Table_5_Genomic and Phenotypic Biology of Novel Strains of Dickeya zeae Isolated From Pineapple and Taro in Hawaii: Insights Into Genome Plasticity, Pathogenicity, and Virulence Determinants.DOCX

Dickeya zeae, a bacterial plant pathogen of the family Pectobacteriaceae, is responsible for a wide range of diseases on potato, maize, rice, banana, pineapple, taro, and ornamentals and significantly reduces crop production. D. zeae causes the soft rot of taro (Colocasia esculenta) and the heart rot of pineapple (Ananas comosus). In this study, we used Pacific Biosciences single-molecule real-time (SMRT) sequencing to sequence two high-quality complete genomes of novel strains of D. zeae: PL65 (size: 4.74997 MB; depth: 701x; GC: 53.6%) and A5410 (size: 4.7792 MB; depth: 558x; GC: 53.5%) isolated from economically important Hawaiian crops, taro, and pineapple, respectively. Additional complete genomes of D. zeae representing three additional hosts (philodendron, rice, and banana) and other species used for a taxonomic comparison were retrieved from the NCBI GenBank genome database. Genomic analyses indicated the truncated type III and IV secretion systems (T3SS and T4SS) in the taro strain, which only harbored one and two genes of T3SS and T4SS, respectively, and showed high heterogeneity in the type VI secretion system (T6SS). Unlike strain EC1, which was isolated from rice and recently reclassified as D. oryzae, neither the genome PL65 nor A5410 harbors the zeamine biosynthesis gene cluster, which plays a key role in virulence of other Dickeya species. The percentages of average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) between the two genomes were 94.47 and 57.00, respectively. In this study, we compared the major virulence factors [plant cell wall-degrading extracellular enzymes and protease (Prt)] produced by D. zeae strains and evaluated the virulence on taro corms and pineapple leaves. Both strains produced Prts, pectate lyases (Pels), and cellulases but no significant quantitative differences were observed (p > 0.05) between the strains. All the strains produced symptoms on taro corms and pineapple leaves, but the strain PL65 produced symptoms more rapidly than others. Our study highlights the genetic constituents of pathogenicity determinants and genomic heterogeneity that will help to understand the virulence mechanisms and aggressiveness of this plant pathogen.

泽氏迪基氏菌（Dickeya zeae）是果胶杆菌科（Pectobacteriaceae）的植物病原细菌，可侵染马铃薯、玉米、水稻、香蕉、菠萝、芋及多种观赏植物，引发多种病害，显著降低作物产量。该菌可引发芋（Colocasia esculenta）软腐病与菠萝（Ananas comosus）心腐病。本研究采用太平洋生物科学单分子实时测序（Pacific Biosciences single-molecule real-time, SMRT）技术，对两株新泽氏迪基氏菌的高质量完整基因组进行测序：PL65（基因组大小4.74997 Mb，测序深度701×，GC含量53.6%）和A5410（基因组大小4.7792 Mb，测序深度558×，GC含量53.5%），二者分别分离自夏威夷具有经济价值的作物芋和菠萝。另外，从NCBI GenBank基因组数据库中调取了另外3种寄主（心叶蔓绿绒、水稻和香蕉）来源的泽氏迪基氏菌完整基因组，以及用于分类学比较的其他相关物种基因组。基因组分析显示，芋源菌株PL65存在截短的Ⅲ型分泌系统（type III secretion system, T3SS）和Ⅳ型分泌系统（type IV secretion system, T4SS），二者分别仅包含1个和2个编码基因；同时该菌株的Ⅵ型分泌系统（type VI secretion system, T6SS）呈现高度异质性。与分离自水稻、近期被重新归类为稻氏迪基氏菌（D. oryzae）的EC1菌株不同，PL65和A5410基因组均不携带泽胺生物合成基因簇——该基因簇在其他迪基氏菌的致病过程中发挥关键作用。两株菌株基因组的平均核苷酸同源性（average nucleotide identity, ANI）和数字化DNA-DNA杂交（digital DNA–DNA hybridization, dDDH）值分别为94.47%和57.00%。本研究对泽氏迪基氏菌菌株产生的主要致病因子——植物细胞壁降解胞外酶与蛋白酶（protease, Prt）——进行了比较，并测定了两株菌株对芋球茎和菠萝叶片的致病力。两株菌株均可产生蛋白酶、果胶酸裂解酶（pectate lyases, Pels）和纤维素酶，但二者之间无显著的数量差异（p>0.05）。所有供试菌株均可在芋球茎和菠萝叶片上引发症状，但PL65菌株的致病速度显著快于其他菌株。本研究揭示了该植物病原细菌的致病决定因子遗传组成与基因组异质性，可为解析其致病机制与侵染致病能力提供重要依据。