Phylogenetic Analysis of Phytoplasma Strains Associated with Decline Diseases of Coconut in the Niger Delta Region of Nigeria

Phytoplasma-associated decline diseases of coconut are a growing concern across the Niger Delta, where affected palms show irreversible yellowing, premature nut drop, and death within three to five years of symptom onset. The phylogenetic identity of phytoplasma strains infecting coconut in the Nigerian Niger Delta has not been systematically resolved, limiting regional disease surveillance and international reporting obligations. This study conducted phylogenetic analysis of phytoplasma strains collected from 54 symptomatic coconut palms across Bayelsa, Delta, and Rivers States, using polymerase chain reaction amplification of the 16S rRNA, rp, and tuf gene targets, followed by restriction fragment length polymorphism profiling and maximum likelihood phylogenetic reconstruction. All 54 samples yielded phytoplasma-positive polymerase chain reaction products, with restriction fragment length polymorphism profiling placing 80 percent of strains in the 16SrIV group associated with coconut lethal yellowing and 20 percent in the 16SrI group associated with aster yellows phytoplasmas. Maximum likelihood phylogenetic trees placed the 16SrIV strains in a subclade distinct from previously described Caribbean and Ghanaian coconut lethal yellowing strains, suggesting the possible existence of a Nigeria-specific lineage. Comparative analysis with reference sequences from GenBank confirmed the novelty of three haplotypes exclusive to Rivers State samples. Vector species surveys identified Myndus crudus-related planthoppers as suspect vectors in all three states. These findings establish the phylogenetic framework for Nigerian coconut phytoplasma surveillance and inform international quarantine risk assessments. Keywords: coconut phytoplasma, lethal yellowing, phylogenetic analysis, Niger Delta, Nigeria.