一株人参细菌性软腐病致病假单胞菌的基因组特征与毒力基因分析  

Genomic characteristics and virulence genes of Pseudomonas glycinae,the causal agent of bacterial soft rot in ginseng

作　　者：刘坤 孙文松 张天静[1,2] 沈宝宇 李晓丽[1,2] LIU Kun;SUN Wensong;ZHANG Tianjing;SHEN Baoyu;LI Xiaoli(Liaoning Research Institute of Cash Crops,Liaoyang 111000,Liaoning,China;Institute of Medical Plants,Liaoning Academy of Agricultural Sciences,Liaoyang 111000,Liaoning,China)

机构地区：[1]辽宁省经济作物研究所,辽宁辽阳111000 [2]辽宁省农业科学院药用植物研究所,辽宁辽阳111000

出　　处：《微生物学通报》2024年第11期4667-4686,共20页Microbiology China

基　　金：国家中药材产业技术体系辽阳综合试验站项目(CARS-21-06);辽宁省农业科学院学科建设项目(2019DD144221);辽宁省农业科学院协同创新专项(2022XTCX0503);辽宁省应用基础研究计划(联合计划)项目(2022JH2/101300284)。

摘　　要：【背景】细菌性软腐病是植物根部主要病害之一,可在作物生长期和储藏期造成巨大损失。2023年本团队首次发现并报道了由Pseudomonas glycinae引起的人参细菌性软腐病。【目的】探索Pseudomonas glycinae XJFL-1菌株的基因组特征,并通过与属内和种内代表性菌株的比较基因组学分析,初步探讨P.glycinae的遗传特性以及菌株XJFL-1基因组中可能编码的致病相关的毒力因子和Ⅱ型、Ⅲ型分泌系统效应因子。【方法】通过基因组注释、比较基因组学分析和基因家族分析等探索基因组的特征、遗传特性及毒力基因。【结果】基因组注释发现编码了碳水化合物、氨基酸和蛋白质代谢相关酶类,以及与鞭毛运动、膜形成和群体感应相关的重要基因;平均核苷酸一致性(average nucleotide identity,ANI)、数字DNA-DNA杂交分析(digital DNA-DNA hybridization,dDDH)及共线性分析结果确认该菌株为P.glycinae,并且P.glycinae物种的直系同源基因集具有较高的种内保守性;植物细胞壁降解酶系(plant cell wall degrading enzyme,PCWDE)分析结果显示,菌株XJFL-1可编码37种PCWDE,主要为糖苷水解酶(glycoside hydrolase,GH)、碳水化合物酯酶(carbohydrate esterase,CE)和多糖裂解酶(polysaccharide lyase,PL);预测到的Ⅱ型分泌系统效应因子基因主要有编码脂肪酶的lapA、lapB和lapC,编码碱性磷酸酶的phoA2,编码磷脂酶的plcA和编码几丁质酶的cbpD;Ⅲ型分泌系统中E3泛素连接酶效应因子是XJFL-1编码的优势基因,包括IpaH家族的ipaH9.8、ipaH7.8、ipaH4.5、ipaH3和ipaH1.4,SLRP家族的slrP,以及sspH2、sspH1和NGR_a03640,但未注释到编码果胶酶的相关基因。果胶酶活力测定结果显示,菌株XJFL-1确实不能分泌果胶酶类。【结论】比较基因组学和基因家族分析结果明确了菌株XJFL-1与假单胞菌属(Pseudomonas)内代表性菌株的亲缘关系,以及P.glycinae的种内遗传特性;毒力基因预测结果发现,菌�[Background]Bacterial soft rot poses a significant threat to plant roots,resulting in substantial agricultural losses.Our team identified Pseudomonas glycinae as the causative agent of bacterial soft rot in ginseng in 2023.[Objective]To delve into the genomic characteristics of P.glycinae XJFL-1,conduct a comparative genomics analysis for XJFL-1 with intra-and intergenus strains,and predict putative virulence factors and effectors of type II and III secretion systems(T2SS and T3SS,respectively).[Methods]We performed genome annotation,comparative genomics analysis,and gene family analysis to predict the genomic characteristics,genetic characteristics,and virulence genes.[Results]Genome annotation revealed the presence of genes encoding the enzymes involved in carbohydrate,amino acid,and protein metabolism,as well as key genes associated with flagellar movement,membrane biogenesis,and quorum sensing.Strain XJFL-1 was identified as P.glycinae based on ANI,dDDH,and collinearity analyses,and a high degree of intraspecific gene conservation was found for P.glycinae.Strain XJFL-1 encoded 37 plant cell wall-degrading enzymes(PCWDEs)including glycoside hydrolases(GHs),carbohydrate esterases(CEs),and polysaccharide lyases(PLs).In addition,the strain carried the genes encoding effectors of T2SS(e.g.lapA,lapB,lapC,phoA2,plcA,and cbpD)and T3SS(e.g.ipaH9.8,ipaH7.8,ipaH4.5,ipaH3,ipaH1.4,slrP,sspH2,sspH1,and NGR_a03640).However,pectinase genes were conspicuously absent.The results of the pectinase activity assay indicated that strain XJFL-1 was unable to secrete pectinase.[Conclusion]The results of comparative genomics and gene family analyses clarified the genetic relationship of strain XJFL-1 with representative strains of Pseudomonas and the intraspecific genetic characterization of P.glycinae.Additionally,the strain carried abundant genes encoding PCWDEs and effectors of T2SS and T3SS associated with pathogenicity.

关 键 词：基因组 比较基因组学分析 效应因子 植物细胞壁降解酶 Pseudomonas glycinae XJFL-1 

分 类 号：S435.675[农业科学—农业昆虫与害虫防治]