黄栌枯萎病拮抗细菌CCBC3-3-1的全基因组测序及比较基因组分析

Whole Genome Sequencing and Comparative Genomic Analysis of Antagonistic Bacterium CCBC3-3-1 against Verticillium dahlia

【目的】从黄栌枝干内部分离到的细菌CCBC3-3-1菌株对黄栌枯萎病菌(Verticilliumdahliae)表现出较强的拮抗作用,从基因组层面深入研究其拮抗机理,为进一步研发生防菌剂提供理论依据。【方法】利用PacBio RS测序平台完成CCBC3-3-1的全基因组测序,根据16S rDNA序列信息构建系统发育树,并与同属近缘种菌株进行比较基因组学分析;对其发酵液进行LC-MS非靶标代谢组检测。【结果】CCBC3-3-1基因组总长度为5.16 Mb,由1条环状双链染色体和3个环状质粒组成,GC含量48.08%,含有5013个编码基因。经过antiSMASH预测,CCBC3-3-1基因组中有8个抗生素及次生代谢物合成相关的基因簇,其中2个与已知基因簇相似度较低,5个基因簇功能未知,其发酵液中检测出6种已知抗生素类物质。比较基因组学分析结果表明CCBC3-3-1基因组与泛菌属内4个近缘种均有显著差异,而且CCBC3-3-1在16S rDNA系统发育树上形成一个相对独立的分支。【结论】CCBC3-3-1是泛菌属的一个新变异种Pantoeasp.,能够产生多种抗生素类物质,在黄栌枯萎病生物防治方面具有重要应用潜力。

【Objective】A bacterial strain CCBC3-3-1 isolated from the branch of Cotinus coggygria,has strong growth inhibition activity on the causal agent of Verticillium wilt of Cotinus coggygria.Gaining further understanding about the antagonistic mechanism of this strain at the genomic level will provide theoretical basis for developing a new biocontrol agent.【Method】PacBio RS sequencing platform was used to have the whole genome sequencing of CCBC3-3-1,a phylogenetic tree was constructed based on 16S rDNA sequences,comparative genomic analysis with genetically closed species was carried out,and LC-MS based untargeted metabolomics analysis were performed.【Result】The genome size of CCBC3-3-1 was 5.16 Mb with a GC content of 48.08%,and it contained a circular chromosome and three circular plasmids.A total of 5013 coding DNA sequences(CDSs)were predicted.Through antiSMASH prediction,it was found that there were eight antibiotic and secondary metabolite gene clusters in the genome of CCBC3-3-1,two of which clusters had low similarity with the known ones,and five others had unknown functions.Six known antibiotics were identified in the fermentation broth of CCBC3-3-1.The results of comparative genomic analysis showed that there were significant differences between the genome of CCBC3-3-1 and other four closely related Pantoea species.CCBC3-3-1 strain formed a relatively independent branch on the 16S rDNA phylogenetic tree.【Conclusion】CCBC3-3-1 strain is a new variant species of Pantoea genus,which can produce various antibiotics.It has important application potential in the biological control of the Verticillium wilt of C.coggygria.