Comparative genomic analysis of Ralstonia solanacearum reveals candidate genes for host specificity

Background

Ralstonia solanacearum is a vascular soil-borne plant pathogen with an unusually broad host range. This economically destructive and globally distributed bacterium has thousands of distinct lineages within a heterogeneous and taxonomically disputed species complex. Some lineages include highly host-adapted strains (ecotypes), such as the banana Moko disease-causing strains, the cold-tolerant potato brown rot strains (also known as R3bv2) and the recently emerged Not Pathogenic to Banana (NPB) strains.

Results

These distinct ecotypes offer a robust model to study host adaptation and the emergence of ecotypes because the polyphyletic Moko strains include lineages that are phylogenetically close to the monophyletic brown rot and NPB strains. Draft genomes of eight new strains belonging to these three model ecotypes were produced to complement the eleven publicly available R. solanacearum genomes. Using a suite of bioinformatics methods, we searched for genetic and evolutionary features that distinguish ecotypes and propose specific hypotheses concerning mechanisms of host adaptation in the R. solanacearum species complex. Genome-wide, few differences were identified, but gene loss events, non-synonymous polymorphisms, and horizontal gene transfer were identified among type III effectors and were associated with host range differences.

Conclusions

This extensive comparative genomics analysis uncovered relatively few divergent features among closely related strains with contrasting biological characteristics; however, several virulence factors were associated with the emergence of Moko, NPB and brown rot and could explain host adaptation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1474-8) contains supplementary material, which is available to authorized users.     

Isolation of Endophytic Actinomycetes from Different Cultivars of Tomato and their Activities Against Ralstonia solanacearum in Vitro

The populations of endophytic actinomycetes from healthy and wilting tomato plants (tomato cultivars resistant and susceptible to Ralstonia solanacearum) grown in three different sites from Guangzhou, Guangdong Province, South China were investigated by cultivation methods. Most of the isolates belonged to streptomycetes. The Aureus group of Streptomyces was the most frequently isolated group. The population composition of Streptomyces varied according to tomato cultivars, physiological status and soil types. The proportions of antagonistic Streptomyces strains from healthy plants were higher than that from wilting plants (P < 0.05), although the difference among the proportions of antagonistic Streptomyces strains from different cultivars of healthy tomato was not significant, the similar result was found from wilting plants. No significant difference was found in the proportions of siderophere-producing Streptomyces strains from the same site (P > 0.05), but the difference was found from the different sampling sites (P < 0.05). The percentage of bacterial cell wall-degrading streptomycetes from wilting tomato was higher than that from healthy plants (P < 0.05). These results indicated that the cultivar of the host plant, physiological status and sampling sites would influence the proportion of endophytic streptomycetes with different physiological traits. Diversity of endophytic Streptomyces and their physiological diversity should be involved in developing potential biocontrol agents.     

Heat shock,with recovery,promotes protection of Nicotiana tabacum during subsequent exposure to Ralstonia solanacearum

Host–pathogen interactions in plants are complex and potentially influenced by heat shock/stress (HS). Host HS proteins (HSPs) induced prior to bacterial exposure may facilitate the folding of newly synthesized defense proteins and promote incompatible host–pathogen interactions. We hypothesized that a non-lethal HS, with recovery, promotes protection of Nicotiana tabacum during subsequent exposure to avirulent soilborne necrotrophic pathogen Ralstonia solanacearum. The objective of this study included investigating the effects of HS with or without recovery on the outcome of bacterial exposure to a virulent and avirulent biovar of R. solanacearum in N. tabacum cell suspensions. This was assessed by quantifying host Hsp70/Hsc70 levels, mitochondrial electron (e⁻) transport activity as a marker of viability, and phosphatidylserine externalization and DNA fragmentation as markers of apoptosis. Our findings support the hypothesis that HS, with recovery, promotes protection of N. tabacum during subsequent exposure to R. solanacearum, suggesting a role for Hsp70/Hsc70 in the observed protection of e⁻ transport, increased apoptosis, and DNA fragmentation.     

Fertile Solanum tuberosum+S. commersonii somatic hybrids as sources of resistance to bacterial wilt caused by Ralstonia solanacearum

 The wild potato relative Solanum commersonii is reported to carry resistance to bacterial wilt disease caused by Ralstonia solanacearum. To overcome sexual incompatibilites due to differences in ploidy and endosperm balance numbers, somatic hybrids were made that combine the S. tuberosum and S. commersonii genomes. The resulting somatic hybrid plants are vigorous, but their disease resistance level and their fertility was unknown. We therefore tested the S. commersonii and S. tuberosum source material cv Superior, potato cv Atlantic and six somatic hybrid lines for resistance to a virulent strain of R. solanacearum (race 3, biovar 2) at 28°C. As expected, S. commersonii was significantly more wilt-resistant than the cultivated potatoes. In five of the six somatic hybrid lines, disease resistance levels were similar to that of the resistant S. commersonii parent. The resistance level of the sixth somatic hybrid was intermediate, significantly different from both S. commersonii and S. tuberosum. In controlled crosses, the somatic hybrids in this study proved both to be male- and female-fertile and were self-compatible. More importantly, the somatic hybrids can be crossed with S. tuberosum to produce viable seeds. Received: 23 June 1998 / Accepted: 13 October 1998     

Genetic diversity and population structure in the tomato-like nightshades Solanum lycopersicoides and S. sitiens

Background and Aims

Two closely related, wild tomato-like nightshade species, Solanum lycopersicoides and Solanum sitiens, inhabit a small area within the Atacama Desert region of Peru and Chile. Each species possesses unique traits, including abiotic and biotic stress tolerances, and can be hybridized with cultivated tomato. Conservation and utilization of these tomato relatives would benefit from an understanding of genetic diversity and relationships within and between populations.

Methods

Levels of genetic diversity and population genetic structure were investigated by genotyping representative accessions of each species with a set of simple sequence repeat (SSR) and allozyme markers.

Key Results

As expected for self-incompatible species, populations of S. lycopersicoides and S. sitiens were relatively diverse, but contained less diversity than the wild tomato Solanum chilense, a related allogamous species native to this region. Populations of S. lycopersicoides were slightly more diverse than populations of S. sitiens according to SSRs, but the opposite trend was found with allozymes. A higher coefficient of inbreeding was noted in S. sitiens. A pattern of isolation by distance was evident in both species, consistent with the highly fragmented nature of the populations in situ. The populations of each taxon showed strong geographical structure, with evidence for three major groups, corresponding to the northern, central and southern elements of their respective distributions.

Conclusions

This information should be useful for optimizing regeneration strategies, for sampling of the populations for genes of interest, and for guiding future in situ conservation efforts.     

Characterization of Resistance in a Somatic Hybrid of Solanum bulbocastanum and S. tuberosum,to Meloidogyne chitwoodi

A somatic hybrid, CBP-233, between resistant Solanum bulbocastanum (SB-22) and susceptible S. tuberosum (R4) was tested for resistance to Meloidogyne chitwoodi race 1. One week after inoculation, only 0.04-0.4% of the initial inoculum (Pi, 5,000 eggs) as second stage-juveniles infected SB-22 and CBP-233 root systems, compared to 2% in R4. After 8 weeks, the number of M. chitwoodi in SB-22 and CBP-233 roots remained lower (0.3-1.5% of Pi) compared to R4, which increased from 2% to ca. 27%. Development of M. chitwoodi was delayed on SB-22 and CBP-233 by at least 2 weeks, and only half of the infective nematodes established feeding sites and matured in resistant clones compared to 99% in susceptible R4. Necrotic tissue surrounded nematodes that failed to develop in SB-22 and CBP-233. The reproductive factor (ratio of final number of eggs recovered from roots to Pi) was <0.01 for both SB-22 and CBP-233 and 46.8 for R4. Delaying inoculation of CBP-233 from 1 to 3 months after planting did not increase the chance or rate of tuber infection. Only a few M. chitwoodi developed to maturity on CBP-233 tubers and deposited a small number of eggs. SB-22 rarely produced tubers in these experiments, and like CBP-233 were resistant to M. chitwoodi. It appeared that the mechanisms of resistance to M. chitwoodi in roots and tubers of CBP-233 are similar.     

Genomic variation in tomato,from wild ancestors to contemporary breeding accessions

Background

Domestication modifies the genomic variation of species. Quantifying this variation provides insights into the domestication process, facilitates the management of resources used by breeders and germplasm centers, and enables the design of experiments to associate traits with genes. We described and analyzed the genetic diversity of 1,008 tomato accessions including Solanum lycopersicum var. lycopersicum (SLL), S. lycopersicum var. cerasiforme (SLC), and S. pimpinellifolium (SP) that were genotyped using 7,720 SNPs. Additionally, we explored the allelic frequency of six loci affecting fruit weight and shape to infer patterns of selection.

Results

Our results revealed a pattern of variation that strongly supported a two-step domestication process, occasional hybridization in the wild, and differentiation through human selection. These interpretations were consistent with the observed allele frequencies for the six loci affecting fruit weight and shape. Fruit weight was strongly selected in SLC in the Andean region of Ecuador and Northern Peru prior to the domestication of tomato in Mesoamerica. Alleles affecting fruit shape were differentially selected among SLL genetic subgroups. Our results also clarified the biological status of SLC. True SLC was phylogenetically positioned between SP and SLL and its fruit morphology was diverse. SLC and “cherry tomato” are not synonymous terms. The morphologically-based term “cherry tomato” included some SLC, contemporary varieties, as well as many admixtures between SP and SLL. Contemporary SLL showed a moderate increase in nucleotide diversity, when compared with vintage groups.

Conclusions

This study presents a broad and detailed representation of the genomic variation in tomato. Tomato domestication seems to have followed a two step-process; a first domestication in South America and a second step in Mesoamerica. The distribution of fruit weight and shape alleles supports that domestication of SLC occurred in the Andean region. Our results also clarify the biological status of SLC as true phylogenetic group within tomato. We detect Ecuadorian and Peruvian accessions that may represent a pool of unexplored variation that could be of interest for crop improvement.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1444-1) contains supplementary material, which is available to authorized users.     

Mapping of resistance to the potato cyst nematode Globodera rostochiensis from the wild potato species Solanum vernei

A population of diploid potato (Solanum tuberosum) was used for the genetic analysis and mapping of a locus for resistance to the potato cyst nematode Globodera rostochiensis, introgressed from the wild potato species Solanum vernei. Resistance tests of 108 genotypes of a F₁ population revealed the presence of a single locus with a dominant allele for resistance to G. rostochiensis pathotype Ro1. This locus, designated GroV1, was located on chromosome 5 with RFLP markers. Fine-mapping was performed with RAPD and SCAR markers. The GroV1 locus was found in the same region of the potato genome as the S. tuberosum ssp. andigena H1 nematode resistance locus. Both resistance loci could not excluded to be allelic. The identification of markers flanking the GroV1 locus offers a valuable strategy for marker-assisted selection for introgression of this nematode resistance.Abbreviations BSA bulked segregant analysis - RAPD random-amplified polymorphic DNA - RFLP restriction fragment length polymorphism - SCAR sequence-characterized amplified region     

Effects of the Mi-1 and the N root-knot nematode-resistance gene on infection and reproduction of Meloidogyne enterolobii on tomato and pepper cultivars

Meloidogyne enterolobii is widely considered to be an aggressive root-knot nematode species that is able to reproduce on root-knot nematode-resistant tomato and pepper cultivars. In greenhouse experiments, M. enterolobii isolates 1 and 2 from Switzerland were able to reproduce on tomato cultivars carrying the Mi-1 resistance gene as well as an N-carrying pepper cultivar. Reproduction factors (Rf) ranged between 12 and 109 depending on the plant cultivar, with M. enterolobii isolate 2 being more virulent when compared to isolate 1. In contrast, M. arenaria completely failed to reproduce on these resistant tomato and pepper cultivars. Although some variability in virulence and effectiveness of root-knot nematode-resistance genes was detected, none of the plant cultivars showed Rf values less than 1 or less than 10% of the reproduction observed on the susceptible cv. 'Moneymaker' (Rf = 23-44) used to characterize resistance. The ability of M. enterolobii to overcome the resistance of tomato and pepper carrying the Mi-1 and the N gene makes it difficult to manage this root-knot nematode species, particularly in organic farming systems where chemical control is not an option.     

Evaluation of rhizosphere bacterial antagonists for their potential to bioprotect potato (Solanum tuberosum) against bacterial wilt (Ralstonia solanacearum)

Bacterial wilt (Ralstonia solanacearum) is one of the production constraints of potato (Solanum tuberosum). The intent of the study was to evaluate potential of bacterial antagonists to suppress bacterial wilt disease development and evaluate the role of the strains as plant growth-promoting rhizobacteria (PGPR) in potato. One hundred-twenty rhizosphere bacterial isolates were screened against virulent strain of Ralstonia solanacearum PPRC-Rs. After in vitro screening, six antagonistic strains (PFMRI, BS-DFS, PF9, PF20, BC, and BS-wly) with inhibition diameter >11 mm were selected and studied further in the greenhouse, in vivo. During in vivo study, the strains were evaluated for their effect in suppressing disease development in terms of area under disease progress curve (AUDPC) and increasing biomass (plant height and dry weight) of potato. Accordingly, PFMRI, BS-DFS, and PF9, significantly reduced AUDPC by 78.6, 66, and 64.3%, and wilt incidence by 82.7, 66.2, and 65.7%, respectively, compared to the control. During the sole application, the strains significantly (P < 0.0001) increased plant height by 35.6, 45.9, and 45%, and dry matter by 111, 130.4, and 129%, respectively compared to non-bacterized control. In the presence of the pathogen strain PFMRI, BS-DFS, and PF9 increased plant height by 66, 50, and 48.2%, and dry matter by 153.8, 96.8, and 92.5%, respectively compared to the pathogen treated control. Hence, the study shows that PFMRI, BS-DFS, and PF9 strains have potential use in potato bioprotection, as PGPR or in an integrated bacterial wilt management; whose effectiveness under a variety of field conditions should be investigated.