Gene expression profiling of the plant pathogenic basidiomycetous fungus Rhizoctonia solani AG 4 reveals putative virulence factors

Lakshman, Dilip K.; Alkharouf, Nadim W.; Roberts, Daniel P.; Natarajan, Savithiry; Mitra, Amitava

doi:10.3852/11-226

Cited by 22 publications

(16 citation statements)

References 90 publications

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“…Thus, the resulting differential cDNA In this study, six contigs (3, 4, 6, 7, 32 and 33) representing nearly 37 % of the EST sequences showed no significant similarity to known protein sequences, reflecting the necessity of sequence annotation in fungi. This high frequency of orphan sequences is similar to that observed in previous fungal EST projects (Shim et al 2004;Viaud et al 2005) and is consistent with findings of other fungal EST studies on different plant pathogens (Lakshman et al 2012;Neumann and Dobinson 2003;Trail et al 2003;Viaud et al 2005). However, the lack of similarity of these EST sequences to entries in protein databases could be due to the fact that they might be derived from 5′ and 3′ un-translated regions (UTRs) (Skinner et al 2001).…”

Section: Discussionsupporting

confidence: 91%

Suppression subtractive hybridization and comparative expression of a pore-forming toxin and glycosyl hydrolase genes in Rhizoctonia solani during potato sprout infection

et al. 2014

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Rhizoctonia solani is a plant pathogenic fungus that causes black scurf on tubers and stem and stolon canker on underground parts of potato plant. Early in the season, the fungus attacks germinating sprouts underground before they emerge from the soil. Damage at this stage results in delayed emergence of weakened plants with poor and uneven stands. The mechanism underlying this phenomenon has been investigated in this study by coupling a cDNA-suppression subtractive hybridization (SSH) library to differential screening to identify transcripts of R. solani that are down-regulated during infection of potato sprouts. We report on the identification of 33 unique genes with functions related to carbohydrate binding, vitamin synthesis, pathogenicity, translation, ATP and nucleic acid binding and other categories. RACE-PCR was used to clone and characterize the first full-length cDNA clones, RSENDO1 and RSGLYC1 that encode for an eukaryotic delta-endotoxin CytB protein and an intracellular glycosyl hydrolase, respectively. Quantitative real-time PCR revealed the down-regulation of RSENDO1 during infection of potato sprouts and the up-regulation of RSGLYC1 when the fungus was grown on a cellulose-based nutrient medium. In contrast, additional experiments have highlighted the down-regulation of RSENDO1 when R. solani was co-cultured with the mycoparasite Stachybotrys elegans and the bacterial antagonist Bacillus subtilis B26. These results advance our understanding of R. solani-potato interaction in subterranean parts of the plant. Such approaches could be considered in building an efficient integrated potato disease management program.

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Section: Discussionsupporting

confidence: 91%

Suppression subtractive hybridization and comparative expression of a pore-forming toxin and glycosyl hydrolase genes in Rhizoctonia solani during potato sprout infection

et al. 2014

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“…Balali and Kowsari (2004) suggest that heterokaryosis could directly influence AG 4 pathogenicity and that isolates which have heterokaryons with genetically diverse nuclei could result in more virulent AG 4 isolates. Other authors have acknowledged that most AG or subgroups of R. solani exhibit a wide range of virulence and genetic diversity, perhaps due to genetic and environmental factors (Farrokhi-Nejad et al 2007;González et al 2012;Lakshman et al 2012;Strausbaugh et al 2011).…”

Section: Discussionmentioning

confidence: 99%

Isolates of Rhizoctonia solani Can Produce both Web Blight and Root Rot Symptoms in Common Bean (Phaseolus vulgaris L.)

Torres¹,

Vargas

Godoy‐Lutz³

et al. 2016

Plant Disease

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In common bean (Phaseolus vulgaris L.), Rhizoctonia solani Kühn is an important pathogen causing web blight (WB) in the tropics, and it is also a soilborne pathogen causing root rot (RR) worldwide. This pathogen is a species complex classified into 14 anastomosis groups (AG). AG 1-IA, AG 1-IB, AG 1-IE, AG 1-IF, AG 2-2, and AG 4 have been reported to cause WB of the aboveground structures of the plant, while AG 4 and AG 2-2 have been associated with RR. There is limited information, however, concerning the ability of particular isolates of specific AG to cause both diseases in common bean. Nine R. solani isolates, including three AG 1 and three AG 4 WB isolates and three AG 4 RR isolates collected from both leaves and roots, respectively, of common bean in Puerto Rico, were used to evaluate the response of 12 common bean genotypes to WB inoculated using a detached-leaf method and to RR inoculated using a solution suspension of R. solani mycelia in the greenhouse. All R. solani isolates were able to induce both RR and WB symptoms. RR readings were generally more severe than the WB readings. The RR isolate RR1 (AG 4) produced the most severe RR scores. A few bean lines had mean RR scores ≤4.4 for specific R. solani isolates on a scale of 1 to 9, with 1 representing resistant and 9 highly susceptible. However, all of the bean lines had mean RR scores ≥5.0 when inoculated with the isolates RR1, RR2, and RR3, which were determined to be AG 4 in this study. Significant line–isolate interactions were observed for the WB and RR inoculations for the three planting dates, suggesting a differential response of the common bean lines to the pathogen. This genotypic interaction may require bean breeders and pathologists to monitor the virulence patterns of R. solani in specific growing environments, while the compatibility of specific R. solani isolates to both aerial and root tissue needs to be considered for disease control strategies.

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“…Significant genomic resources for other AGs of R. solani have also recently become publicly available, formerly being limited to EST libraries of AG1-IA [24] and AG4 [25]. The recent generation of whole genome sequences of R. solani AGs presents new opportunities for comparative genomics between R. solani anastomosis groups.…”

Section: Introductionmentioning

confidence: 99%

Genome Sequencing and Comparative Genomics of the Broad Host-Range Pathogen Rhizoctonia solani AG8

et al. 2014

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Rhizoctonia solani is a soil-borne basidiomycete fungus with a necrotrophic lifestyle which is classified into fourteen reproductively incompatible anastomosis groups (AGs). One of these, AG8, is a devastating pathogen causing bare patch of cereals, brassicas and legumes. R. solani is a multinucleate heterokaryon containing significant heterozygosity within a single cell. This complexity posed significant challenges for the assembly of its genome. We present a high quality genome assembly of R. solani AG8 and a manually curated set of 13,964 genes supported by RNA-seq. The AG8 genome assembly used novel methods to produce a haploid representation of its heterokaryotic state. The whole-genomes of AG8, the rice pathogen AG1-IA and the potato pathogen AG3 were observed to be syntenic and co-linear. Genes and functions putatively relevant to pathogenicity were highlighted by comparing AG8 to known pathogenicity genes, orthology databases spanning 197 phytopathogenic taxa and AG1-IA. We also observed SNP-level “hypermutation” of CpG dinucleotides to TpG between AG8 nuclei, with similarities to repeat-induced point mutation (RIP). Interestingly, gene-coding regions were widely affected along with repetitive DNA, which has not been previously observed for RIP in mononuclear fungi of the Pezizomycotina. The rate of heterozygous SNP mutations within this single isolate of AG8 was observed to be higher than SNP mutation rates observed across populations of most fungal species compared. Comparative analyses were combined to predict biological processes relevant to AG8 and 308 proteins with effector-like characteristics, forming a valuable resource for further study of this pathosystem. Predicted effector-like proteins had elevated levels of non-synonymous point mutations relative to synonymous mutations (dN/dS), suggesting that they may be under diversifying selection pressures. In addition, the distant relationship to sequenced necrotrophs of the Ascomycota suggests the R. solani genome sequence may prove to be a useful resource in future comparative analysis of plant pathogens.

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Gene expression profiling of the plant pathogenic basidiomycetous fungus Rhizoctonia solani AG 4 reveals putative virulence factors

Abstract: Lakshman, Dilip K.; Alkharoud, Nadim; Roberts, Daniel P.; Natarajan, Savithiry S.; and Mitra, Amitava, "Gene expression profiling of the plant pathogenic basidiomycetous fungus Rhizoctonia solani AG 4 reveals putative virulence factors" (2012

Cited by 22 publications

References 90 publications

Suppression subtractive hybridization and comparative expression of a pore-forming toxin and glycosyl hydrolase genes in Rhizoctonia solani during potato sprout infection

Suppression subtractive hybridization and comparative expression of a pore-forming toxin and glycosyl hydrolase genes in Rhizoctonia solani during potato sprout infection

Isolates of Rhizoctonia solani Can Produce both Web Blight and Root Rot Symptoms in Common Bean (Phaseolus vulgaris L.)

Genome Sequencing and Comparative Genomics of the Broad Host-Range Pathogen Rhizoctonia solani AG8

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