Time-resolved comparative genomics of ‘Candidatus Carsonella ruddii’ across psyllid lineages reveals a conserved core genome and contrasting secondary symbiont dynamics
Psyllids harbour the obligate nutritional symbiont ‘
Candidatus
Carsonella ruddii’ (
Ca
Cr), yet complete
Ca
Cr genomes remain unevenly sampled across Psylloidea, limiting both comparative analysis and temporal inference. Here, seven complete
Ca
Cr genomes (165–174 kb) were assembled and annotated from psyllid hosts representing four families, including lineages for which genome-grade resources had previously been unavailable. We integrated whole-genome phylogenomics, pangenome analysis, fossil-calibrated relaxed-clock dating and quantitative PCR (based on 16S rRNA) screening of secondary symbionts. Across hosts,
Ca
Cr retained an extremely reduced, AT-rich (>82%) and gene-dense (>90% coding) genome architecture with a conserved core of 155 genes, while the accessory fraction was limited and lineage-specific. Most variable genes belonged to amino-acid metabolism or proteins of unknown function, suggesting differential erosion of peripheral functions around a stable translational and informational core. Phylogenomically,
Ca
Cr diversification broadly tracked deep host diversification, although the
Ca
Cr lineage from
Diaphorina citri
grouped with Triozidae-associated lineages rather than with other sampled Psyllidae. Using two host fossil-informed soft calibrations, we estimated that major
Ca
Cr divergences occurred mainly from the Paleogene to the Miocene, with crown diversification of
Cacopsylla
-associated
Ca
Cr at 15.95–18.99 Ma. In contrast to the stability of the primary symbiosis, secondary symbionts showed patchy host distributions:
Wolbachia-
and
Arsenophonus
-like lineages occurred in multiple hosts, ‘
Candidatus
Profftella armatura’ was restricted to
D. citri
, and no secondary symbiont was detected in
Cacopsylla chinensis
. These results provide a time-resolved comparative framework for
Ca
Cr evolution in psyllids and underscore the different evolutionary stability of primary and facultative associates.