Comparative genomic analysis of subspecies of Pantoea stewartii reveals distinct variations
Pantoea stewartii subsp. stewartii (Pnss) and P. stewartii subsp. indologenes (Pnsi) are closely related plant pathogens that differ in their host specificities. Pnss is the causal agent of Stewart’s wilt of corn, whereas Pnsi causes disease on millets but not corn. Comparative genomics is a valuable method for characterizing the differences between genomes, but there are few studies on this important quarantine pathogen. Here, we compared publicly available genomes of seven strains of Pnss and three strains of Pnsi. Pan- and core-genome analyses showed that strains isolated from close geographical regions are more similar in their genome structures. Gene content and collinearity analyses further revealed numerous strain-specific genes. In particular, the Pnss type strain DC283 contained over 1200 additional genes compared with other strains. Importantly, we also identified eleven genes that are only present in Pnsi genomes and thus may be useful to distinguish between Pnss and Pnsi strains. Overall, this study characterized the common and distinct genomic features of Pnss and Pnsi, which lay the foundation for future development of molecular methods to detect the Stewart’s wilt pathogen in maize for quarantine regulations and distinguish its two subspecies.
KeywordsQuarantine pathogen Maize Virulence variation Genome evolution
This work was supported by the State Key Laboratory for Conservation and Utilization of Subtropical Agro–bioresources (No. SKLCUSA–b201715). National Key Project for Basic Research of China (973 Program, No. 2015CB150600).
PL and XZ designed the experiments, PL, YZ, YS, XY, ZY, and XZ analyzed the data and wrote the paper, XW, ZW, JZ and XZ revised the manuscript.
Compliance with ethical standards
The authors declare no potential conflicts of interest, and the research involving no human participants and/or animals.
- Comandatore F, Sassera D, Montagna M, Kumar S, Koutsovoulos G, Thomas G, Repton C, Babayan SA, Gray N, Cordaux R, Darby A, Makepeace B, Blaxter M (2013) Phylogenomics and analysis of shared genes suggest a single transition to mutualism in Wolbachia of nematodes. Genome Biol Evol 5:1668–1674CrossRefGoogle Scholar
- Fegan M, Prior P (2005) How complex is the Ralstonia solanacearum species complex. In: Allen C, Prior P, Hayward A (eds) Bacterial wilt disease and the Ralstonia solanacearum species complex. American Phytopathological Society, Madison, pp 449–461Google Scholar
- Li P, Wang DC, Yan JL, Zhou JN, Yue DY, Jiang ZD, Cao BH, He ZF, Zhang L-H (2016) Genomic analysis of phylotype I strain EP1 reveals substantial divergence from other strains in the Ralstonia solanacearum species complex. Front Microbiol 7:01719Google Scholar
- Mergaert J, Verdonck L, Kersters K (1993) Transfer of Erwinia ananas (synonym, Erwinia uredovora) and Erwinia stewartii to the genus Pantoea emend as Pantoea ananas (serrano 1928) comb. nov. and Pantoea stewartii (smith 1898) comb. nov., respectively, and description of Pantoea stewartii subsp indologenes subsp. nov. Int J Syst Bacteriol 43:162–173CrossRefGoogle Scholar
- Pataky J, Ikin R (2003a) Pest risk analysis : the risk of introducing Erwinia stewartii in maize seed. The Innternational Seed Federation, NyonGoogle Scholar
- Pataky J, Ikin R (2003b) Pest risk analysis: the risk of introducing Erwinia stewartii in maize seed. The International Seed Federation, NyonGoogle Scholar