Comparative genome analyses of four rice-infecting Rhizoctonia solani isolates reveal extensive enrichment of homogalacturonan modification genes

Abstract

Background Plant pathogenic isolates of Rhizoctonia solani anastomosis group 1-intraspecific group IA (AG1-IA) infect a wide range of crops causing diseases such as rice sheath blight (ShB). ShB has become a serious disease in rice production worldwide. Additional genome sequences of the rice-infecting R. solani isolates from different geographical regions will facilitate the identification of important pathogenicity-related genes in the fungus. Results Rice-infecting R. solani isolates B2 (USA), ADB (India), WGL (India), and YN-7 (China) were selected for whole-genome sequencing. Single-Molecule Real-Time (SMRT) and Illumina sequencing were used for de novo sequencing of the B2 genome. The genomes of the other three isolates were then sequenced with Illumina technology and assembled using the B2 genome as a reference. The four genomes ranged from 38.9 to 45.0 Mbp in size, contained 9715 to 11,505 protein-coding genes, and shared 5812 conserved orthogroups. The proportion of transposable elements (TEs) and average length of TE sequences in the B2 genome was nearly 3 times and 2 times greater, respectively, than those of ADB, WGL and YN-7. Although 818 to 888 putative secreted proteins were identified in the four isolates, only 30% of them were predicted to be small secreted proteins, which is a smaller proportion than what is usually found in the genomes of cereal necrotrophic fungi. Despite a lack of putative secondary metabolite biosynthesis gene clusters, the rice-infecting R. solani genomes were predicted to contain the most carbohydrate-active enzyme (CAZyme) genes among all 27 fungal genomes used in the comparative analysis. Specifically, extensive enrichment of pectin/homogalacturonan modification genes were found in all four rice-infecting R. solani genomes. Conclusion Four R. solani genomes were sequenced, annotated, and compared to other fungal genomes to identify distinctive genomic features that may contribute to the pathogenicity of rice-infecting R. solani. Our analyses provided evidence that genomic conservation of R. solani genomes among neighboring AGs was more diversified than among AG1-IA isolates and the presence of numerous predicted pectin modification genes in the rice-infecting R. solani genomes that may contribute to the wide host range and virulence of this necrotrophic fungal pathogen.

Genome duplication and transposon mediated gene alteration shapes the pathogenicity of Rhizoctonia solani AG1-IA

“…Further, to determine the period of divergence of different AGs of R. solani we plotted the rate of synonymous substitution per synonymous site (Ks) between the orthogroups in the syntenic blocks between AG1-IA and the other sequenced AGs against the percentage of orthologous pairs. We considered the average rate in change of Ks value as 1.3x10 - 8 per year, as reported earlier in case of fungi. The maximum likelihood-based phylogenetic tree constructed using the single-copy orthogroups expectedly predicted AG1-IA and AG1-IB to be phylogenetically closest and they seems to have diverged around 28 million years ago (mya).…”

“…This has been proposed to cause diversification of host range and increasing virulence. Previous genome based studies had revealed expansion/emergance of gene families/orthogoups in different AGs of R. solani 8, 14 . We have observed similar expansion of gene families in AG1-IA in comparison to its closest relative AG1-IB especially, the genes located in the duplicated gene blocks.…”

“…Notably, silencing of one of them i.e Rs_01468 (encoding GH61, LPMO_AA9 domain containing protein) significantly compromised pathogenesis of R. solani . The LPMO domain containing proteins are widespread in filamentous fungi including R. solani and enables the pathogens to degrade different components of the host cell wall 8, 38 . In Colletotrichum , induction of LPMO has been associated with switching between biotrophic and necrotrophic phases 39 .…”

Improving the Genome Annotation of Rhizoctonia solani Using Proteogenomics

“…The RNA-Seq reads were assembled as follows: Trinity --seqType fq --left reads_1.fq --right reads_2.fq --CPU 10 --max_memory 30G. Besides, the protein sequence, genomic sequence, and GFF file of R. solani AG1, AG3, AG4, AG5, AG6, and AG8 have all been released in 2021 [ 34 - 37 ] and downloaded from https://api.ncbi.nlm.nih.gov/datasets/v1alpha/genome/download .…”

Comparative Mitogenomic Analysis and the Evolution of Rhizoctonia solani Anastomosis Groups

“…In recent years, R. solani pathogenesis has been studied at the genomic and transcriptomic level, including AG1-IA that causes sheath blight in rice ( Oryza sativa ), corn ( Zea mays ), and soybeans ( Gl ycine max; Zheng et al, 2013 ; Nadarajah et al, 2017 ; Xia et al, 2017 ; Yamamoto et al, 2019 ; Lee et al, 2021 ; Li et al, 2021a ), AG1-IB that infects lettuce ( Wibberg et al, 2015 ; Verwaaijen et al, 2017 ), AG3 that infects potatoes ( Cubeta et al, 2014 ; Patil et al, 2018 ; Zrenner et al, 2020 ), and AG8 that infects wheat ( Hane et al, 2014 ).…”