Metagenomics-Based Discovery of Novel Phytopathogens in Symptom-Expressing Crops Across Nigeria’s Six Geopolitical Zones

Conventional plant disease diagnostics detect only known pathogens against which specific assays have been developed, creating surveillance blind spots in which novel or emerging pathogens cause undiagnosed yield losses. Metagenomic sequencing of plant material presents a transformative approach to unbiased pathogen discovery, but has not been applied at national scale to Nigerian crop disease diagnostics. This doctoral research conducts the first systematic metagenomics-based phytopathogen discovery programme across all six geopolitical zones of Nigeria, targeting symptomatic plant material from cassava, maize, tomato, yam, sorghum, and cowpea crops. A total of 360 symptomatic plant samples, 60 per geopolitical zone representing diverse symptom types across the six target crops, are subjected to total nucleic acid extraction, ribosomal depletion, and next-generation sequencing using the Illumina NovaSeq platform. Bioinformatic pipelines incorporating de novo assembly, viral, bacterial, oomycete, and fungal taxonomic classification against curated phytopathogen reference databases are used to characterise pathogen communities. Novel sequence contigs not assignable to known pathogen taxa are subjected to structure-based protein analysis and phylogenetic placement. Sixteen putative novel or country-first-record pathogens are identified, including four candidate novel viruses, two potentially novel Phytophthora species, and a Candidatus phytoplasma lineage not previously described. The dissertation establishes a national crop pathobiome baseline, a publicly accessible curated sequence database, and a methodological framework for ongoing metagenomic surveillance of Nigerian plant health. Keywords: metagenomics, pathogen discovery, plant disease, Nigeria, surveillance.