Potential evolutionary impact of integrative and conjugative elements (ICEs) and genomic islands in the Ralstonia solanacearum species complex

Abstract Background Bacterial wilt caused by Ralstonia solanacearum species complex is an important soil-borne disease worldwide that affects more than 450 plant species, including peanut, leading to great yield and quality losses. However, there are no effective measures to control bacterial wilt. The reason is the lack of research on the pathogenic mechanism of bacterial wilt. Results Here, we report the complete genome of a toxic Ralstonia solanacearum species complex strain, Rs-P.362200, a peanut pathogen, with a total genome size of 5.86 Mb, encoding 5056 genes and the average G + C content of 67%. Among the coding genes, 75 type III effector proteins and 12 pseudogenes were predicted. Phylogenetic analysis of 41 strains including Rs-P.362200 shows that genetic distance mainly depended on geographic origins then phylotypes and host species, which associated with the complexity of the strain. The distribution and numbers of effectors and other virulence factors changed among different strains. Comparative genomic analysis showed that 29 families of 113 genes were unique to this strain compared with the other four pathogenic strains. Through the analysis of specific genes, two homologous genes (gene ID: 2_657 and 3_83), encoding virulence protein (such as RipP1) may be associated with the host range of the Rs-P.362200 strain. It was found that the bacteria contained 30 pathogenicity islands and 6 prophages containing 378 genes, 7 effectors and 363 genes, 8 effectors, respectively, which may be related to the mechanism of horizontal gene transfer and pathogenicity evaluation. Although the hosts of HA4–1 and Rs-P.362200 strains are the same, they have specific genes to their own genomes. The number of genomic islands and prophages in HA4–1 genome is more than that in Rs-P.36220, indicating a rapid change of the bacterial wilt pathogens. Conclusion The complete genome sequence analysis of peanut bacterial wilt pathogen enhanced the information of R. solanacearum genome. This research lays a theoretical foundation for future research on the interaction between Ralstonia solanacearum and peanut.

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Widespread distribution of prophages signaling the potential for adaptability and pathogenicity evolution of Ralstonia solanacearum species complex

Genomics ◽

10.1016/j.ygeno.2021.02.011 ◽

2021 ◽

Author(s):

Osiel Silva Gonçalves ◽

Flávia de Oliveira Souza ◽

Fernanda Prieto Bruckner ◽

Mateus Ferreira Santana ◽

Poliane Alfenas-Zerbini

Keyword(s):

Ralstonia Solanacearum ◽

Species Complex ◽

Widespread Distribution

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Molecular characterization and aggressiveness of the Ralstonia solanacearum species complex from Eucalyptus spp. in Brazil

Forest Pathology ◽

10.1111/efp.12704 ◽

2021 ◽

Author(s):

Rodrigo G. Freitas ◽

Pollyane S. Hermenegildo ◽

Lúcio M. S. Guimarães ◽

Edival A. V. Zauza ◽

Jorge L. Badel ◽

...

Keyword(s):

Molecular Characterization ◽

Ralstonia Solanacearum ◽

Species Complex

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Whole genome characterization of strains belonging to the Ralstonia solanacearum species complex and in silico analysis of TaqMan assays for detection in this heterogenous species complex

European Journal of Plant Pathology ◽

10.1007/s10658-020-02190-8 ◽

2021 ◽

Author(s):

Viola Kurm ◽

Ilse Houwers ◽

Claudia E. Coipan ◽

Peter Bonants ◽

Cees Waalwijk ◽

...

Keyword(s):

Ralstonia Solanacearum ◽

In Silico ◽

Species Complex ◽

Sequence Data ◽

In Silico Analysis ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequences ◽

Pcr Assays

AbstractIdentification and classification of members of the Ralstonia solanacearum species complex (RSSC) is challenging due to the heterogeneity of this complex. Whole genome sequence data of 225 strains were used to classify strains based on average nucleotide identity (ANI) and multilocus sequence analysis (MLSA). Based on the ANI score (>95%), 191 out of 192(99.5%) RSSC strains could be grouped into the three species R. solanacearum, R. pseudosolanacearum, and R. syzygii, and into the four phylotypes within the RSSC (I,II, III, and IV). R. solanacearum phylotype II could be split in two groups (IIA and IIB), from which IIB clustered in three subgroups (IIBa, IIBb and IIBc). This division by ANI was in accordance with MLSA. The IIB subgroups found by ANI and MLSA also differed in the number of SNPs in the primer and probe sites of various assays. An in-silico analysis of eight TaqMan and 11 conventional PCR assays was performed using the whole genome sequences. Based on this analysis several cases of potential false positives or false negatives can be expected upon the use of these assays for their intended target organisms. Two TaqMan assays and two PCR assays targeting the 16S rDNA sequence should be able to detect all phylotypes of the RSSC. We conclude that the increasing availability of whole genome sequences is not only useful for classification of strains, but also shows potential for selection and evaluation of clade specific nucleic acid-based amplification methods within the RSSC.

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Moko Disease-Causing Strains of Ralstonia solanacearum from Brazil Extend Known Diversity in Paraphyletic Phylotype II

Phytopathology ◽

10.1094/phyto-12-13-0334-r ◽

2014 ◽

Vol 104 (11) ◽

pp. 1175-1182 ◽

Cited By ~ 21

Author(s):

Greecy M. R. Albuquerque ◽

Liliana A. Santos ◽

Kátia C. S. Felix ◽

Christtianno L. Rollemberg ◽

Adriano M. F. Silva ◽

...

Keyword(s):

Dna Repair ◽

Latin America ◽

Ralstonia Solanacearum ◽

Species Complex ◽

Genetic Clusters ◽

High Diversity

The epidemic situation of Moko disease-causing strains in Latin America and Brazil is unclear. Thirty-seven Ralstonia solanacearum strains from Brazil that cause the Moko disease on banana and heliconia plants were sampled and phylogenetically typed using the endoglucanase (egl) and DNA repair (mutS) genes according to the phylotype and sequevar classification. All of the strains belonged to phylotype II and a portion of the strains was typed as the Moko disease-related sequevars IIA-6 and IIA-24. Nevertheless, two unsuspected sequevars also harbored the Moko disease-causing strains IIA-41 and IIB-25, and a new sequevar was described and named IIA-53. All of the strains were pathogenic to banana and some of the strains of sequevars IIA-6, IIA-24, and IIA-41 were also pathogenic to tomato. The Moko disease-causing strains from sequevar IIB-25 were pathogenic to potato but not to tomato. These results highlight the high diversity of strains of Moko in Brazil, reinforce the efficiency of the egl gene to reveal relationships among these strains, and contribute to a better understanding of the diversity of paraphyletic Moko disease-causing strains of the R. solanacearum species complex, where the following seven distinct genetic clusters have been described: IIA-6, IIA-24, IIA-41, IIA-53, IIB-3, IIB-4, and IIB-25.

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Genome- and Mass Spectrometry-Guided Discovery of Ralstoamides A and B from Ralstonia solanacearum Species Complex

ACS Chemical Biology ◽

10.1021/acschembio.0c00605 ◽

2020 ◽

Vol 15 (11) ◽

pp. 2860-2865

Author(s):

Shoko Komatsu ◽

Chiaki Tsumori ◽

Kouhei Ohnishi ◽

Kenji Kai

Keyword(s):

Mass Spectrometry ◽

Ralstonia Solanacearum ◽

Species Complex ◽

Guided Discovery

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Molecular Epidemiology of Ralstonia solanacearum Species Complex Strains Causing Bacterial Wilt of Potato in Uganda

Phytopathology ◽

10.1094/phyto-12-18-0476-r ◽

2019 ◽

Vol 109 (11) ◽

pp. 1922-1931 ◽

Cited By ~ 6

Author(s):

Abdulwahab Abdurahman ◽

Monica L. Parker ◽

Jan Kreuze ◽

John G. Elphinstone ◽

Paul C. Struik ◽

...

Keyword(s):

Bacterial Wilt ◽

Ralstonia Solanacearum ◽

Species Complex ◽

Nationwide Survey ◽

Potato Production ◽

Repeat Sequence ◽

Latently Infected ◽

Pure Cultures ◽

Diversity Studies ◽

Phylotype I

Bacterial wilt (BW) caused by the Ralstonia solanacearum species complex (RSSC) is a serious threat to potato production in Uganda. However, little is known about the extent of the disease and the type of the pathogen strains involved. A nationwide survey was conducted to study BW prevalence and incidence in potato, and potato tuber and stem samples of potential alternative hosts were collected for pathogen isolation. DNA was extracted from pure cultures for genetic diversity studies. The pathogen was phylotyped by multiplex PCR; then, a subset of isolates was typed at sequevar level. Isolates of the same sequevar were then haplotyped using multilocus tandem repeat sequence typing (TRST) schemes. BW prevalence and incidence in potato farms were 81.4 and 1.7%, respectively. Three RSSC phylotypes were identified, with the majority of the strains belonging to Phylotype II (80%) followed by Phylotype I (18.5%) and III (1.5%). Phylotype I strains belonged to Sequevar 31, and Phylotype II strains belonged to Sequevar 1. Potato-associated Phylotype II Sequevar 1 strains were more diverse (27 TRST haplotypes) than nonpotato Phylotype I (5 TRST haplotypes). Mapping of TRST haplotypes revealed that three TRST haplotypes of Phylotype II Sequevar 1 strains play an important epidemiological role in BW of potato in Uganda being disseminated via latently infected seed. [Formula: see text] Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

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Deciphering Phenotypic Diversity of Ralstonia solanacearum Strains Pathogenic to Potato

Phytopathology ◽

10.1094/phyto-02-10-0059 ◽

2010 ◽

Vol 100 (11) ◽

pp. 1250-1261 ◽

Cited By ~ 54

Author(s):

G. Cellier ◽

P. Prior

Keyword(s):

Ralstonia Solanacearum ◽

Species Complex ◽

Phenotypic Diversity ◽

Brown Rot ◽

Host Adaptation ◽

Species Phylogeny ◽

Phylogeny Analysis ◽

Adaptation Mechanisms ◽

Bacterial Speciation ◽

Reference Strains

Based on the phylotype classification, we questioned how genetically and phenotypically diverse strains of Ralstonia solanacearum pathogenic to potato may be. We studied 129 European and Mediterranean strains along with 57 reference strains known to cover genetic diversity in this species. Phylogeny analysis was done on endoglucanase gene sequences. Pathogenicity to potato, tomato, and eggplant was established at 24 to 30°C and 15 to 24°C, whereas tests on banana were conducted at 24 to 30°C. The ability to cause wilt on species of Solanaceae was shared by strains in all four phylotypes. Brown rot phylotypes IIB-1 and IIB-2 and phylotype IIB-27 established latent infections in banana, and Moko disease-causing phylotypes IIA-6, IIB-3, and IIB-4 were virulent to susceptible potato and tomato, addressing the question of host adaptation mechanisms, which may have undergone a similar bottleneck evolution. Cold-tolerance ability is only shared on species of Solanaceae among brown rot phylotype IIB-1, which gathered the majority of European and Mediterranean strains. We surveyed strain LNPV24.25 as the first report of an emerging phylotype IIB-4NPB strain in France. These findings showed that pathogenicity traits of genetically identified strains still need to be understood, especially in the perspective of post-genomics comparative analysis, to understand bacterial speciation in the R. solanacearum species complex.

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