Paula Cristina de Magalhães, Andrei Giacchetto Felice, Siomar Soares (2026).
Pangenomic and genomic plasticity analyses of the genus Rickettsia.
Brazilian Journal of Microbiology. 10.1007/s42770-026-02030-7
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Pangenomic and genomic plasticity analyses of the genus Rickettsia
Understanding how obligate intracellular pathogens like Rickettsia diversify genomically is key to identifying virulence factors and vaccine targets — especially for species that are hard to culture in vitro.
Background
Rickettsia are arthropod-borne, obligate intracellular bacteria that cause zoonoses including spotted fever and typhus. Because in vitro cultivation is difficult, in silico comparative genomics is a practical route to characterize their diversity. This study asks how open the Rickettsia pangenome is, how plasticity varies across species, and what functional categories dominate the core versus accessory genome.
Methods
- Dataset: 165 genomes spanning 31 Rickettsia species from NCBI RefSeq.
- Orthology and pangenome classification: OrthoFinder was used to partition genes into core, shared, and singleton categories, and to estimate Heaps’ law α.
- Similarity and synteny: ANIclustermap and Gegenees for genome-wide similarity; Mauve for synteny and structural rearrangement detection.
- Statistics: Correlations between pangenome openness (α), core genome size, and singleton counts.
Key findings
- Open pangenome at the genus level: α = 0.842, consistent with high genetic variability and continued gene acquisition.
- Species-level contrasts:
- R. typhi: α = 0.999 (nearly closed), high genomic conservation and strong synteny.
- R. rhipicephali: α = 0.876 (open), extensive structural reorganization and intraspecies diversity.
- Functional partitioning: Core genes were enriched for essential/housekeeping functions; singletons were enriched for mobility-related genes, consistent with horizontal gene transfer.
- Correlations: Core genome size remained stable regardless of pangenome expansion, and singleton counts were inversely correlated with α.
The authors interpret this as evidence for contrasting evolutionary trajectories within the genus: conserved, specialized lineages coexisting with genetically dynamic, niche-flexible ones.
Limitations and open questions
- Analyses are entirely in silico and rely on the composition/quality of RefSeq genomes, which is uneven across species.
- Species with few available genomes may bias α estimates toward apparent closure.
- The functional inferences for singletons (e.g., HGT origin, virulence relevance) remain to be validated experimentally, which the authors flag as a target for future work on virulence factors and vaccine candidates.
Original 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.
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