寄主间未表现明显分化。通过进一步分析发现，有80个基因是芭蕉芋和香蕉菌株所特有的，42个基因则是水稻菌株所特有的。在芭蕉芋和香蕉菌株的特异基因中，功能预测发现有2个基因簇分别与脂肪酸合成酶和群体感应相关；然而较多的水稻菌株特异基因则与碳水化合物转运和代谢相关，另外有一个水稻菌株特异基因簇存在于CRISPR的邻接位点。【结论】比较基因组学分析确定了芭蕉芋菌株和香蕉菌株、水稻菌株间的遗传亲缘关系，并发现了数个可能与不同类型寄主互作相关的基因位点，为D. zeae病原细菌侵染与香蕉、水稻等重要作物亲缘关系较为接近的不同作物提出风险预警。

Abstract:

[Background] Dickeya zeae causes bacterial soft rot of several important crops such as banana and rice and may cause heavy losses. Canna edulis is resistant to many biotic and abiotic stressors and only a few pests are reported for this plant. Bacterial soft rot of C. edulis caused by D. zeae CE1 was first reported by our research group. [Objective] This study was conducted to sequence the whole genome of D. zeae CE1 and to compare this strain genomically with the other Guangdong strains of this pathogen from banana (strains MS1 and MS2) and rice (strains EC1, EC2 and ZJU1202), in order to explore any genetic differentiation related to the interaction between pathogenic D. zeae bacteria and their hosts. [Methods] The third-generation sequencing combined with next-generation sequencing method was used to construct the complete genome of strain CE1. Next, comparative genomics was adopted to compare the evolutionary relationships and genomic characteristics of strain CE1 with other strains of the pathogen isolated from banana and rice plants. [Results] The complete genome size of CE1 was 4 714 731 bp, with 4 052 coding genes predicted. Similarly with the taxonomic relation between C. edulis and banana, the strains from C. edulis and banana were closely related showing by the phylogenetic tree, but they were notably different from rice strains. The OrthoMCL analysis revealed that the bacterial gene clusters encoding important pathogenic factors such as: bacterial secretion systems, flagellar proteins, extracellular polysaccharides, and the clustered regularly interspaced short palindromic repeats (CRISPR), did not have obvious differences that corresponded to different types of hosts. Further analysis revealed that 80 genes were specific to the C. edulis and banana strains, while 42 genes were specific to the rice strains. According to the functional prediction, two of the gene clusters found in the specific loci of C. edulis and banana strains were related to fatty acid synthase and quorum sensing, respectively. However, more rice strain-specific genes were involved in carbohydrates transport and metabolism compared to the C. edulis and banana strains; in addition, there was a specific gene cluster from rice strains found in the adjacent genomic locus of the CRISPR array. [Conclusion] comparative genomic analysis have determined the phylogenetic relationship among C. edulis strain, banana strains, and rice strains and found several gene loci that might be involved in the interaction between these D. zeae strains and the hosts of different types. It is recommend providing an early warning to growers that crops closely related to banana and rice may be at risk of infection from these important pathogenic bacteria.