Genomic Features of Rickettsia heilongjiangensis Revealed by Intraspecies Comparison and Detailed Comparison With Rickettsia japonica
Genomic Features of Rickettsia heilongjiangensis Revealed by Intraspecies Comparison and Detailed Comparison With Rickettsia japonica
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DOI：
10.3389/fmicb.2019.02787
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发表时间：
2019-12-06
影响因子：
5.2
通讯作者：
Hayashi, Tetsuya
中科院分区：
文献类型：
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作者：
Kasama, Kentaro;Fujita, Hiromi;Hayashi, Tetsuya
黑龙江立克次体是远东斑点热(FESF)的病原体。在日本，2008年在宫城县仙台发现了一例FESF人间病例，并从疑似感染地理区域采集的直立血蜱中分离出黑龙血吸虫细菌。虽然对立克次体的种内基因组多样性研究很少，但我们最近的分析发现，日本立克次体基因组多样性极低，它是日本斑点热病的病原体，是黑龙立克次体的近亲。为了研究黑龙江立克动物基因组的多样性，了解中日两国间的亲缘关系，本研究对采自仙台的3个黑龙江硬蜱分离物和内蒙古采集的1个黑龙江硬蜱分离物中国进行了测序，并与黑龙江省森林革螨的模式菌株中国进行了基因组序列比较。虽然这三个日本株是在2008年、2009年和2012年分离的，但它们的基因组序列是相同的，这表明携带一个黑龙江立克隆氏杆菌克隆体的扁虱已经在日本仙台分布。在这5个黑龙江乳杆菌分离株中，尽管这些分离株在地理和时间上存在显著差异，但只发现了81个SNPs和13个插入/缺失位点。81个SNP中有很大一部分(16/81)是重组基因。这些结果表明，与日本刺参一样，黑龙江刺参的基因组多样性较低。此外，我们还对黑龙江大熊猫和日本大黄进行了详细的基因组比较，以准确地确定保守的和物种特异的基因。这一分析表明，尽管编码RelA/Spot家族蛋白和主要表面蛋白的串联重复序列的基因组座位存在显著差异，但两个物种之间的基因谱仅有很小的差异，这表明SNPs和小Indels是导致两个物种之间功能或生理差异的原因。通过这一分析，还确定了几个物种特异的基因组区域，这些区域可以作为区分黑龙江大黄和日本大黄的理想的PCR目标。
Rickettsia heilongjiangensis is the causative agent of Far-Eastern spotted fever (FESF). In Japan, a human case of FESF was identified in Sendai in Miyagi Prefecture in 2008, and R. heilongjiangensis bacteria were isolated from Haemaphysalis concinna ticks collected in the suspected geographical area of infection. Although the intraspecies genome diversity of Rickettsia has been poorly investigated, our recent analysis revealed extremely low genomic diversity of R. japonica, the agent of Japanese spotted fever, which is a close relative of R. heilongjiangensis. In this study, to investigate the genomic diversity of R. heilongjiangensis and understand the genetic relationship between Japanese and Chinese isolates, we sequenced three isolates from H. concinna ticks collected in Sendai and one isolate from a H. concinna tick collected in Inner Mongolia, China, and performed genomic comparisons between these isolates and strain 054, the type strain isolated from a Dermacentor silvarum tick in Heilongjiang Province, China. Although the three Japanese strains were isolated in 2008, 2009, and 2012, their genome sequences were identical, indicating that H. concinna ticks carrying a single R. heilongjiangensis clone have been distributed in Sendai, Japan. Among the five R. heilongjiangensis isolates, only 81 SNPs and 13 insertion/deletion sites were identified, despite the significant differences in these isolates both geographically and temporally. A significant portion of the 81 SNPs (16/81) were found to be recombinogenic. These results indicate low genomic diversity of R. heilongjiangensis, as observed in R. japonica. We further performed a detailed genomic comparison of R. heilongjiangensis and R. japonica to accurately define conserved and species-specific genes. This analysis revealed that although notable variations were found in the genomic loci encoding RelA/SpoT family proteins and tandem repeats in major surface proteins, there was only a small difference in the gene repertoire between the two species, suggesting that SNPs and small InDels are responsible for the functional or physiological differences between the two species, if present. Through this analysis, several species-specific genomic regions that can serve as ideal PCR targets for distinguishing R. heilongjiangensis and R. japonica were also identified.