Multilocus next-generation sequencing of leafhopper-associated phytoplasmas highlights gaps in knowledge for some phytoplasma lineages and genetic loci

Analysis of DNA sequence data for 6 housekeeping genes obtained from leafhopper-associated phytoplasmas using anchored hybrid enrichment next-generation sequencing yielded a well resolved phylogeny largely congruent with previous phylogenetic estimates, despite the substantial amounts of missing data. In general, phytoplasmas belonging to previously well studied groups (e.g., 16SrI) were placed on the phylogeny with high confidence while the placements of strains belonging to poorly studied groups were less stable. This suggests that major gaps in knowledge of phytoplasma diversity remain, especially for groups largely distributed in the tropics.