Dataset Information

Genome sequence of the rice-pathogenic bacterium Acidovorax avenae subsp. avenae RS-1.

ABSTRACT: Acidovorax avenae subsp. avenae is a phytobacterium which is the causative agent of several plant diseases with economic significance. Here, we present the draft genome sequence of strain RS-1, which was isolated from rice shoots in a rice field in China. This strain can cause bacterial stripe of rice.

SUBMITTER: Xie GL

PROVIDER: S-EPMC3165674 | biostudies-literature | 2011 Sep

REPOSITORIES: biostudies-literature

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Genome sequence of the rice-pathogenic bacterium Acidovorax avenae subsp. avenae RS-1.

Xie Guan-Lin GL Zhang Guo-Qing GQ Liu He H Lou Miao-Miao MM Tian Wen-Xiao WX Li Bin B Zhou Xue-Ping XP Zhu Bo B Jin Gu-Lei GL

Journal of bacteriology 20110708 18

Acidovorax avenae subsp. avenae is a phytobacterium which is the causative agent of several plant diseases with economic significance. Here, we present the draft genome sequence of strain RS-1, which was isolated from rice shoots in a rice field in China. This strain can cause bacterial stripe of rice. ...[more]

PMID: 21742879

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Project description:Determining how a bacterial pathogen responds to its host and other bacterial species by altering gene expression is key to understand its pathogenesis and environmental adaption. Here, we used RNA-Seq to comprehensively and quantitatively assess the transcriptional response of the rice bacterial pathogen Acidovorax avenae subsp. avenae strain RS-1 cultivated in vitro, in vivo and in co-culture with rice rhizobacterium Burkholderia seminalis R456. Results revealed a surprisingly large number of regulatory differences between these conditions indicating adaptation of A. avenae subsp. avenae to specific ecological conditions. In particular, a number of potential virulence factors such as type 3 secretion system proteins were specifically expressed under in vivo conditions, whereas genes whose protein products are involved in inter-bacterial interaction such as auxin efflux carrier, small mechanosensitive ion channel protein, and ureidoglycolate hydrolase were among those specifically up-regulated under co-culture conditions. In addition, global genomic analysis of strain RS-1 identified 406 putative non-coding (nc) RNA genes. Interestingly, 8 ncRNA genes that were uniquely expressed under in vivo may be linked to pathogenicity while 4 ncRNA genes that were uniquely expressed under coculture conditions may be involved in adaption to co-cultivation with B. seminalis. Expression data obtained by RNA-Seq were also confirmed for selected genes by quantitative real-time PCR and two-dimensional gel electrophoresis as well as knockout analysis. Aaa strain RS-1 and B. seminalis strain R456 was isolated from diseased rice plants (Li et al., 2011; Xie et al., 2011) and rice rhizosphere (Zhang et al., 2007; Li et al., 2011), respectively, in our previous studies, and were stored in 20-30% sterile glycerol at -80°C. The samples of Aaa strain RS-1 for in vitro and in vivo analysis were prepared as described before (Ibrahim et al., 2012). The co-culture analysis of Aaa strain RS-1 with B. seminalis strain R456 were conducted according to Ruiz et al. (2009) and Di Cagno et al. (2009). Briefly, Aaa strain RS-1 and B. seminalis strain R456 was inoculated and incubated in chambers of a double culture vessel apparatus separated by a 0.4-μm membrane filter (Millipore Isopore™). In order to avoid the possible contamination during in vivo and co-culture operation, all bacterial samples were further confirmed based on the sequence analysis of 16S-rRNA (Li et al., 2011). Then samples were processed for RNA harvesting, mRNA purification and cDNA synthesis.

Dataset Information

Genome sequence of the rice-pathogenic bacterium Acidovorax avenae subsp. avenae RS-1.

Publications

Genome sequence of the rice-pathogenic bacterium Acidovorax avenae subsp. avenae RS-1.

Similar Datasets

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