Comparative Genomics of Xanthomonas axonopodis Pathovars Infecting Cassava and Cowpea in Nigeria: Pathogenicity Determinants and Horizontal Gene Transfer

Xanthomonas axonopodis represents a species complex whose pathovars cause economically significant bacterial diseases of cassava and cowpea in Nigeria, yet the comparative genomic architecture linking host specificity, virulence factor repertoire, and horizontal gene transfer history among Nigerian isolates has not been investigated. This research gap constrains the development of DNA-based diagnostics, resistance breeding targets, and biosecurity risk assessments for these pathovars. This doctoral research uses whole-genome comparative genomics of 90 X. axonopodis isolates, including pv. manihotis from cassava and pv. vignicola from cowpea collected across all six geopolitical zones of Nigeria, to characterise pathogenicity determinants and reconstruct horizontal gene transfer history. Pan-genome analysis, effector gene cataloguing targeting TAL effector and type III effector families, core genome phylogeny reconstruction, and horizontal gene transfer detection using alien gene hunter and comparative island analysis tools are conducted. The research specifically tests the hypothesis that cross-crop horizontal transfer of TAL effector genes between cassava-infecting and cowpea-infecting populations has occurred in zones of geographic co-cultivation, potentially expanding host range. Original contributions include the first pan-genome characterisation of Nigerian X. axonopodis pathovar populations, identification of Nigerian-specific TAL effector variants with novel repeat variable di-residue sequences, and a geographically resolved horizontal gene transfer network for X. axonopodis in Nigeria. Results will directly inform the design of broad-spectrum resistance strategies targeting conserved pathogenicity determinants shared across both pathovars. Keywords: Xanthomonas axonopodis, comparative genomics, horizontal gene transfer, pathogenicity, Nigeria.