铜绿假单胞菌HZ15全基因组和比较基因组学分析

Whole-genome and comparative genomic analysis of Pseudomonas aeruginosa strain HZ15

  • 摘要: 【目的】 挖掘铜绿假单胞菌(Pseudomonas aeruginosa)菌株HZ15抑菌物质合成相关基因及其抑菌机理,探究不同来源铜绿假单胞菌的遗传多样性及特异性,为菌株HZ15的实际应用提供理论依据。【方法】 采用Nanopore第三代测序技术对分离自鳞翅目幼虫的铜绿假单胞菌菌株HZ15进行全基因组测序,并结合多种数据库对其基因组进行注释,同时与来自不同环境(人体、土壤、植物、废水)的另外9株铜绿假单胞菌进行比较基因组学和泛基因组分析。【结果】 菌株HZ15含有1条6722482 bp的染色体,平均GC含量66.14%,共注释到6173个编码基因,总长度6018345 bp,编码区占基因组全长的89.53%。比较基因组学分析结果显示,10株铜绿假单胞菌在基因组大小、基因数量等方面均存在差异。菌株HZ15含有61个抗生素耐受基因、8个前噬菌体、53个水平基因转移及225个毒力因子。CAZy数据库注释发现,菌株HZ15含有多种可能与其抑菌活性相关的糖苷水解酶(GH18、GH19、GH23、GH73和GH103)。此外,菌株HZ15拥有编码3种金属螯合剂[Pf-5 pyoverdine、伪帕林(pseudopaline)和绿脓杆菌螯铁蛋白(pyochelin)]以及lankaci‐din C、氰化氢(hydrogen cyanide)、双环霉素(bicyclomycin)等抑菌活性成分的基因簇,还特有套索肽(lassopeptide)的次级代谢合成相关基因。泛基因组分析发现10株铜绿假单胞菌有10517个泛基因组基因,5278个核心基因组基因。泛基因组中,菌株HZ15拥有231个独特基因,其中aphA_2bla基因与抗生素耐受性相关。【结论】 菌株HZ15可能通过破坏病原菌细胞壁、释放毒素和抑菌活性成分等抑制病原菌生长,并因其具有较强环境适应能力,在生物防治领域具有良好的应用潜力。

     

    Abstract: 【Objective】 The objective was to identify genes related to the synthesis of antibacterial substances in Pseudomonas aeruginosa strain HZ15,explore its antibacterial mechanisms,and investigate the genetic diversity and specificity of P. aeruginosa from different sources,providing theoretical basis for the practical application of strain HZ15. 【Method】 Using Nanopore third-generation sequencing technology,the whole-genome of P. aeruginosa strain HZ1,5 which was isolated from Lepidoptera larvae,was sequenced. Genome annotation was performed using various databases. Comparative genomics and pan-genomics analysis were conducted with 9 other P. aeruginosa strains from different environments(human,soil,plant and wastewater). 【Result】 Strain HZ15 possessed a single chromosome of 6722482 bp, with an average GC content of 66.14%. A total of 6173 coding genes were annotated,the total length was 6018345 bp, with the coding region accounting for 89.53% of the entire genome. The comparative genomics analysis revealed variations in genome size and gene number among the 10 P. aeruginosa strains. Strain HZ15 contained 61 antibiotic resistance genes,8 prophages,53 horizontally transferred genes,and 225 virulence factors. Annotation using the CAZy database revealed that strain HZ15 possessed several glycoside hydrolases(GH18,GH19,GH23,GH73 and GH103)that might be related to its antibacterial activity. Furthermore,strain HZ15 harbored gene clusters encoding 3 types of metal chelators (Pf-5 pyoverdine,pseudopaline and pyochelin),as well as gene clusters for antibacterial active substances such as lankacidin C,hydrogen cyanide and bicyclomycin,along with its unique secondary metabolic synthesis related genes of lassopeptide. Pan-genomic analysis revealed that the 10 strains of P. aeruginosa had 10517 pan-genome genes and 5278 core genome genes. Within the pan-genome,strain HZ15 had 231 unique genes,among which,aphA_2 and bla genes related to antibiotic resistance. 【Conclusion】 Strain HZ15 likely inhibits pathogens through cell wall disruption,toxin release,and the production of antibacterial compounds. Its strong environmental adaptability suggests potential for application in biocontrol.

     

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