Abstract: While specialized metabolites are thought to mediate ecological interactions, the evolutionary processes driving their diversification, particularly among closely related lineages, remain poorly understood. Here, we examine the evolutionary dynamics governing the distribution of natural product biosynthetic gene clusters (BGCs) using 118 strains within the marine actinomycete genus Salinispora. While previous evidence indicated that horizontal gene transfer (HGT) largely contributed to BGC diversity, we find that a majority of BGCs in Salinispora genomes are conserved through processes of vertical descent. In particular, vertical inheritance maintained BGCs over evolutionary timescales (millions of years) allowing for BGC diversification among Salinispora species. By coupling the genomic analyses with high-resolution tandem mass spectrometry (LC-MS/MS), we identified that BGC evolution in Salinispora proceeds largely through gene gain/loss events and constrained recombination that contributes to interspecies diversity at the gene, pathway, and metabolite levels. Consequently, the evolutionary processes driving BGC diversification had direct consequences for compound production and contributed to chemical diversification, as exemplified in our case study of the medically relevant proteosome inhibitors, the salinosporamides. Together, our results support the concept that specialized metabolites, and their cognate BGCs, represent functional traits associated with niche differentiation among Salinispora species. GRAPHICAL SIGNIFICANCE Natural products are traditionally exploited for their pharmaceutical potential; yet what is often overlooked is that the evolution of the biosynthetic gene clusters (BGCs) encoding these small molecules likely affects the diversification of the produced compounds and implicitly has an impact on the compounds’ activities and ecological functions. And while the prevailing dogma in natural product research attributes frequent and widespread horizontal gene transfer (HGT) as an integral driver of BGC evolution, we find that the majority of BGC diversity derives from processes of vertical descent, with HGT events being rare. This understanding can facilitate informed biosynthetic predictions to identify novel natural products, in addition to uncovering how these specialized metabolites contribute to the environmental distribution of microbes.
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