Comparative Genomics and Biosynthetic Pathway Elucidation of Cryptolepine Production in Cryptolepis sanguinolenta Populations Across Nigerian Ecological Zones

Cryptolepine, the principal indoloquinoline alkaloid of Cryptolepis sanguinolenta, is a pharmacologically pivotal compound with documented antiplasmodial, antibacterial, and antifungal activity. Cryptolepis sanguinolenta populations distributed across the rainforest and forest-savannah transition zones of Nigeria's South West, South East, and South South regions show considerable phenotypic and phytochemical variation, suggesting underlying genomic diversity. No study has employed comparative genomics to elucidate cryptolepine biosynthetic pathway genes or to correlate genomic variation with alkaloid yield across Nigerian ecotypes. This PhD research characterises the genome architecture, biosynthetic gene cluster organisation, and cryptolepine production efficiency of Cryptolepis sanguinolenta populations from Cross River (South South), Ondo (South West), and Anambra (South East) States using long-read PacBio sequencing, biosynthetic pathway transcriptomics, and metabolomics-genotype correlation analysis. Full draft genomes of three population representatives were assembled and annotated using MAKER2. Biosynthetic gene clusters for the indoloquinoline pathway were identified by comparison with the strictosidine-based monoterpene indole alkaloid pathway and manual genome mining. Differential gene expression of biosynthetic pathway genes was correlated with cryptolepine yield quantified by HPLC across 30 individual plant specimens per population. Significant inter-population genomic variation was detected in cytochrome P450 and O-methyltransferase loci critical to cryptolepine biosynthesis. The Cross River population demonstrated highest cryptolepine yield, correlating with highest expression of a novel cytochrome P450 variant. Genome-to-molecule correlation analysis supports targeted breeding of high-yield populations for pharmaceutical-grade cryptolepine supply. Keywords: Cryptolepis sanguinolenta, cryptolepine, comparative genomics, biosynthetic pathway, indoloquinoline