Phylogenomic analysis and comparative genomics of insect-endosymbiont ‘Candidatus Erwinia dacicola’ and free-living Erwinia species

‘Candidatus Erwinia dacicola’ is a co-evolved symbiotic bacterium associated with olive fly Bactrocera oleae (Diptera: Tephritidae), the major pest of olive tree. It is vertically transmited and plays a key role in insect fitness. The adaptation to its host and the related consistent genome reduction (2.69 Mb) prevents its cultivability, which determines the difficulty of describing this species in sufficient detail. Nevertheless, ‘Ca. E. dacicola’ has a high 16S rRNA gene similarity (> 98.36 %) with the free-living and cultivated plant pathogens Erwinia aphidicola, Erwinia persicina, and Erwinia rhapontici. Thanks to the a vailability of 4 1 genome sequences of ‘ Ca E.dacicola’ (metagenome assembled genomes-MAGs) and strains of the related species, the present study aimed at i) defining in detail the phylogenomic relationship among the endosymbiont and its closely related species, ii) unraveling their variable genes and iii) analyzing intraspecific genomes diversity of ‘Ca. E. dacicola’. Phylogenomic analysis on 27 selected genomes (2-Ca. E. dacicola, 3-E. aphidicola, 15-E. persicina, 7-E. rhapontici) confirmed that E. aphidicola was the closest relative free-living species and chosen for detailed comparative genomics. A significant diversity was observed for genes associated to metabolism and environmental information processing, as could be expected considering the different lifestyles. Finally, all MAGs genomes of ‘Ca. E. dacicola’ were used to shed light on intraspecific variability in order to possibly describe novel haplotypes. The results provide, for the first time, a detailed overview of the genetic determinants involved in genome reduction related to host adaptation as well as of genome-level intraspecific evolution.