Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, USA.
Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea.
BMC Genomics. 2021 Apr 7;22(1):242. doi: 10.1186/s12864-021-07549-7.
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.
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.
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.
根肿菌属 1 号吻合组内组 IA（AG1-IA）的植物病原分离物感染范围广泛的作物，导致水稻纹枯病（ShB）等疾病。ShB 已成为全球水稻生产中的严重疾病。来自不同地理区域的感染水稻的根肿菌分离物的额外基因组序列将有助于鉴定真菌中重要的致病性相关基因。
选择感染水稻的根肿菌分离物 B2（美国）、ADB（印度）、WGL（印度）和 YN-7（中国）进行全基因组测序。使用单分子实时（SMRT）和 Illumina 测序对 B2 基因组进行从头测序。然后使用 Illumina 技术对其他三个分离物的基因组进行测序，并使用 B2 基因组作为参考进行组装。四个基因组的大小分别为 38.9 至 45.0 Mbp，包含 9715 至 11505 个蛋白质编码基因，共享 5812 个保守直系同源物。与 ADB、WGL 和 YN-7 相比，B2 基因组中转座元件（TEs）的比例和 TE 序列的平均长度分别高出近 3 倍和 2 倍。尽管在四个分离物中鉴定出 818 至 888 个推定分泌蛋白，但其中只有 30%被预测为小分泌蛋白，这一比例低于通常在谷类坏死真菌基因组中发现的比例。尽管缺乏推定的次生代谢物生物合成基因簇，但预测感染水稻的根肿菌基因组包含在比较分析中使用的所有 27 个真菌基因组中最多的碳水化合物活性酶（CAZyme）基因。具体而言，在所有四个感染水稻的根肿菌基因组中都发现了丰富的果胶/半乳糖醛酸聚糖修饰基因。
对四个根肿菌基因组进行了测序、注释，并与其他真菌基因组进行了比较，以鉴定可能导致感染水稻的根肿菌致病性的独特基因组特征。我们的分析提供了证据，表明相邻 AG 之间根肿菌基因组的基因组保守性比 AG1-IA 分离物之间的多样性更大，并且感染水稻的根肿菌基因组中存在大量预测的果胶修饰基因，这可能有助于这种坏死真菌病原体的广泛宿主范围和毒力。
