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RNAseq analysis of Xcc strain B100 in minimum media

ABSTRACT: RNAseq analysis of Xcc strain B100 in minimum media

PROVIDER: PRJEB20201 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1906039_1.fastq.gz	Fastqsanger.gz
	ERR1906039_2.fastq.gz	Fastqsanger.gz

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Project description:Xanthomonas campestris pathovar campestris (Xcc), the causal agent of black rot disease of cruciferous plants worldwide, is composed of phenotypically heterogeneous groups of strains. The knowledge about the genome diversity and phylogenetic relationships between Xcc strains with different origins are of great interest as they provide insight into the mechanisms of pathogenicity, host preferences and evolution of this pathogen. In our present work, eighteen Xcc strains collected from different geographical area of China mainland were investigated concerning of the genome composition by comparative genomic hybridization (CGH) using microarray slides spotted with PCR-based intragenic DNA fragments of 4273 open reading frames (ORFs) representing the non-redundant genome content of Xcc strain 8004. The common genome backbone of Chinese strains was estimated to contain about 3404 ORFs, which was considered to maintain the basic characteristics of Xcc, i.e. the yellow mucoid colony on nutrient solid medium as well as the pathogenicity to induce black rot disease on host plants. A flexible gene pool of 729 ORFs in Xcc was characterized, of which 402 ORFs were clustered in twenty-seven highly variable genomic regions in Xcc 8004. Of these highly variable genomic regions, five are absolutely absent from Chinese strains, which constitutes the main genomic differences between the Xcc 8004 and Chinese strains. Transcriptome analysis of Xcc 8004 grown in the rich medium NYG and the defined medium XVM2 indicated that the expression of some certain genes in highly variable genomic regions are significantly activated in XVM2, which included the predicted pathogencity and avirulence genes. Candidate genes for cultivar-specificity of Xcc were identified in the variable genomic regions: the avrXccC and avrXccE1 were demonstrated to confer the avirulence on the host plants Mustard cultivar (cv.) Guangtou and Chinese cabbage cv. Zhongbai 83, respectively; and the avrBs1 showed to correlate with the hypersensitive reaction (HR) on the non-host plant pepper ECW10R. This study revealed the common genome backbone of Xcc maintained the basic function in essential metabolisms and basic pathogencity, and the variable genomic determinants contributed to the cultivar-specificity of the pathogen, suggesting that the Xcc genome, with a compact function core carrying essential genes for survival, reproduction, and invasion, is constantly diversifying by acquiring and losing DNA segments, or by DNA degeneration, to improve the genetic novelty for the adaptation during the evolution. Keywords: CGH analysis and transcriptome analysis

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RNAseq analysis of Xcc strain B100 in minimum media

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