Evolutionary and genomic comparisons of hybrid uninucleate and nonhybrid Rhizoctonia fungi

Abstract

The basidiomycetous fungal genus, Rhizoctonia, can cause severe damage to many plants and is composed of multinucleate, binucleate, and uninucleate species differing in pathogenicity. Here we generated chromosome-scale genome assemblies of the three nuclear types of Rhizoctonia isolates. The genomic comparisons revealed that the uninucleate JN strain likely arose by somatic hybridization of two binucleate isolates, and maintained a diploid nucleus. Homeolog gene pairs in the JN genome have experienced both decelerated or accelerated evolution. Homeolog expression dominance occurred between JN subgenomes, in which differentially expressed genes show potentially less evolutionary constraint than the genes without. Analysis of mating-type genes suggested that Rhizoctonia maintains the ancestral tetrapolarity of the Basidiomycota. Long terminal repeat-retrotransposons displayed a reciprocal correlation with the chromosomal GC content in the three chromosome-scale genomes. The more aggressive multinucleate XN strain had more genes encoding enzymes for host cell wall decomposition. These findings demonstrate some evolutionary changes of a recently derived hybrid and in multiple nuclear types of Rhizoctonia.

Salicylic Acid Is Required for Broad-Spectrum Disease Resistance in Rice

“…Lesion lengths caused by the challenge of R. solani XN strain were markedly reduced upon knockout of OsSAH3 (sah3KO), and both OsSAH2 and OsSAH3 (sah2&sah3KO) plants, whereas the lesion lengths were increased in the CDU::SAH3-and 35S::SAH3-GFP-overexpressing plants (Figure 4d). Furthermore, the plants harboring OsSAH3-overexpressing constructs were infected with a weak virulent uninucleate Rhizoctonia JN isolate [29]. OsSAH3-overexpressing plants were more susceptible to JN isolate than the ZH17 control plants (Figure S9).…”

Phylogenomic analysis of the Neocallimastigomycota: Proposal of Caecomycetaceae fam. nov., Piromycetaceae fam. nov., and emended description of the families Neocallimastigaceae and Anaeromycetaceae

“…[51,52], with genome-based quantitative comparisons (e.g. Jaccard index of genomic distance (the fraction of shared k-mers), identification of syntenic blocks, and Average Nucleotide Identity (ANI) [15,18]) being more heavily utilized and often for delineating lower taxonomic level (e.g. species) boundaries.…”

“…Comparative genomics approaches (e.g. calculation of shared Kmer (Kmer overlap) [15,16], average nucleotide identity (ANI) [17], identification of genomic syntenic blocks [18]) have been increasingly utilized in taxonomic studies, aided by the development of lower cost high . CC-BY-ND 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.…”

Genomic Analysis of Sarcomyxa edulis Reveals the Basis of Its Medicinal Properties and Evolutionary Relationships

“…It also has an explicit evolutionary model for data and better accounting for branch length ( Mishler, 2006 ). For example, Li et al (2021) and Xu et al (2020) used the ML algorithm in RAxML to construct a genome-based phylogenetic tree. In this study, based on the ML/NJ phylogenetic analysis of S. edulis and 31 other species of fungus, it was shown that the Sarcomyxa genus is a distinct group.…”