A Meta-analysis of the known Global Distribution and Host Range of the<i>Ralstonia</i>Species Complex

Lowe‐Power, Tiffany M.; Chipman, Kyle C.

doi:10.1101/2020.07.13.189936

Cited by 21 publications

(24 citation statements)

References 242 publications

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“…However, it should be noted that the reports describing the genetic diversity of the RSSC according to the phylotype–sequevar system are relatively concentrated in recent years; some RSSC strains with completely different genetic backgrounds have been classified as the same sequevars, resulting in confusion over the sequevar numbering in relevant reports. In 2020, Lowe‐Power and Chipman (2020) consolidated the scattered information on the RSSC genetic diversity into a frequently updated database. This can solve the confusion of sequevar information caused by name overlapping to some extent.…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity of Ralstonia solanacearum species complex strains obtained from Guangxi, China and their pathogenicity on plants in the Cucurbitaceae family and other botanical families

Chen²,

Zhang

et al. 2021

Plant Pathology

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Bacterial wilt, caused by the Ralstonia solanacearum species complex (RSSC), is one of the most destructive bacterial plant diseases. It is distributed worldwide but is more intense in tropical and subtropical regions (Mansfield et al., 2012). The RSSC infects the roots of plants through the soil and water and multiplies through the xylem, where it clogs the vascular tissues and ultimately collapses the host (Mansfield et al., 2012). This group of bacterial pathogens has an extensive host range and can infect over 450 plant species representing 54 botanical families (Hayward, 1991;Wicker et al., 2007). Members of the RSSC are highly diverse pathogens with multiple taxonomic

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Section: Discussionmentioning

confidence: 99%

Genetic diversity of Ralstonia solanacearum species complex strains obtained from Guangxi, China and their pathogenicity on plants in the Cucurbitaceae family and other botanical families

Chen²,

Zhang

et al. 2021

Plant Pathology

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“…Logically, mutants with strong fitness defects in rich medium are excluded from the libraries because they would not have grown on the selection plates. Interestingly, we observed 9 that more mutants had gain-of-fitness phenotypes in minimal (4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20) and rich media (2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19) than in xylem sap (0-1). We next determined which genes influence fitness in a single condition and which genes have intersecting fitness contributions in two or more conditions (Fig 2D).…”

Section: Rb-tnseq Experiments Identify Mutants With Altered Fitness In Xylem Sap Andmentioning

confidence: 98%

“…Ralstonia solanacearum, R. pseudosolanacearum, and R. syzygii (hereafter, "Ralstonia") comprise the monophyletic but diverse species complex of plant wilt pathogens (1,2). Ralstonia strains are adapted to plant hosts belonging to over 50 botanical families and are distributed worldwide in in warm tropics and temperate subtropical highlands with year-round precipitation (3)(4)(5)(6)(7). Most Ralstonia strains invade plant roots, gain entry to the water-transporting xylem vasculature, and spread systemically, which disrupts xylem function and fatally wilts the host The mutant libraries were created by conjugation with the pKMW3 E. coli donor library (16), which carries a pool of over 10 8 mariner transposon delivery vectors in which each transposon is marked by a unique 20 base pair sequence.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification of tomato xylem sap fitness factors for three plant-pathogenicRalstoniaspecies

Georgoulis

Shalvarjian

Helmann

et al. 2020

Preprint

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Plant pathogenic Ralstonia spp. colonize plant xylem and cause wilt diseases on a broad range of host plants. To identify genes that promote growth of diverse Ralstonia strains in xylem sap from tomato plants, we performed genome-scale genetic screens (random barcoded transposon mutant sequencing screens; RB-TnSeq) in Ralstonia pseudosolanacearum GMI1000 and R. syzygii PSI07. Contrasting mutant fitness phenotypes in culture media versus in xylem sap suggest that Ralstonia strains are adapted to sap and that culture media impose foreign selective pressures. Although wild-type Ralstonia grew in sap and in rich medium with similar doubling times and to a similar carrying capacity, more genes were essential for growth in sap than in rich medium. Multiple mutants lacking amino acid biosynthesis and central metabolism functions had fitness defects in xylem sap and minimal medium. Our screen identified > 26 genes in each strain that contributed to growth in xylem sap but were dispensable for growth in culture media. Many sap-specific fitness factors are associated with bacterial stress responses: envelope remodeling and repair processes such as peptidoglycan peptide formation (murI and RSc1177), LPS O-antigen biosynthesis (RSc0684), periplasmic protein folding (dsbA), drug efflux (tolA and tolR), and stress responses (cspD3). Our genome-scale genetic screen identified Ralstonia fitness factors that promote growth in xylem sap, an ecologically relevant condition.ImportanceTraditional transposon mutagenesis genetic screens pioneered molecular plant pathology and identified core virulence traits like the type III secretion system. TnSeq approaches that leverage next-generation sequencing to rapidly quantify transposon mutant phenotypes are ushering in a new wave of biological discovery. Here we have adapted a genome-scale approach, random barcoded transposon mutant sequencing (RB-TnSeq), to discover fitness factors that promote growth of two related bacterial strains in a common niche, tomato xylem sap. Fitness of wild-type and mutants show that Ralstonia spp. are adapted to grow well in xylem sap from their natural host plant, tomato. Our screen identified multiple sap-specific fitness factors with roles in maintaining the bacterial envelope. These factors are putative adaptations to resist plant defenses, including antimicrobial proteins and specialized metabolites that damage bacterial membranes.

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“…The global plant pathology community has widely adopted the sequevar taxonomic system to classify Ralstonia strains at the within-species level. Over 5,000 strains from over 88 regions have been assigned to over 70 sequevar groups [64]. Because the sequevar system is based on a single genetic marker (750 bp of the egl gene), and RSSC genomes often recombine, we predicted that the egl gene may have recombined between strains.…”

Section: Comparing Sequevars (Egl Trees) With the Core Genome Phylogeny And Populationsmentioning

confidence: 99%

Meta Analysis of the Ralstonia solanacearum species complex (RSSC) based on comparative evolutionary genomics and reverse ecology

Sharma

Johnson

Mazloom

et al. 2021

Preprint

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Ralstonia solanacearum species complex (RSSC) strains are bacteria that colonize plant xylem and cause vascular wilt diseases. However, individual strains vary in host range, optimal disease temperatures, and physiological traits. To increase our understanding of the evolution, diversity, and biology of the RSSC, we performed a meta-analysis of 100 representative RSSC genomes. These 100 RSSC genomes contain 4,940 genes on average, and a pangenome analysis found that there are 3,262 genes in the core genome (~60% of the mean RSSC genome) with 13,128 genes in the extensive flexible genome. Although a core genome phylogenetic tree and a genome similarity matrix aligned with the previously named species (R. solanacearum, R. pseudosolanacearum, R. syzygii) and phylotypes (I-IV), these analyses also highlighted an unrecognized sub-clade of phylotype II. Additionally, we identified differences between phylotypes with respect to gene content and recombination rate, and we delineated population clusters based on the extent of horizontal gene transfer. Multiple analyses indicate that phylotype II is the most diverse phylotype, and it may thus represent the ancestral group of the RSSC. Additionally, we also used our genome-based framework to test whether the RSSC sequence variant (sequevar) taxonomy is a robust method to define within-species relationships of strains. The sequevar taxonomy is based on alignments of a single conserved gene (egl). Although sequevars in phylotype II describe monophyletic groups, the sequevar system breaks down in the highly recombinogenic phylotype I, which highlights the need for an improved cost-effective method for genotyping strains in phylotype I. Finally, we enabled quick and precise genome-based identification of newly sequenced Ralstonia strains by assigning Life Identification Numbers (LINs) to the 100 strains and by circumscribing the RSSC and its sub-groups in the LINbase Web service.

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A Meta-analysis of the known Global Distribution and Host Range of theRalstoniaSpecies Complex

Cited by 21 publications

References 242 publications

Genetic diversity of Ralstonia solanacearum species complex strains obtained from Guangxi, China and their pathogenicity on plants in the Cucurbitaceae family and other botanical families

Genetic diversity of Ralstonia solanacearum species complex strains obtained from Guangxi, China and their pathogenicity on plants in the Cucurbitaceae family and other botanical families

Genome-wide identification of tomato xylem sap fitness factors for three plant-pathogenicRalstoniaspecies

Meta Analysis of the Ralstonia solanacearum species complex (RSSC) based on comparative evolutionary genomics and reverse ecology

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