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.

Keywords: Homogalacturonan/pectin modification genes; Plant cell wall degrading enzymes; Rhizoctonia solani AG1-IA; Rice sheath blight.

Fig. 1

Evolutionary closeness of the genomes of rice-infecting R. solani AG1-IA and to that of the selected fungal outgroups used in this study. a Single-copy orthogroup, maximum likelihood-based phylogenetic tree illustrating the evolutionary proximity of R. solani isolates relative other members of the Basidiomycota and Ascomycota. b Intra- and inter- anastomosis group comparisons of orthogroups shared among the genomes of R. solani depicted in Venn diagrams

Fig. 2

Genomic level synteny between R. solani anastomosis groups and proteome-level conservation of genes among and between the selected comparison groups. a Circos plot depicting the syntenic region size of all R. solani genomes used in this study. The outer block represents accumulated syntenic region size in Mbp calculated by PROmer. Red and blue blocks and ribbons represent AG1 and the rest of the anastomosis groups, respectively. b Comparison of the protein-coding gene proximity of five closely-related groups. Each consists of protein-coding genes of intra-AG-IA (rice-infecting R. solani AG1-IA), inter-AGs (AG1-IA B2, AG1-IB, AG2, AG3 and AG8), Basidiomycetes (Piriformospora indica, Pleurotus ostreatus, Armillaria ostoyae, Heterobasidion irregulare, Dacryopinax sp.), Ustilago and Trametes. The asterisks represent significant differences in distribution according to the t-test (P over 0.05, ∗∗∗P ≤ 0.001)

Fig. 3

Distribution of small secreted proteins in R. solani isolates and other fungal species. a The number of small secreted proteins in the total secretome of each fungal genome. Gray and red bars represent the size of secretome and the number of small secreted proteins, respectively. b The number of SSPs in relation to the number of total protein-coding genes. Red, blue, gray dots represent genomes belonging to intra-AGs, inter-AGs, and other fungal species. c The heatmap shows the conservation of 272 SSPs in B2 against the other R. solani genome sequences. Exonerate 2.4.0 was utilized to perform protein to genome sequence alignments of the SSPs

Fig. 4

Distribution of gene families in rice-infecting R. solani AG1-IA isolates and the fungal outgroups used in this study. Phylogenetic tree with information of contracted and expanded gene families. Abundance of genes in carbohydrate-binding module (CBM), glycoside hydrolase (GH), carbohydrate esterase (CE), glycosyltransferase (GT), polysaccharide lyase (PL) and auxillary activity (AA) families. Expansion and contraction of enriched pectin lyase and pectate lyase (PL/PNL: PL1–1 (EC 4.2.2.2), PL1–2 (EC 4.2.2.10), PL3–1 (EC 4.2.2.2), PL4, PL9–1 (EC 4.2.2.2)), polygalacturonase (PG: GH28–1 (EC 3.2.1.15), GH28–2 (EC 3.2.1.67)), pectin methylesterase (PME: CE8) pectin acetylesterase (PAE: CE12–1 (EC 3.1.-)), and other GHs (GH105–1 (EC 3.2.1.172), GH88–1 (EC 3.2.1.-), GH78–1 (EC 3.2.1.40)) in all 27 fungal genomes used in this study indicated. Red circle indicates the gain EC in R. solani monophyletic