Genomic Analysis of Phylotype I Strain EP1 Reveals Substantial Divergence from Other Strains in the Ralstonia solanacearum Species Complex.

Peng Li,Zide Jiang,Yinyue Deng,Zifu He,Bihao Cao,Jianuan Zhou,Jinli Yan,Dechen Wang,Lianhui Zhang

doi:10.3389/fmicb.2016.01719

Abstract

Ralstonia solanacearum species complex is a devastating group of phytopathogens with an unusually wide host range and broad geographical distribution. R. solanacearum isolates may differ considerably in various properties including host range and pathogenicity, but the underlying genetic bases remain vague. Here, we conducted the genome sequencing of strain EP1 isolated from Guangdong Province of China, which belongs to phylotype I and is highly virulent to a range of solanaceous crops. Its complete genome contains a 3.95-Mb chromosome and a 2.05-Mb mega-plasmid, which is considerably bigger than reported genomes of other R. solanacearum strains. Both the chromosome and the mega-plasmid have essential house-keeping genes and many virulence genes. Comparative analysis of strain EP1 with other 3 phylotype I and 3 phylotype II, III, IV strains unveiled substantial genome rearrangements, insertions and deletions. Genome sequences are relatively conserved among the 4 phylotype I strains, but more divergent among strains of different phylotypes. Moreover, the strains exhibited considerable variations in their key virulence genes, including those encoding secretion systems and type III effectors. Our results provide valuable information for further elucidation of the genetic basis of diversified virulences and host range of R. solanacearum species.

Highlights

Ralstonia solanacearum, a destructive bacterial pathogen that causes bacterial wilt diseases in over 400 plant species, has been recently ranked as the second most important bacterial plant pathogen (Mansfield et al, 2012)
Comparative genomic analysis have uncovered some divergent features among closely related strains, including putative virulence effectors associated with host adaptation(Ailloud et al, 2015), and presented evidences on the horizontal gene transfer between R. solanacearum strains (Guidot et al, 2009)
R. solanacearum species complex is considered one of the best models to understand the micro- and macro-evolution patterns leading to the formation of emerging ecotypes adapting to local environmental conditions (Genin and Denny, 2012)

Summary

Introduction

A destructive bacterial pathogen that causes bacterial wilt diseases in over 400 plant species, has been recently ranked as the second most important bacterial plant pathogen (Mansfield et al, 2012). 54 R. solanacearum species have been sequenced (data from NCBI database; Sep. 2016); while most of these genome assemblies were in a “draft” status, the genomes of strains GMI1000 (phylotype I, France), YC45 (phylotype I, China), FQY_4 (phylotype I, China), PO82 (phylotype II, Mexico), CMR15 (phylotype III, Cameroon), and PSI07 (phylotype IV, Indonesia) were completely determined (Remenant et al, 2010; Xu et al, 2011; Cao et al, 2013; She et al, 2015) These genome data open up the possibilities for characterizing the global regulation mechanisms that govern the bacterial virulence, analyzing the genomic diversity within the R. solanacearum species complex, and may present a good opportunity to study the R. solanacearum evolution and the genes contributing to host-range determination. Comparative genomic analysis have uncovered some divergent features among closely related strains, including putative virulence effectors associated with host adaptation(Ailloud et al, 2015), and presented evidences on the horizontal gene transfer between R. solanacearum strains (Guidot et al, 2009)

Methods

Results

Conclusion