Evolutionary genomics and divergence of Cacopsylla species with a special focus on the apple proliferation vectors Cacopsylla melanoneura and Cacopsylla picta

Abstract Background The psyllid genus Cacopsylla includes several species that act as vectors for phytoplasma-associated diseases affecting plantations across Europe. Among them, Cacopsylla melanoneura and Cacopsylla picta are the primary vectors of ‘Candidatus Phytoplasma mali’, the phloem-restricted bacterium responsible for Apple Proliferation disease in Europe. To explore whether vector competence in these species reflects shared ancestry or independent evolution, we assembled mitochondrial and draft nuclear genomes of Italian populations of C. melanoneura and C. picta and reconstructed time-calibrated phylogenies using 13 mitochondrial protein-coding genes from 12 Cacopsylla species. Results Phylogenetic analyses revealed two major Cacopsylla clades (Clade I and II) whose divergence times range from the Early Miocene (18.4 MYA; 95% HPD: 10.8–27.5) to the Middle Miocene (12.7 MYA; 95% HPD: 9.7–16.0). Both C. melanoneura and C. picta are within Clade I, which is predominantly composed of univoltine species that overwinter on conifers. Within this clade, Cacopsylla melanoneura is more closely related to the plum psyllid Cacopsylla pruni than to the apple-associated Cacopsylla picta and Cacopsylla mali, the latter belonging to Clade II. Draft nuclear genomes revealed significant differences in size (438 Mb in C. melanoneura vs. 631 Mb in C. picta), largely attributed to repetitive elements. Comparative analyses of repetitive elements across Cacopsylla species revealed a recent expansion of transposable elements, particularly LINE elements, which were slightly more abundant in Clade I and contributed to the larger genome size observed in C. picta. Conclusions Collectively, our findings provide the first genomic resources for C. melanoneura, C. picta, and several other phytoplasma-vectoring Cacopsylla species. We established a robust mitogenomic phylogeny with divergence estimated for this genus showing the presence of two clades with the representatives predominantly associated with different overwintering strategies. Our results further indicate that vectorial capacity in Cacopsylla reflects an independent evolutionary trajectory rather than a shared ancestral origin. This evolutionary framework advances our understanding of the biology and origin of vector competence in this agriculturally important group.