Abstract
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.
Highlights
Dickeya and Pectobacterium are Gram-negative, rod-shaped bacteria, which belongs to the family Pectobacteriaceae, and are devastating phytopathogens (Adeolu et al, 2016)
Previous comparative genomic analyses revealed that the genes related to the production of plant cell-wall-degrading enzymes (PCWDEs) include multiple Pels, pectin lyase (Pnl), Pehs, pectin methyl esterase (Pme), pectin acetyl esterases, feruloyl esterases, rhis, and one periplasmic Gan (GanA) exist in various Dickeya species and are highly conserved (Zhou et al, 2015; Duprey et al, 2019)—our analyses demonstrated concordant results
We present two high-quality complete genome sequences of novel D. zeae strains PL65 and A5410 isolated from taro and pineapple in Hawaii
Summary
Dickeya and Pectobacterium are Gram-negative, rod-shaped bacteria, which belongs to the family Pectobacteriaceae (order Enterobacteriales), and are devastating phytopathogens (Adeolu et al, 2016). The D. zeae strains were isolated from a wide and diverse range of hosts such as pineapple, potato, maize, rice, banana, hyacinth, clivia, Brachiaria, chrysanthemum, and philodendron (Sinha and Prasad, 1977; Samson et al, 2005; Sławiak et al, 2009; Toth et al, 2011; Li et al, 2012; Bertani et al, 2013; Pritchard et al, 2013; Zhang et al, 2014; Hu et al, 2018). Among the Dickeya species, D. solani, D. dadantii, and D. zeae often cause serious economic losses, especially on potato, rice, pineapple, and banana (Hussain et al, 2008; Sławiak et al, 2009; Lin et al, 2010; Toth et al, 2011; Zhou J. et al, 2011; Marrero et al, 2013; Zhang et al, 2014)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
