Genome Sequencing of Ralstonia solanacearum CQPS-1, a Phylotype I Strain Collected from a Highland Area with Continuous Cropping of Tobacco

Abstract

Ralstonia solanacearum , an agent of bacterial wilt, is a highly variable species with a broad host range and wide geographic distribution. As a species complex, it has extensive genetic diversity and its living environment is polymorphic like the lowland and the highland area, so more genomes are needed for studying population evolution and environment adaptation. In this paper, we reported the genome sequencing of R. solanacearum strain CQPS-1 isolated from wilted tobacco in Pengshui, Chongqing, China, a highland area with severely acidified soil and continuous cropping of tobacco more than 20 years. The comparative genomic analysis among different R. solanacearum strains was also performed. The completed genome size of CQPS-1 was 5.89 Mb and contained the chromosome (3.83 Mb) and the megaplasmid (2.06 Mb). A total of 5229 coding sequences were predicted (the chromosome and megaplasmid encoded 3573 and 1656 genes, respectively). A comparative analysis with eight strains from four phylotypes showed that there was some variation among the species, e.g., a large set of specific genes in CQPS-1. Type III secretion system gene cluster ( hrp gene cluster) was conserved in CQPS-1 compared with the reference strain GMI1000. In addition, most genes coding core type III effectors were also conserved with GMI1000, but significant gene variation was found in the gene ripAA : the identity compared with strain GMI1000 was 75% and the hrp II box promoter in the upstream had significantly mutated. This study provided a potential resource for further understanding of the relationship between variation of pathogenicity factors and adaptation to the host environment.

Complete Genome Sequence of Industrial Biocontrol Strain Paenibacillus polymyxa HY96-2 and Further Analysis of Its Biocontrol Mechanism

“…However, the polymyxin-related gene clusters in strains SC2 and E681 displayed low identities with that in strain HY96-2 of only 63.21 and 54.94%, respectively. Bacterial plant diseases are mainly caused by G - bacteria, such as those belonging to the genera Ralstonia ( Liu et al, 2017c ), Erwinia ( Bell et al, 2004 ), Pseudomonas ( Wang et al, 2018 ), and Xanthomonas ( Islam et al, 2018 ). Strain HY96-2 has been found to effectively control many G - bacteria plant diseases in the field ( Table 1 ), such as bacterial wilt, a soil-borne disease caused by R. solanacearum that has been referred to as “plant cancer,” and angular leaf spot on cucumbers, a leaf disease caused by P. syringae .…”

Pangenomic type III effector database of the plant pathogenicRalstoniaspp.

“…A few research groups added a significant amount of host-compatibility information for a set of strains (Ailloud et al, 2015; Cho et al, 2018; Lebeau et al, 2011). Other groups have performed host-compatibility experiments and shared this information with us, for example, tobacco strain CQPS-1 (Liu et al, 2017) is also mildly pathogenic on tomato (Prof. W Ding, 2019, personal communication), while the blueberry strains P816, P822 and P824 (Bocsanczy, Espindola & Norman, 2019), are very aggressive on tomato (Dr. DJ Norman, 2019, personal communication). In our repertoire comparison, we allow a tolerance of presence for the Rip in the interval of strains between the total number of strains n , and n -5%, this allows to compensate the effect of unequal set of strains to compare.…”

“…5; Table 3). Eight of them are conserved in the different species: RipB (absent only in R. pseudosolanacearum CQPS-1 (Liu et al, 2017)); RipH2 (absent only in R. pseudosolanacearum RSCM isolated from Cucurbita maxima in China (She et al, 2017)); RipR (absent only in R. solanacearum UW181, a plantain banana strain (Wicker et al, 2012), and R. syzygii BDB_RUN1347, no host of isolation reported); RipW (absent only in R. pseudosolanacearum strain SL3822 isolated form potato in Korea (Cho et al, 2018); RipAB (absent only in R. pseudosolanacearum strain YC40-M, no host of isolation reported, and R. solanacearum strain MolK2 (Remenant et al, 2010)); RipAI (absent only in R. pseudosolanacearum strain HA4-1 a Chinese peanut strain); RipAO (absent only in R. pseudosolanacearum strain SL3755 isolated form potato in Korea (Cho et al, 2018)). The only strictly conserved T3E among these 84 strains is RipAJ.…”

Overexpression of NtPR-Q Up-Regulates Multiple Defense-Related Genes in Nicotiana tabacum and Enhances Plant Resistance to Ralstonia solanacearum

“…Ralstonia solanacearum CQPS-1 (phylotype I, race 1, biovar 3) ( Liu et al, 2017a ) was maintained in our laboratory and was isolated from Chongqing Municipality, China. R. solanacearum strains were cultured at 180 rpm, 30°C in NB medium (3 g⋅L -1 beef extract, 1 g⋅L -1 yeast extract, 5 g⋅L -1 peptone and 10 g⋅L -1 glucose), and bacterial suspension was cultured to about 1 × 10 9 CFU mL -1 .…”