Cutting the Gordian knot: taking a stab at corky root rot of tomato

Ekengren, Sophia

doi:10.5511/plantbiotechnology.25.265

Cited by 10 publications

(6 citation statements)

References 40 publications

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“…However, the prohibition of soil fumigation with methyl bromide and high costs of grafting plants restrict the availability of these control methods. No resistant cultivars are commonly available in spite of the determination of resistant sources to this pathogen on tomato plants (Bubici et al 2006;Ekengren 2008).…”

Section: Introductionmentioning

confidence: 99%

Molecular, physiological and pathogenic variability of Pyrenochaeta lycopersici associated with corky rot disease of tomato plants in Turkey

Bayraktar

Oksal²

2011

Phytoparasitica

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Isolates of Pyrenochaeta lycopersici, the causal agent of corky root rot on tomato plants, were assessed for physiological and genetic characteristics using conventional and molecular techniques. All isolates were able to produce necrosis on tomato roots and classified into temperature group according to the optimal growth temperatures. Specific-PCR assays and DNA sequence analysis of the ribosomal DNA (rDNA) internal transcribed spacer region confirmed the existence of both types (Type 1 and Type 2) of the pathogen among the isolates tested. All isolates were identified as Type 2 except for isolate Pl-4, which was classified as Type 1. Restriction fragment length polymorphism (RFLP) analysis with six enzymes resulted in three distinct banding patterns among the isolates depending on the length and restriction profiles of the rDNA intergenic spacer region. Inter-simple sequence-repeat analysis revealed a high level of genetic diversity among the isolates in agreement with the data of RFLP analysis. These results indicated that there were three different intraspecific groups among Turkish isolates of P. lycopersici. The presented study is the first attempting to characterize Turkish isolates of P. lycopersici. The results obtained will be useful in screening of tomato seedlings for resistance to P. lycopersici.

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Section: Introductionmentioning

confidence: 99%

Molecular, physiological and pathogenic variability of Pyrenochaeta lycopersici associated with corky rot disease of tomato plants in Turkey

Bayraktar

Oksal²

2011

Phytoparasitica

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“…It is pathogenic to tomato and other agronomically important Solanaceous species [ 1 , 2 ]. The pathogen is the agent of Corky Root Rot (CRR), a disease widespread especially under intensive tomato production systems and in greenhouse, with yield losses of 30–40% or more [ 3 , 4 ]. The pathogen attacks the main root causing the typical corky aspect, but the disease, especially in the field, tends to be underestimated, due to the lack of significant symptoms on the aerial parts of the plant.…”

Section: Introductionmentioning

confidence: 99%

The genome assembly of the fungal pathogen Pyrenochaeta lycopersici from Single-Molecule Real-Time sequencing sheds new light on its biological complexity

et al. 2018

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The first draft genome sequencing of the non-model fungal pathogen Pyrenochaeta lycopersici showed an expansion of gene families associated with heterokaryon incompatibility and lacking of mating-type genes, providing insights into the genetic basis of this “imperfect” fungus which lost the ability to produce the sexual stage. However, due to the Illumina short-read technology, the draft genome was too fragmented to allow a comprehensive characterization of the genome, especially of the repetitive sequence fraction. In this work, the sequencing of another P. lycopersici isolate using long-read Single Molecule Real-Time sequencing technology was performed with the aim of obtaining a gapless genome. Indeed, a gapless genome assembly of 62.7 Mb was obtained, with a fraction of repetitive sequences representing 30% of the total bases. The gene content of the two P. lycopersici isolates was very similar, and the large difference in genome size (about 8 Mb) might be attributable to the high fraction of repetitive sequences detected for the new sequenced isolate. The role of repetitive elements, including transposable elements, in modulating virulence effectors is well established in fungal plant pathogens. Moreover, transposable elements are of fundamental importance in creating and re-modelling genes, especially in imperfect fungi. Their abundance in P. lycopersici, together with the large expansion of heterokaryon incompatibility genes in both sequenced isolates, suggest the presence of possible mechanisms alternative to gene re-assorting mediated by sexual recombination. A quite large fraction (~9%) of repetitive elements in P. lycopersici, has no homology with known classes, strengthening this hypothesis. The availability of a gapless genome of P. lycopersici allowed the in-depth analysis of its genome content, by annotating functional genes and TEs. This goal will be an important resource for shedding light on the evolution of the reproductive and pathogenic behaviour of this soilborne pathogen and the onset of a possible speciation within this species.

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“…The majority of commercial varieties are susceptible to P. lycopersici and sources of partial genetic resistances occur only in wild tomato species [ 6 ]. The use of susceptible cultivars combined with continuous cropping and the lack of effective soil treatments has encouraged the rapid spread of CRR disease resulting in fruit yield losses of up to 75% [ 7 , 8 ]. The sequencing of 18S nrDNA (SSU) and 28S nrDNA (LSU) indicate that P. lycopersici is an ascomycete in the order Pleosporales, along with other necrotrophic and hemibiotrophic plant pathogens representing genera such as Cochliobolus, Pyrenophora, Phaeosphaeria, Leptosphaeria, Pleospora, Phoma and Didymella [ 9 ] .…”

Section: Introductionmentioning

confidence: 99%

De novo genome assembly of the soil-borne fungus and tomato pathogen Pyrenochaeta lycopersici

et al. 2014

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BackgroundPyrenochaeta lycopersici is a soil-dwelling ascomycete pathogen that causes corky root rot disease in tomato (Solanum lycopersicum) and other Solanaceous crops, reducing fruit yields by up to 75%. Fungal pathogens that infect roots receive less attention than those infecting the aerial parts of crops despite their significant impact on plant growth and fruit production.ResultsWe assembled a 54.9Mb P. lycopersici draft genome sequence based on Illumina short reads, and annotated approximately 17,000 genes. The P. lycopersici genome is closely related to hemibiotrophs and necrotrophs, in agreement with the phenotypic characteristics of the fungus and its lifestyle. Several gene families related to host–pathogen interactions are strongly represented, including those responsible for nutrient absorption, the detoxification of fungicides and plant cell wall degradation, the latter confirming that much of the genome is devoted to the pathogenic activity of the fungus. We did not find a MAT gene, which is consistent with the classification of P. lycopersici as an imperfect fungus, but we observed a significant expansion of the gene families associated with heterokaryon incompatibility (HI).ConclusionsThe P. lycopersici draft genome sequence provided insight into the molecular and genetic basis of the fungal lifestyle, characterizing previously unknown pathogenic behaviors and defining strategies that allow this asexual fungus to increase genetic diversity and to acquire new pathogenic traits.

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Cutting the Gordian knot: taking a stab at corky root rot of tomato

Cited by 10 publications

References 40 publications

Molecular, physiological and pathogenic variability of Pyrenochaeta lycopersici associated with corky rot disease of tomato plants in Turkey

Molecular, physiological and pathogenic variability of Pyrenochaeta lycopersici associated with corky rot disease of tomato plants in Turkey

The genome assembly of the fungal pathogen Pyrenochaeta lycopersici from Single-Molecule Real-Time sequencing sheds new light on its biological complexity

De novo genome assembly of the soil-borne fungus and tomato pathogen Pyrenochaeta lycopersici

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