Draft Genome Sequence of Rhizoctonia solani Anastomosis Group 1 Subgroup 1A Strain 1802/KB Isolated from Rice

Karmakar

Plant Biotechnology Journal

et al. 2020

191

163

Summary Rice sheath blight disease, caused by the basidiomycetous necrotroph Rhizoctonia solani, became one of the major threats to the rice cultivation worldwide, especially after the adoption of high‐yielding varieties. The pathogen is challenging to manage because of its extensively broad host range and high genetic variability and also due to the inability to find any satisfactory level of natural resistance from the available rice germplasm. It is high time to find remedies to combat the pathogen for reducing rice yield losses and subsequently to minimize the threat to global food security. The development of genetic resistance is one of the alternative means to avoid the use of hazardous chemical fungicides. This review mainly focuses on the effort of better understanding the host–pathogen relationship, finding the gene loci/markers imparting resistance response and modifying the host genome through transgenic development. The latest development and trend in the R. solani–rice pathosystem research with gap analysis are provided.

Section: Application Of Omics Technologies To Understand the Pathogenmentioning

confidence: 99%

Section: Application Of Omics Technologies To Understand the Pathogenmentioning

confidence: 99%

Understanding sheath blight resistance in rice: the road behind and the road ahead

Karmakar

Plant Biotechnology Journal

et al. 2020

191

163

“…This will provide us with the understanding of the adaptive nature of these organisms, their mechanism of survival and pathogenicity. The advent of the genomic era has resulted in a surge in the availability of microbial genome sequences, including that of the destructive fungal phytopathogens [7]. Through genome information, characterization at the molecular level of fungal phytopathogens has enabled researchers to unravel their lifestyle [8,9].…”

Section: Introductionmentioning

confidence: 99%

Transposable Elements Adaptive Role in Genome Plasticity, Pathogenicity and Evolution in Fungal Phytopathogens

Razali

Cheah

Nadarajah

2019

IJMS

Self Cite

Transposable elements (TEs) are agents of genetic variability in phytopathogens as they are a source of adaptive evolution through genome diversification. Although many studies have uncovered information on TEs, the exact mechanism behind TE-induced changes within the genome remains poorly understood. Furthermore, convergent trends towards bigger genomes, emergence of novel genes and gain or loss of genes implicate a TE-regulated genome plasticity of fungal phytopathogens. TEs are able to alter gene expression by revamping the cis-regulatory elements or recruiting epigenetic control. Recent findings show that TEs recruit epigenetic control on the expression of effector genes as part of the coordinated infection strategy. In addition to genome plasticity and diversity, fungal pathogenicity is an area of economic concern. A survey of TE distribution suggests that their proximity to pathogenicity genes TEs may act as sites for emergence of novel pathogenicity factors via nucleotide changes and expansion or reduction of the gene family. Through a systematic survey of literature, we were able to conclude that the role of TEs in fungi is wide: ranging from genome plasticity, pathogenicity to adaptive behavior in evolution. This review also identifies the gaps in knowledge that requires further elucidation for a better understanding of TEs’ contribution to genome architecture and versatility.

“…In fact, until now, draft genome assemblies belonging to only 4 of the 13 AGs have been reported viz. AG1-IA (16), AG1-IB (17), AG2-2IIIB (13), AG3-Rhs1AP (18), AG3-PT isolate Ben-3 (19) and AG8 (20). This limited availability of genome sequences and the predicted proteomes across the 13 different AGs and their subgroups is one of the important barriers hindering the understanding of functional complexity and temporal dynamics in R. solani AGs and their subgroups.…”

Section: Introductionmentioning

confidence: 99%

Pangenome analysis of the soil-borne fungal phytopathogenRhizoctonia solaniand development of a comprehensive web resource: RsolaniDB

Kaushik

Roberts²,

Ramaprasad

et al. 2020

Preprint

Rhizoctonia solani is a collective group of genetically and pathologically diverse basidiomycetous fungus that damages economically important crops. Its isolates are classified into 13 Anastomosis Groups (AGs) and subgroups having distinctive morphology and host range. The genetic factors driving the unique features of R. solani pathology are not well characterized due to the limited availability of its annotated genomes. Therefore, we performed genome sequencing, assembly, annotation and functional analysis of 12 R. solani isolates covering 7 AGs and selected subgroups (AG1-IA, AG1-IB, AG1-IC, AG2-2IIIB, AG3-PT (isolates Rhs 1AP and the hypovirulent Rhs1A1), AG3-TB, AG4-HG-I (isolates Rs23 and R118-11), AG5, AG6, and AG8), in which six genomes are reported for the first time, wherein we discovered unique and shared secretomes, CAZymes, and effectors across the AGs. Using a pangenome comparative analysis of 12 R. solani isolates and 15 other basidiomycetes, we also elucidated the molecular factors potentially involved in determining the AG-specific host preference, and the attributes distinguishing them from other Basidiomycetes. Finally, we present the largest repertoire of R. solani genomes and their annotated components as a comprehensive database, viz. RsolaniDB, with tools for large-scale data mining, functional enrichment and sequence analysis not available with other state-of-the-art platforms, to assist mycologists in formulating new hypotheses.