Diversidade genômica, arquitetura do pangenoma e variação funcional no gênero Yersinia

Abstract

The genus Yersinia comprises species widely distributed across diverse environments and hosts, including medically and veterinary relevant pathogens such as Y. pestis, Y. enterocolitica, and Y. pseudotuberculosis, as well as species associated with broad lifestyles. This ecological diversity reflects the extensive genomic variability observed within the genus, particularly in the accessory genome, which may be associated with adaptation to different ecological niches. In this study, we investigated the genomic diversity of the genus Yersinia through the integration of average nucleotide identity (ANI) analyses, phylogenomic reconstruction, pangenome characterization, functional annotation, and metadata analysis related to isolation sources and hosts available in public databases. To this end, a publicly available genome dataset was used and deduplicated to reduce redundancy and sampling bias. A strong bias in genome distribution was observed, with a predominance of Y. enterocolitica and Y. pestis, followed by a substantial reduction of the dataset after filtering. ANI-based analysis allowed the delineation of genomic clusters compatible with previously described species, which were further supported by phylogenomic structure. The pangenome exhibited an open behavior, with a predominance of accessory genes over the persistent genome. In addition, gene content organized the genomes into three major clusters, congruent with the main evolutionary clades of the genus. Functionally, the persistent genome was mainly represented by categories related to metabolism and cellular information processing, whereas accessory genes showed higher variability and part was associated with mobile genetic elements. Metadata analysis revealed subtle distribution patterns, partially structured among species and clusters, although with extensive overlap across isolation sources, hosts, and environments. Overall, the results indicate that the genomic diversity of the genus Yersinia is structured at hierarchical levels, with agreement between gene content organization, phylogenetic structure, and taxonomic delimitation, as well as partially consistent ecological patterns.