Pangenomic and genomic plasticity analyses of the genus Rickettsia
TL;DR
The findings demonstrate the existence of contrasting evolutionary trajectories within the Rickettsia genus, with conserved, specialized species coexisting alongside genetically dynamic species that are more adaptable to different niches.
Abstract
The Rickettsia genus comprises obligate intracellular bacteria transmitted by arthropods and responsible for clinically relevant zoonoses, rickettsioses, such as spotted fever and typhus. The difficulty of cultivating these bacteria in vitro reinforces the importance of in silico approaches, such as pangenomic and genomic plasticity analyses. This study analyzed 165 genomes from 31 Rickettsia species available in the REFSEQ (NCBI) database. Tools such as Orthofinder, ANIclustermap, Gegenees, and Mauve were used to classify genes into core, shared, and singletons, assess genomic similarity, and identify structural rearrangements. The results indicate that the genus has an open pangenome (α = 0,842), suggesting high genetic variability and adaptive and expansion potential. Species such as R. typhi exhibited a nearly closed pangenome (α = 0,999), with high genomic conservation, whereas R. rhipicephali showed an open pangenome (α = 0,876), reflecting greater plasticity and intraspecies diversity. Functional categorization of genes revealed that the core genome is associated with vital functions, while singletons include genes related to genetic mobility, indicating possible acquisition through horizontal transfer. Synteny analysis demonstrated high gene conservation in R. typhi and extensive structural reorganization in R. rhipicephali. Statistical correlation reinforced the stability of the core genome regardless of pangenome expansion and revealed an inverse relationship between the number of singletons and the value of α. The findings demonstrate the existence of contrasting evolutionary trajectories within the Rickettsia genus, with conserved, specialized species coexisting alongside genetically dynamic species that are more adaptable to different niches. Thus, this study expands the understanding of clonality, genomic plasticity, and functional diversity within the genus, providing support for future investigations into virulence factors, vaccine targets, and bacterial evolution.