Integrated genomic and transcriptomic analysis of 2-oxoglutarate-dependent dioxygenases mediating resistance to Xpm in cassava

Cassava bacterial blight (CBB), caused by Xanthomonas phaseoli pv. Manihotis ( Xpm ), remains a primary constraint to global cassava yields, necessitating the identification of genomic components that orchestrate host immune responses. The 2-oxoglutarate-dependent dioxygenase superfamily, renowned for modulating specialized metabolites and defense signaling in model plants, represents a promising but largely untapped genetic resource for enhancing disease resistance in cassava. In this study, RNA-seq revealed that the differentially expressed genes (DEGs) in cassava following Xpm inoculation were predominantly enriched in the MAPK signaling pathway and plant-pathogen interaction pathways. Notably, the 2OGD superfamily emerged as a predominant metabolic hub among significantly enriched defense-related enzyme families. Genome-wide identification characterized 138 Me2OGD gene family members, phylogenetically categorized into DOXA and DOXC subfamilies. Evolutionary analysis demonstrated that while these genes maintain structural conservation, they have undergone clade-specific diversification, likely driven by purifying selection to adapt to tropical pathogen pressures. Weighted Gene Co-expression Network Analysis (WGCNA) was employed to pinpoint the “khaki1” module, which exhibited an infection-stage-specific expression pattern. Within this network, Me2OGD61 was identified as a central hub gene, co-expressed with 27 core defense regulators and exhibiting strong early induction in cassava. Integrated expression profiling and qRT-PCR confirmed its pivotal regulatory potential. Finally, functional validation via Virus-Induced Gene Silencing (VIGS) demonstrated that silencing Me2OGD61 significantly increased cassava susceptibility to CBB, confirming its role as a positive regulator of resistance. This study provides a comprehensive genomic framework for the Me2OGD gene family and identifies Me2OGD61 as a high-value molecular target for breeding CBB-resistant cassava varieties.