Pangenome analysis of Nocardia brasiliensis reveals phylogenetic divergence, high genomic diversity and widespread distribution of biosynthetic gene clusters involved in secondary metabolite biosynthesis.

Abstract

Actinobacteria are a diverse and heterogeneous group of bacteria with complex taxonomy that produce most of the natural products used in medicine. Although comparative genomic studies of Nocardia species have been reported, comprehensive species-level analyses integrating phylogenomics, pangenome structure, and biosynthetic gene cluster distribution in N. brasiliensis remain limited. In this study, we performed phylogenomic orthology inference, analyzed pangenome composition, and evaluated the potential of Nocardia brasiliensis as a source of secondary metabolites using comparative genomics. Four clinical strains from Mexico and 22 publicly accessible genomes were included. Genomic identification was performed, orthologous genes were identified, core genome and pangenome composition were estimated, and phylogenomic orthology inference was assessed. All genomes were searched for known BGCs, secondary metabolites were predicted, and data on reported biological activity were collected. A pangenome comprising 17,715 clusters was calculated, with the core genome accounting for 22.76 % and the cloud genome for 48.17 %. The trend in the gene accumulation curve indicated that the species had an open pangenome, as the continuous increase in gene clusters with the addition of new genomes suggests a high level of genomic diversity and ongoing gene acquisition within the species, reflecting its capacity for environmental adaptation and evolutionary plasticity. Phylogenomic analysis showed that geographical origin and isolation conditions affect evolutionary divergence within N. brasiliensis. Computational BGC prediction detected PKS, NRPS, NAPAA, terpenes, aminopolycarboxylic acids, hybrids, and other clusters coding for secondary metabolites with antimicrobial activity (ε-Poly-L-lysine, brasiliquinones A-B), antitumor activity (rhizomides A-C, anthramycin), antioxidant activity (isorenieratene), and a fertilizer for calcareous soils ([S, S]-EDDS). The results reveal significant genomic diversity and a wide distribution of biosynthetic clusters within the Nocardia brasiliensis pangenome, demonstrating its genomic plasticity and the variability in metabolic potential across strains.