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本研究选取采自江西的感染柑橘溃疡病的脐橙样品进行病原分离,采用Illumina Miseq测序平台对分离得到的A型jx-6菌株进行全基因组测序,并与已发表的2株A型菌株和2株A~W型菌株进行比较基因组学分析。直系同源分析表明两种菌株核心基因簇3 887个,只有A~W型菌株具有特异基因簇,特异基因簇为216个。对这些特异基因簇进行分析结果显示大部分与生物代谢和细胞代谢过程有关。基因组共线性分析结果显示相比于A型菌株,A~W型菌株基因组存在翻转、易位、倒位等基因组重排事件。另外,对A型菌株和A~W型菌株的全基因组上存在的前噬菌体进行预测分析,结果显示A型菌株基因组含有3个前噬菌体区域,A~W型菌株基因组含有5个前噬菌体区域。通过比对发现A型菌株中的prophage2与A~W型菌株中的prophage2属于同一种噬菌体,其中A~W型菌株中的prophage4和prophage5两个前噬菌体区域正好插入在两个菌株共线性程度较低的部分。这些前噬菌体的插入及基因组重排有可能是导致A~W型菌株寄主专化性的原因所在。基于7个看家基因(atp D,dna K,efp,fyu A,gln A,gyrB,rpoD)的系统发育进化分析表明所有的A型菌株聚为一支,A~W型菌株聚为一支,这一结果与基因同源聚类分析的结果相一致。
In this study, navel orange samples from citrus canker isolated from Jiangxi were selected for pathogen isolation. Genomic sequencing of the isolated strains of type A jx-6 was carried out using Illumina Miseq sequencing platform and compared with the published 2 strains of type A and 2 Strains A ~ W strain comparative genomics analysis. Homologous analysis showed that there were 3 887 core gene clusters in both strains, of which only A to W strains had specific gene clusters and 216 specific gene clusters. The analysis of these specific gene clusters showed that most of them were related to biological metabolism and cellular metabolism. Genome collinearity analysis showed that compared with type A strains, genotype A ~ W strains had overturn, translocation, transposition and other genomic rearrangements. In addition, the prediction of the prophage present on the genomes of type A and type A-W strains showed that the type A strain genome contained three pre-phage regions and that the genotypes A-W contained five pre-phage regions. By comparison, it was found that prophage2 in type A strain belongs to the same type of phage as prophage2 in type A ~ W strain. The prophage4 and prophage5 regions in type A ~ W strains are inserted exactly between the two strains Low part. These pro-phage insertions and genomic rearrangements are likely responsible for the host specificity of A to W strains. Phylogenetic analysis based on seven housekeeping genes (atp D, dna K, efp, fyu A, gln A, gyrB, rpoD) showed that all type A strains clustered together and that type A to W strains clustered together , This result is consistent with the result of gene homology clustering analysis.