Surveillance of Pathogenicity of Rhizoctonia solani Japanese Isolates with Varied Anastomosis Groups and Subgroups on Arabidopsis thaliana.
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ABSTRACT:
SUBMITTER: Abdelghany MMA
PROVIDER: S-EPMC8781544 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Sheath blight disease caused by Rhizoctonia solani Kuhn (teleomorph; Thanatephorus cucumeris) is a major constraint in rice production. Among the different anastomosis groups (AGs) of Rhizoctonia solani, AG1-IA causes sheath blight of rice, which induce necrotic lesions on leaf sheaths of the infected plants. Several reports contradict the host specificity of anastomosis groups in Rhizoctonia solani. There is lack of information on the pathogenicity genes of these Rhizoctonia solani anastomosis groups during sheath blight infection in rice. In the present study, Rhizoctonia solani isolates collected from diverse rice growing regions of India were screened for anastomosis groups and two groups namely, AG1-IA, AG2-2 were identified. Accordingly, comparative studies were made with AG1-IA (GenBank ID: 16,395) and AG2-2 (GenBank ID: 2,318,768) group sequences, which enabled the identification of specific gene clusters (119 in AG1-IA and 604 in AG2-2) belonging to these groups. Pathogen Host Interaction (PHI) blast with these specific gene clusters could further identify genes involved in host pathogen interaction (38 in AG1_IA and 150 in AG2-2), which were shortlisted for qRT-PCR validation based on qcov cutoff values representing different phenotypic categories of PHI blast. Expression analysis-based validation in sheath blight susceptible (Pusa Basmati 1) and resistant (Pusa 1908-13-12-5) rice genotypes showed that most of the genes expressed significantly higher in the susceptible variety Pusa Basmati 1. The genes like inorganic phosphate transporter (AG1_IPT), Bromodomain containing protein (AG1_BrD), Aldehyde dehydrogenase (AG1_AldD), AMP binding domain (AG1_AMP) and Heme peroxidase (AG1_HmPr) were upregulated in the susceptible genotype, PB 1 at 72hpi compared to Pusa 1908-13-12-5. Among these, inorganic phosphate transporter (AG1_IPT), Bromodomain containing protein (AG1_BrD) and Heme peroxidase (AG1_HmPr) were specific to Rhizoctonia solani AG1-IA. Through the present study, we could demonstrate the AG1-IA-specific interactions of Rhizoctonia solani causing sheath blight disease of rice, which is a step forward in understanding the specificity of Rhizoctonia solani with reference to sheath blight disease of rice.Supplementary informationThe online version contains supplementary material available at 10.1007/s13205-021-02934-1.
| S-EPMC8329123 | biostudies-literature
Project description:Mitochondria are the major energy source for cell functions. However, for the plant fungal pathogens, mitogenome variations and their roles during the host infection processes remain largely unknown. Rhizoctonia solani, an important soil-borne pathogen, forms different anastomosis groups (AGs) and adapts to a broad range of hosts in nature. Here, we reported three complete mitogenomes of AG1-IA RSIA1, AG1-IB RSIB1, and AG1-IC, and performed a comparative analysis with nine published Rhizoctonia mitogenomes (AG1-IA XN, AG1-IB 7/3/14, AG3, AG4, and five Rhizoctonia sp. mitogenomes). These mitogenomes encoded 15 typical proteins (cox1-3, cob, atp6, atp8-9, nad1-6, nad4L, and rps3) and several LAGLIDADG/GIY-YIG endonucleases with sizes ranging from 109,017 bp (Rhizoctonia sp. SM) to 235,849 bp (AG3). We found that their large sizes were mainly contributed by repeat sequences and genes encoding endonucleases. We identified the complete sequence of the rps3 gene in 10 Rhizoctonia mitogenomes, which contained 14 positively selected sites. Moreover, we inferred a robust maximum-likelihood phylogeny of 32 Basidiomycota mitogenomes, representing that seven R. solani and other five Rhizoctonia sp. lineages formed two parallel branches in Agaricomycotina. The comparative analysis showed that mitogenomes of Basidiomycota pathogens had high GC content and mitogenomes of R. solani had high repeat content. Compared to other strains, the AG1-IC strain had low substitution rates, which may affect its mitochondrial phylogenetic placement in the R. solani clade. Additionally, with the published RNA-seq data, we investigated gene expression patterns from different AGs during host infection stages. The expressed genes from AG1-IA (host: rice) and AG3 (host: potato) mainly formed four groups by k-mean partitioning analysis. However, conserved genes represented varied expression patterns, and only the patterns of rps3-nad2 and nad1-m3g18/mag28 (an LAGLIDADG endonuclease) were conserved in AG1-IA and AG3 as shown by the correlation coefficient analysis, suggesting regulation of gene repertoires adapting to infect varied hosts. The results of variations in mitogenome characteristics and the gene substitution rates and expression patterns may provide insights into the evolution of R. solani mitogenomes.
| S-EPMC8488467 | biostudies-literature
Project description:Rhizoctonia solani Kühn (teleomorph = Thanatephorus cucumeris (Frank) Donk) is one of the important soil-borne fungal pathogen, which infects tomato with typical symptoms of seedling damping-off and foot rot. During surveys (2014 and 2015 crop season) of nine tomato growing areas in Pothohar region of Pakistan, symptoms of foot rot were noted on approximately 33.4% of the plants observed at soil line level of the stem. Lesions on infected plant stems were irregular in shape, water-soaked, brown in colour manifesting sunken appearance. Fungal colonies isolated from stem portions of the diseased plants on malt extract agar medium were light grey to brown in colour with abundant mycelial growth and branched hyphae. A septum was always present in the branch of hyphae near the originating point with a slight constriction at the branch. No conidia or conidiophores were observed. All isolates were multinucleate when subjected to DAPI (4',6-diamidino-2-phenylindole) stain. Based on morphological characteristics of fungal hyphae, isolates were identified as R. solani. Restriction analysis of PCR-amplified ribosomal DNA with four discriminant enzymes (MseI, AvaII, HincII, and MunI) and hyphal interactions with known tester strains confirmed these isolates belong to AG-3-PT (64.2%), AG-2-1 (14.2%), AG-2-2 (9.5%), AG-5 (7.1%) and AG-4-HGI (4.7%). AG-3-PT was widely distributed to major tomato growing areas while other groups were confined to distinct locations. Internal transcribed spacer (ITS) region of rDNA was amplified with the primers ITS1/ITS4 and sequenced which had 99-100% identity with the corresponding gene sequences of respective R. solani AGs. To confirm Koch's postulates, four week old tomato plants were transplanted into 1.5 L plastic pots containing sterilized potting mixture i.e. sand: clay: farmyard manure, at the rate of 1:1:1. Soil inoculum containing 10 g of barley grains colonized with each isolate of R. solani for 14 days was mixed in the upper 2 cm layer of soil (Taheri and Tarighi, 2012). A set of uninoculated plants was used as a control. Ambient conditions were provided under the greenhouse. 21 days after inoculation, water-soaked greyish to brown lesions similar to the symptoms of the previous infection were observed on stem portions of all inoculated plants while control plants remained symptomless. Fungus re-isolated from infections was confirmed as R. solani by microscopic appearance of the hyphae. Present study is the first report of AG composition of R. solani infecting tomato in Pakistan which will be useful to breeding programs working on varietal evaluation.
| S-EPMC6405938 | biostudies-literature
Project description:Proper management of agricultural disease is important to ensure sustainable food security. Staple food crops like rice, wheat, cereals, and other cash crops hold great export value for countries. Ensuring proper supply is critical; hence any biotic or abiotic factors contributing to the shortfall in yield of these crops should be alleviated. Rhizoctonia solani is a major biotic factor that results in yield losses in many agriculturally important crops. This paper focuses on genome informatics of our Malaysian Draft R. solani AG1-IA, and the comparative genomics (inter- and intra- AG) with four AGs including China AG1-IA (AG1-IA_KB317705.1), AG1-IB, AG3, and AG8. The genomic content of repeat elements, transposable elements (TEs), syntenic genomic blocks, functions of protein-coding genes as well as core orthologous genic information that underlies R. solani's pathogenicity strategy were investigated. Our analyses show that all studied AGs have low content and varying profiles of TEs. All AGs were dominant for Class I TE, much like other basidiomycete pathogens. All AGs demonstrate dominance in Glycoside Hydrolase protein-coding gene assignments suggesting its importance in infiltration and infection of host. Our profiling also provides a basis for further investigation on lack of correlation observed between number of pathogenicity and enzyme-related genes with host range. Despite being grouped within the same AG with China AG1-IA, our Draft AG1-IA exhibits differences in terms of protein-coding gene proportions and classifications. This implies that strains from similar AG do not necessarily have to retain similar proportions and classification of TE but must have the necessary arsenal to enable successful infiltration and colonization of host. In a larger perspective, all the studied AGs essentially share core genes that are generally involved in adhesion, penetration, and host colonization. However, the different infiltration strategies will depend on the level of host resilience where this is clearly exhibited by the gene sets encoded for the process of infiltration, infection, and protection from host.
| S-EPMC7926851 | biostudies-literature
Project description:Rhizoctonia solani is a species complex composed of many genetically diverse anastomosis groups (AG) and their subgroups. It causes economically important diseases of soybean worldwide. However, the global genetic diversity and distribution of R. solani AG associated with soybean are unknown to date. In this study, the global genetic diversity and distribution of AG associated with soybean were investigated based on rDNA-ITS sequences deposited in GenBank and published literature. The most prevalent AG, was AG-1 (40%), followed by AG-2 (19.13%), AG-4 (11.30%), AG-7 (10.43%), AG-11 (8.70%), AG-3 (5.22%) and AG-5 (3.48%). Most of the AG were reported from the USA and Brazil. Sequence analysis of internal transcribed spacers of ribosomal DNA separated AG associated with soybean into two distinct clades. Clade I corresponded to distinct subclades containing AG-2, AG-3, AG-5, AG-7 and AG-11. Clade II corresponded to subclades of AG-1 subgroups. Furthermore, AG and/or AG subgroups were in close proximity without corresponding to their geographical origin. Moreover, AG or AG subgroups within clade or subclades shared higher percentages of sequence similarities. The principal coordinate analysis also supported the phylogenetic and genetic diversity analyses. In conclusion, AG-1, AG-2, and AG-4 were the most prevalent AG in soybean. The clade or subclades corresponded to AG or AG subgroups and did not correspond to the AG's geographical origin. The information on global genetic diversity and distribution will be helpful if novel management measures are to be developed against soybean diseases caused by R. solani.
| S-EPMC9777564 | biostudies-literature
Project description:Sheath blight, caused by Rhizoctonia solani anastomosis group 1 subgroup 1A (AG1-1A), is one of the most devastating rice diseases worldwide. Here, we report the draft genome sequence of R. solani AG1-1A strain 1802/KB isolated from a popular Malaysian rice variety. To the best of our knowledge, this is the second reported representative genome from AG1-1A.
| S-EPMC5658503 | biostudies-literature
Project description:Single-basidiospore isolates (SBIs) were obtained from field isolates of Thanatephorus cucumeris (Rhizoctonia solani) AG-1 IC and AG-2-2 IV. Formation of distinctive tufts, a recognized feature of heterokaryon synthesis, was observed, and isolates derived from hyphal-tipped tuft hyphae were obtained following pairings between various strains. Three distinctive types of tufts were formed: the fibrous type of mating-compatible homokaryon-homokaryon (Hom-Hom) pairings, the sparse type between heterokaryon-homokaryon (Het-Hom) pairings originating from one parent, and the compact type between Het-Hom pairings originating from different parents. Amplified Fragment Length Polymorphism (AFLP) profile of fingerprints of these tuft isolates verified that they were all heterokaryotic. Because of heterokaryotic vigor, the growth and pathogenicity of the majority of tuft isolates increased compared with their contributing SBIs. New somatic compatibility groups (SCGs) that were different from parental field isolates occurred following heterokaryon formation within T. cucumeris. Tuft isolates produced by Hom-Hom and Het-Hom pairings among isolates of different parents yielded no somatic compatibility with the original parent isolates and a high frequency of new SCGs (62-100%). This was in contrast to those produced by Hom-Hom and Het-Hom pairings among isolates with a common parent that yielded only 12-37% new SCGs. The SCG diversity of R. solani in the field may be attributed to new fitter heterokaryons formed between a heterokaryon of one pair of parents and a homokaryon of another parent pair. This mechanism greatly contributes to genetic diversity in the field and accounts for the failure to recover the expected distribution of SCGs from a field population.
| S-EPMC4070963 | biostudies-literature
Project description:Cellulose-rich amendments stimulate saprotrophic fungi in arable soils. This may increase competitive and antagonistic interactions with root-infecting pathogenic fungi, resulting in lower disease incidence. However, cellulose-rich amendments may also stimulate pathogenic fungi with saprotrophic abilities, thereby increasing plant disease severity. The current study explores these scenarios, with a focus on the pathogenic fungus Rhizoctonia solani. Saprotrophic growth of R. solani on cellulose-rich materials was tested in vitro. This confirmed paper pulp as a highly suitable substrate for R. solani, whereas its performance on wood sawdusts varied with tree species. In two pot experiments, the effects of amendment of R. solani-infected soil with cellulose-rich materials on performance of beetroot seedlings were tested. All deciduous sawdusts and paper pulp stimulated soil fungal biomass, but only oak, elder and beech sawdusts reduced damping-off of beetroot. Oak sawdust amendment gave a consistent stimulation of saprotrophic Sordariomycetes fungi and of seedling performance, independently of the time between amendment and sowing. In contrast, paper pulp caused a short-term increase in R. solani abundance, coinciding with increased disease severity for beet seedlings sown immediately after amendment. However, damping-off of beetroot was reduced if plants were sown two or four weeks after paper pulp amendment. Cellulolytic bacteria, including Cytophagaceae, responded to paper pulp during the first two weeks and may have counteracted further spread of R. solani. The results showed that fungus-stimulating, cellulose-rich amendments have potential to be used for suppression of R. solani. However, such amendments require a careful consideration of material choice and application strategy.
| S-EPMC8231496 | biostudies-literature
Project description:Rhizoctonia solani is a fungal species complex that causes necrotrophic crop diseases. It comprises several anastomosis groups, some of which include intra-subgroups, such as AG-1 IA and AG-1 IB, exhibiting varying pathogenicity. Owing to its heterozygous and multinucleate features, genomic analyses of R. solani are still challenging, and understanding of its genetic diversity and genic components is limited. In this study, in order to elucidate the molecular basis of this phytopathogen complex, an integrated transcriptome analysis was undertaken for three subgroups of AG-1, i.e. AG-1 IA, AG-1 IB, and AG-1 IC. Sequence variations suggested substantial evolutionary distances within AG-1. Transcript simple sequence repeats showed comparable characteristics among AG-1, but contained polymorphic sites. Intra-subgroup polymorphisms suggested varying genic heterozygosity within AG-1, suggesting their independent evolutionary trajectory. Sequences of pathogenic factors, phytotoxin biosynthesis pathway enzymes, secreted lignocellulosic enzymes, secreted reactive oxygen species detoxification enzymes, apoplastic/cytoplasmic effector candidates, were conserved among those subgroups. dN/dS ratios of a secretome subset suggested core secreted proteins in AG-1 and distinct evolution of Cys-rich small secreted proteins after differentiation of AG-1 subgroups. Identification of likely pathogenic factors including allergen protein homologues, oxidative phosphorylation and ethylene biosynthesis pathways, and diversification of polysaccharide monooxygenases provides molecular insight into key genomic components that play a role in R. solani pathogenesis.
| S-EPMC6928066 | biostudies-literature
Project description:Ninety seven Rhizoctonia isolates were collected from different Brassica species with typical Rhizoctonia symptoms in different provinces of Vietnam. The isolates were identified using staining of nuclei and sequencing of the rDNA-ITS barcoding gene. The majority of the isolates were multinucleate R. solani and four isolates were binucleate Rhizoctonia belonging to anastomosis groups (AGs) AG-A and a new subgroup of A-F that we introduce here as AG-Fc on the basis of differences in rDNA-ITS sequence. The most prevalent multinucleate AG was AG 1-IA (45.4% of isolates), followed by AG 1-ID (17.5%), AG 1-IB (13.4%), AG 4-HGI (12.4%), AG 2-2 (5.2%), AG 7 (1.0%) and an unknown AG related to AG 1-IA and AG 1-IE that we introduce here as AG 1-IG (1.0%) on the basis of differences in rDNA-ITS sequence. AG 1-IA and AG 1-ID have not been reported before on Brassica spp. Pathogenicity tests revealed that isolates from all AGs, except AG-A, induced symptoms on detached leaves of several cabbage species. In in vitro tests on white cabbage and Chinese cabbage, both hosts were severely infected by AG 1-IB, AG 2-2, AG 4-HGI, AG 1-IG and AG-Fc isolates, while under greenhouse conditions, only AG 4-HGI, AG 2-2 and AG-Fc isolates could cause severe disease symptoms. The occurrence of the different AGs seems to be correlated with the cropping systems and cultural practices in different sampling areas suggesting that agricultural practices determine the AGs associated with Brassica plants in Vietnam.
| S-EPMC4221111 | biostudies-literature