基于全基因组测序一株自然形成的耐链霉素果胶杆菌NJAU2的分离鉴定  

Isolation and identification of a spontaneous streptomycin-resistant strain,Pectobacterium aroidearum NJAU2,based on genome-wide analysis

作　　者：杨丽萍 楼望颖 车舒 唐莉栋 邓伟[2] 谷安宇[2] 管俊娇[2] 奎丽梅[2] 安华 王睿 李小林[2] 范加勤[1] YANG Liping;LOU Wangying;CHE Shu;TANG Lidong;DENG Wei;GU Anyu;GUAN Junjiao;KUI Limei;AN Hua;WANG Rui;LI Xiaolin;FAN Jiaqin(College of Plant Protection,Nanjing Agricultural University,Nanjing 210095,China;Institute of Grain Production,Yunnan Academy of Agricultural Science,Kunming 650205,China;Yunnan Grain Industry Group Co.,Ltd,Kunming 650000,China)

机构地区：[1]南京农业大学植物保护学院,南京210095 [2]云南省农业科学院粮食作物研究所,昆明650205 [3]云南省粮食产业集团有限公司,昆明650000

出　　处：《植物病理学报》2024年第6期1198-1214,共17页Acta Phytopathologica Sinica

基　　金：国家重点研究开发项目(2021YFC2600602);江苏省高校一流学科建设项目(PPZY2015B157);云南省科技人才与平台计划(202105AE160009);云南省重大科技专项计划(202302AE090001)。

摘　　要：果胶杆菌属(Pectobacterium)是导致全球农作物经济损失的重要病原细菌之一,抗生素抗性菌株的产生加大了该病害的防控难度。本研究以不同寄主植物分离获得的果胶杆菌为材料,利用平板分析,获得一株野外形成的链霉素抗性菌株。通过基因组测序及比较基因组研究,明确其分类地位,并预测链霉素抗性基因。研究表明,自不同寄主分离的8个菌株中,云南黄花马蹄莲发病株获得的NJAU2,对链霉素存在高度抗性。NJAU2基因组总长5 062 459 bp, GC含量51.83%,N50长度306 378 bp,共有4 568个编码基因。基于果胶杆菌8个管家基因(fliA、fusA、glyA、gyrB、purA、rpoA、rpoS和secY)的MLSA多位点序列分析结果显示NJAU2与标准菌株P.aroidearum SCRI 109~T及已报道的菌株P.aroidearum PC1聚类在同一个分支,该结果与基于16S rRNA基因序列构建的系统发育关系一致,进一步NJAU2与各果胶杆菌的平均核苷酸一致性(ANI)、DNA-DNA杂交(isDDH)分析也支持这一结果。为此,将自然形成的链霉素耐性菌株NJAU2归属于果胶杆菌的新种:Pectobacterium aroidearum,命名为Pectobacterium aroidearum NJAU2。NJAU2的基因组中携带编码链霉素耐药基因集。抗生素耐药性综合数据库(CARD)比对发现NJAU2含有与7类耐药相关的328个耐药基因。此外,NJAU2基因组注释表明:其含有15个编码氨基糖苷类抗生素抗性基因,其中与链霉素抗性相关的基因有rpsL和gidB。马蹄莲软腐病病原菌NJAU2的发现,为果胶杆菌在链霉素抗性方向的研究提供了新材料。Bacteria from the genus of Pectobacterium are the important plant pathogens causing significant economic losses worldwide,and the emergence of antibiotic-resistant strains further exacerbates the challenges in Pectobacterium-caused disease prevention and control.This study used Pectobacteriums isolated from different host plants as materials and used plate analysis to obtain streptomycin-resistant strains formed in the wild.Clarify its taxonomic status through genome sequencing and comparative genome research,and streptomycin resistance genes were predicted.The results shown that among the eight strains isolated from different hosts,NJAU2 obtained from Yunnan yellow-flowered calla lily disease strains is highly resistant to streptomycin.NJAU2 genome was 5062459 bp in length,with G+C content of 51.83%and N50 length of 306378 bp,containing 4568 protein-coding genes.NJAU2 clusters on the same branch as the type strain P.aroidearum SCRI 109^(T) and the reported strain P.aroidearum PC1 based on the Multi-Locus Sequence Analysis results of 8 housekeeping genes(fliA,fusA,glyA,gyrB,purA,rpoA,rpoS,secY).This result is consistent with the phylogenetic relationship constructed based on the 16S rRNA gene sequence.Furthermore,the Average Nucleotide Identity(ANI)and DNA-DNA Hybridization(isDDH)analysis with various Pectobacterium strains also support this classification.Therefore,the naturally occurring streptomycin-resistant strain NJAU2 is classified as a new species within the Pectobacterium genus:Pectobacterium aroidearum,and named Pectobacterium aroidearum NJAU2.P.aroidearum NJAU2 carrying sets of genes encoding proteins for streptomycin-resistanc in its genome.Comparison with the Comprehensive Antibiotic Resistance Database(CARD)identified 328 genes belonging seven types of drug resistance mechanisms.Moreover,in NJAU2 genome,15 genes were annotated encoding aminoglycoside antibiotic resistance,including rpsL and gidB that are related to streptomycin resistance.The discovery of P.aroidearum NJAU2 provides new material for

关 键 词：Pectobacterium aroidearum NJAU2 鉴定 链霉素抗药性 基因组分析 抗性基因 

分 类 号：S432.1[农业科学—植物病理学]