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.

担子菌属真菌丝核菌属可对许多植物造成严重损害，由致病性不同的多核、双核和单核物种组成。在这里，我们生成了三种核型丝核菌分离株的染色体级基因组组装。基因组比较表明，单核 JN 菌株可能由两个双核分离物的体细胞杂交产生，并保持二倍体细胞核。JN 基因组中的同源基因对经历了减速或加速进化。同源基因表达优势发生在 JN 亚基因组之间，其中差异表达的基因比没有差异表达的基因表现出可能更少的进化约束。交配型基因分析表明丝核菌属维持担子菌的祖先四极性。长末端重复逆转录转座子与三个染色体级基因组中的染色体 GC 含量呈相互关联。更具攻击性的多核 XN 菌株具有更多编码宿主细胞壁分解酶的基因。这些发现证明了最近衍生的杂种和多种核类型的丝核菌的一些进化变化。