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Journal of Plant Pathology

, Volume 101, Issue 4, pp 997–1004 | Cite as

Comparative genomic analysis of subspecies of Pantoea stewartii reveals distinct variations

  • Peng LiEmail author
  • Ying Zhang
  • Yuqingqing Sun
  • Xingxing Wu
  • Zhiyuan Wang
  • Jianuan Zhou
  • Xiaofan ZhouEmail author
Original Article

Abstract

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.

Keywords

Quarantine pathogen Maize Virulence variation Genome evolution 

Notes

Acknowledgments

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).

Author contributions

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.

Supplementary material

42161_2019_328_MOESM1_ESM.docx (17 kb)
ESM 1 (DOCX 16 kb)
42161_2019_328_MOESM2_ESM.pdf (669 kb)
SI Fig. 1 Nucleic acid co-linearity of strain DC283 vs strain M073a (A), RSA13 (B), A206 (C), and LMG2632 (D), respectively. The sequence of DC283 is ordered as the reference bacterium based on MUMmer 3.22, then the figure is generated by the Mauve rearrangement viewer. The upper and following axes of co-linear graph are constructed, and pairwised nucleic acid sequence of two alignments is marked in the coordinate diagram according to its position information. The locally collinear blocks (LSB) below a genome’s center line are in the reverse complement orientation relative to the reference genome. Lines between genomes trace each orthologous LCB through every genome. Large gray regions within an LCB signify the presence of lineage-specific sequence at that site. (PDF 669 kb)

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Copyright information

© Società Italiana di Patologia Vegetale (S.I.Pa.V.) 2019

Authors and Affiliations

  1. 1.Ministry of Education Key Laboratory for Ecology of Tropical Islands, Hainan Provincial Key Laboratory for Tropical Plant and Animal Ecology, College of Life SciencesHainan Normal UniversityHaikouChina
  2. 2.Southwest Forestry UniversityKunmingChina
  3. 3.Yunnan Forestry Technological CollegeKunmingChina
  4. 4.Dehong Teachers’ CollegeMangshiChina
  5. 5.Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of AgricultureSouth China Agricultural UniversityGuangzhouChina

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