Identification and functional analysis of AG1-IA specific genes of Rhizoctonia solani

Abstract

Rhizoctonia solani is an important necrotrophic fungal pathogen which causes disease on diverse plant species. It has been classified into 14 genetically distinct anastomosis groups (AGs), however, very little is known about their genomic diversity. AG1-IA causes sheath blight disease in rice and controlling this disease remains a challenge for sustainable rice cultivation. Recently the draft genome sequences of AG1-IA (rice isolate) and AG1-IB (lettuce isolate) had become publicly available. In this study, using comparative genomics, we report identification of 3,942 R. solani genes that are uniquely present in AG1-IA. Many of these genes encode important biological, molecular functions and exhibit dynamic expression during in-planta growth of the pathogen in rice. Based upon sequence similarity with genes that are required for plant and human/zoonotic diseases, we identified several putative virulence/pathogenicity determinants amongst AG1-IA specific genes. While studying the expression of 19 randomly selected genes, we identified three genes highly up-regulated during in-planta growth. The detailed in silico characterization of these genes and extent of their up-regulation in different rice genotypes, having variable degree of disease susceptibility, suggests their importance in rice-Rhizoctonia interactions. In summary, the present study reports identification, functional characterization of AG1-IA specific genes and predicts important virulence determinants that might enable the pathogen to grow inside hostile plant environment. Further characterization of these genes would shed useful insights about the pathogenicity mechanism of AG1-IA on rice.

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

“…However, a smaller genome size of about 28.93 Mb is reported (Nadarajah et al, 2017). Comparative genomics between the different sequenced genome of R. solani anastomosis groups further revealed detail about AG1-1A specific genes and putative virulence factor/effector genes (Ghosh et al, 2014;Hane et al, 2014). Similarly, a study of whole-genome sequencing of 13 inbred rice lines was performed to identify SNPs and candidate genes for sheath blight resistance (Silva et al, 2012).…”

Understanding the direction of evolution in Burkholderia glumae through comparative genomics

“…In contrast, B. glumae LMG 2196 has considerably downsized its genome, losing approximately 1 Mb of information compared to B. glumae BGR1 and B. glumae PG1, which enables B. glumae LMG 2196 to increase their population more quickly by rapidly replicating the genome. The differential virulence in rice cultivars depends on the presence or absence of a small, extra chromosome measuring 1.6 Mb in size, containing avirulence genes in plant pathogenic fungi Pyricularia oryzae (Kusaba et al 2014), and many of the 3942 unique genes that are only present in Rhizoctonia solani AG1-1A are expressed during rice infection and may be virulence factors (Ghosh et al 2014). On the other hand, B. glumae PG1 may have focused on the development of its particular metabolic pathways.…”

A novel cross talk of AtRAV1, an ethylene responsive transcription factor with MAP kinases imparts broad spectrum disease resistance in plants

“…R. solani AG1-IA (BRS1) strain (18) was used to infect A. thaliana and tomato. The R. solani sclerotia pre-germinated in potato dextrose broth (PDB, Himedia, Mumbai, India) at 28°C for 6 hours were used to infect the leaves of A. thaliana plants.…”

“…Similarly Rhizoctonia solani a necrotrophic fungal pathogen infects diverse plants including rice, potato, tomato etc. and imparts huge economic losses (18, 19). Notably R. solani and R. solanacearum share many common hosts, including agriculturally important crops such as tomato, potato, etc.…”