A Perspective on Bridging Legacy Systems and Genomic Advances in Transiting Phytoplasma Taxonomy

Phytoplasmas are uncultivable, wall-less plant pathogens that have long challenged traditional taxonomic frameworks. Historically classified using 16S rRNA gene sequences, many species were described without supporting genomic or ecological data, resulting in ambiguities and inconsistencies. This perspective critically examines the limitations of single-marker systems, including interoperon divergence, RFLP artifacts, and chimeric sequences, and highlights the urgent need to transition toward genome-informed taxonomy. Taxogenomic approaches supported by metrics such as ANI and dDDH offer greater resolution for delineating species boundaries. While technical and infrastructural barriers persist, especially in endemic regions, a hybrid framework that integrates legacy systems with genomic standards is both practical and essential. A unified, inclusive strategy will strengthen taxonomic accuracy and transform classification into a foundation for understanding phytoplasma biology, evolution, and disease management.