Unraveling the Pathogenomics of Rhizoctonia solani infecting Proso millet (Panicum miliaceum L.): Genomic Perspective on Ruthless Virulence and Adaptive Evolution

Prasanna S Koti ¹ T. S. S. K. Patro ^2* K. B. PALANNA ^3* Jeevan B ^4* Porapu Prasanth ² Gutha Venkata Ramesh ⁵ Anuradha N ² Sandhya Rani Y ² Triveni Ungata ² Lavanya Devi K ⁶ Tharana Poonacha T ⁷ Farooq Khan ⁷ Boda Praveen ² Divya M ² Sabina Mary D ² Prasanna Kumari V ⁸ NAGARAJA T. E. ³ R Madhusudhana ⁹ Tara Satyavathi Chellapilla ⁹

• ¹ Department of Plant Biotechnology, University of Agricultural Sciences, GKVK, Bengaluru, Karnataka, India, Bengaluru, Karnataka, India
• ² Agricultural Research Station, Acharya N. G. Ranga Agricultural University, Vizianagaram, Andhra Pradesh, India, Vizianagaram, India
• ³ ICAR-AICRP on Small millets, Project Coordinating (PC) Unit, University of Agricultural Sciences, GKVK, Bengaluru, Karnataka, India, Bengaluru, Karnataka, India
• ⁴ National Rice Research Institute (ICAR), Cuttack, India
• ⁵ Krishi Vigyan Kendra (KVK), Nadia II, Eastern Regional Station, ICAR-National Dairy Research Institute (NDRI), Kalyani, West Bengal, India, Kalyani, India
• ⁶ Functional Genomics and Bioinformatics theme group, The University of Trans-Disciplinary Health Sciences and Technology, Bangalore, India, Bengaluru, India
• ⁷ Department of Plant Pathology, University of Agricultural Sciences, Gandhi Krishi Vigyana Kendra (GKVK), Bengaluru, Karnataka, India, Bengaluru, Karnataka, India
• ⁸ Department of Plant Pathology, Agricultural College, Acharya N.G Ranga Agricultural University, Bapatla, Andra Pradesh, India, Bapatla, India
• ⁹ ICAR-Indian Institute of Millets Research (IIMR), Hyderabad, Telangana, India

Banded sheath blight (BSB), caused by Rhizoctonia solani, poses a significant threat to proso millet production, adversely affecting both yield and grain quality. This study investigates the pathogenomics of R. solani to identify its genetic mechanisms, elucidate key virulence factors, explore host-pathogen interactions, and pinpoint molecular targets for developing effective control strategies. Six isolates of R. solani were collected from different regions of India. These isolates were thoroughly characterized using morphological, molecular, and virulence-based analyses to assess their diversity and pathogenicity. The most virulent isolate, VAP1, was selected for genome sequencing using the Illumina platform, followed by de novo assembly with the SPAdes assembler, yielding a high-quality genome. Functional regions of the genome were annotated using Funannotate, followed by comparative genomics and secretome analysis to provide further insight into the genomic structure and virulence mechanisms. The VAP1 genome was assembled into a 47.12 Mbp sequence, with 17.62% of the genome consisting of repetitive elements, mainly retrotransposons (72%), with DNA transposons comprising 5%. The functional analysis identified enrichment in KEGG pathways related to "Carbohydrate metabolism," "Translation," "Signal transduction," and "Transport and catabolism." Gene Ontology (GO) terms such as "Proteolysis," "Membrane," and "ATP binding" were notably enriched. The secretome of VAP-1 revealed important proteins from the Major Facilitator Superfamily (MFS) transporters, glycosidases, P-loop nucleoside triphosphate hydrolases, and galactose oxidase, with glycoside hydrolases being the largest class of CAZymes identified. A comparative genomic analysis of VAP1 with other R. solani strains infecting different host plants, including rice, sugar beet, and tobacco, showed that VAP1 is genetically closest to rice-infecting strain, while exhibiting greater divergence from strains infecting sugar beet and tobacco. Variations were observed in key secretory proteins, including multiple base deletions in MFS proteins. These findings highlight the genomic diversity within R. solani strains and underscore the importance of secretory proteins in host infection, providing the pathogen with tools for plant cell wall degradation, saccharide release, and energy acquisition. The observed genetic variability suggests potential adaptations that may influence host specificity and pathogenicity.