Date of Graduation


Document Type


Degree Name

Doctor of Philosophy in Agricultural, Food and Life Sciences (PhD)

Degree Level



Entomology and Plant Pathology


Alejandro Rojas

Committee Member

Alverson, Andrew

Second Committee Member

Uehling, Jessie

Third Committee Member

Egan, Martin


Ceratobasidium, Genomic diversity, Mitogenomes, Population genetics, Rhizoctonia, Whole genomes


Rhizoctonia is a complex genus in the phylum Basidiomycota comprised of several taxa distributed across different families in the order Cantharellales. Many species in the genus have been identified as plant pathogens, saprobes, or beneficial mycorrhizal symbionts of orchids. Rhizoctonia isolates are divided into binucleate and multinucleate and then classified into anastomosis groups (AGs) based on the ability of compatible hyphae to fuse. Binucleate Rhizoctonia species (Ceratobasidium spp.) are classified into 21 AGs identified with letters (AG-A to AG-U). Multinucleate Rhizoctonia species (Thanatephorus spp.) are identified with numbers and classified into 14 anastomosis groups (AG-1 to AG-13, and bridging group AG-BI). Rhizoctonia solani is the most studied species within the genus. This is an important plant pathogen, including R. solani AG1-IA, the causal agent of sheath blight of rice and aerial blight of soybean. While several genomes have been reported for different R. solani AGs, only three genomes have been published for Ceratobasidium spp. The large gap between available genomic resources for the two main genera in the Rhizoctonia species complex limits our understanding of their ecology and evolution as well as how their genetic diversity can shape the interactions with different hosts and preferences in lifestyles. We compared genomic features including genome size, gene content and repertoire of pathogenicity related genes of five Ceratobasidium spp. associated with agricultural crops contrasting the genetic differences with an equally less studied species, namely Rhizoctonia zeae, and a reference isolate for the multinucleate pathogen Rhizoctonia solani AG1-IA. To our knowledge this is the first comprehensive comparative genomics study that includes different Rhizoctonia and Ceratobasidium species and we found some core genetic differences to be a good approximation for examining host preference and range. We also explored the composition of the mitochondrial genomes of Ceratobasidium and other Rhizoctonia species, finding differences in length, intronic and intergenic regions, and gene order and a possible correlation between these factors and mitogenome expansion in both genera. Finally, we studied the genetic diversity and population structure of a large population of R. solani AG1-IA obtained from different hosts, geographical locations and years based on genome-wide high-quality SNPs. While year did not influence isolates’ genetic variability, host and geographical origins determined population’s subdivision and pathogen’s reproductive system. In summary, these studies support the advancement of genomic studies in the genus Rhizoctonia that will help understand plant-pathogen interactions and phylogenetic relationships between the two main genera in the family Ceratobasidiaceae. Moreover, the availability of more genomic resources will contribute to the development of molecular tools for pathogen surveillance, disease diagnostics and management. The goal of this study is to contribute to a better understanding of the underlying genetic basis for lifestyle and host preference in both Ceratobasidium and Rhizoctonia species, provide new genetic tools to generate more specific markers than currently available for the identification and classification of Rhizoctonia species and anastomosis groups and ultimately establish a program to monitor pathogens diversity and emergence of new genotypes in areas affected by Rhizoctonia diseases.

Available for download on Thursday, February 13, 2025