Insights into phytoplasma lineages: evaluating single-locus and multilocus trees from next-generation sequencing data

Phytoplasmas detected in insects collected from natural areas provide opportunities to discover new strains and identify potential novel vectors. Integrating these strains into existing phytoplasma phylogenies, which are primarily based on agroecosystem data, enhances the understanding of evolutionary relationships and supports the development of a more robust classification framework. In this study, it was analyzed insect samples collected from natural habitats using both single-locus and multilocus approaches to gain a comprehensive understanding of phytoplasma strain diversity. The results reveal notable differences in tree topologies, with congruent outcomes observed only for samples clustering with reference strains from well-studied phytoplasma groups (e.g., 16SrI). These findings emphasize the importance of multilocus analyses in resolving complex evolutionary histories, particularly for prokaryotic taxa with limited genomic resources. This study highlights the value of multilocus approaches in identifying novel phytoplasma strains and their potential insect vectors, offering insights that can inform future ecological and agricultural research.