Comparative and functional genomics reveals genetic diversity and determinants of host specificity among reference strains and a large collection of Chinese isolates of the phytopathogen Xanthomonas campestris pv. campestris

He, Yong-Qiang; Zhang, Liang; Jiang, Bo-Le; Zhang, Zheng-Chun; Xu, Rong-Qi; Tang, Dong-Jie; Qin, Jing; Jiang, Wei; Zhang, Xia; Liao, Jie; Cao, Jin-Ru; Zhang, Sui-Sheng; Wei, Mei-Liang; Liang, Xiao-Xia; Lu, Guang-Tao; Feng, Jia-Xun; Chen, Baoshan; Cheng, Jing; Tang, Ji-Liang

doi:10.1186/gb-2007-8-10-r218

Table 7 The characteristics of the variable genomic regions in strain 8004

From: Comparative and functional genomics reveals genetic diversity and determinants of host specificity among reference strains and a large collection of Chinese isolates of the phytopathogen Xanthomonas campestris pv. campestris

XVR	Sequence characteristics	Functional description	Occurrence of XVRs*
XVR01	Gene phage related	Regulatory protein cII, putative secreted proteins	II
XVR02	IS elements	Deoxycytidylate deaminase and Rhs protein, genes related T4 phage	I
XVR03	Gene phage related	Methyltransferase	III
XVR04	Integron	Integron, xanthomonadin biosynthesis	III
XVR05	Gene phage related	Type I site-specific deoxyribonuclease	II
XVR06	IS elements	ThiJ/PfpI family protein, oxidoreductase	II
XVR07	IS elements	VirB6 protein	II
XVR08		Transcriptional regulator BlaI family	III
XVR09	Integrase + tRNA-Gly IS elements	Regulatory protein BphR	II
XVR10		Fimbrial assembly protein	III
XVR11		Type IV pilin	III
XVR12	IS elements	VirB cluster for T4SS	III
XVR13	Integrase + tRNA-Gly IS elements	Avirulence proteins, pathogenicity related proteins	II
XVR13.1	IS elements Gene phage related	Adaptation, virulence related protein	II
XVR14	Gene phage related	Prophage	II
XVR15	IS elements	Histidine kinase/response regulator hybrid protein, single-domain response regulator	II
XVR16		Nucleotide sugar transaminase	III
XVR17	IS elements	Arsenite efflux, iron uptake	I
XVR18	Integrase + tRNA-Arg IS elements	Plasmid mobilization protein, hemolysin activation protein	I
XVR19	Integrase + tRNA-Ser IS elements	Avirulence protein, phage related protein	II
XVR20	IS elements Integrase	Phage related protein, helicase	I
XVR21		Metabolic enzymes	II
XVR22		Type I site-specific restriction-modification system, virulence protein	III
XVR23	IS elements	Sugar translocase, O-antigen	IV
XVR24	Flanked by IS elements		II
XVR25	IS elements	Avirulence protein, regulators	II
XVR26	IS elements Gene phage related	Rich in mobile elements	II
XVR27	IS elements	XmnI methyltransferase	I

*There are four possible occurrences of the XVRs predicted in the Xcc genomes: I, recent horizontally acquired sequences; II, horizontally acquired sequences; III, inherited from a common ancestor of xanthomonads and lost from certain Xcc strains at a later stage; IV, inherited from a common ancestor of xanthomonads and degenerated in certain Xcc strains at a later stage.

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