Population genomics and the basis of species delineations in the marine actinomycete Salinispora

The genus Salinispora is a marine actinomycete that is known for producing an assortment of secondary metabolites with anticancer and antibiotic properties. The genus is comprised of three species, S. arenicola, S. pacifica, and S. tropica, and are closely related based on 16S rRNA gene similarity. The goal of this dissertation is to use a population-scale comparative genomics approach to study the evolutionary diversity of Salinispora. Bacterial population genomics allows for the study of genome-wide patterns of sequence variation between closely related species. Aided by the declining costs of Next Generation Sequencing, whole genome analyses have become more commonplace and accessible. Genomes from 119 Salinispora strains representing all 3 species and 11 different geographic locations were sequenced. Ortholog analyses of these genomes reveal the pangenome of the genus and species-specific gene pools are identified, illuminating the composition of their function. Transcriptomics analyses are incorporated into identify differential gene expression as an additional way to identify significant differences between two species. Specifically, chitinase genes as well as genes included in the species core genome are investigated. Bioinformatic predictions suggest S. tropica has the ability to better cope with osmotic stress and may be more affected by nutrient or oxidative stress while S. arenicola has more energetic needs during stationary phase growth potentially due to costly secondary metabolism. Comparative genomics allows us to identify gene content differences between related bacteria and many of these differences can be attributed to lateral gene transfer. This dissertation also examines this type of exchange of genetic information and the introduction of genes and gene clusters from neighboring bacteria which may have conferred an evolutionary advantage. For the first time a molecular clock is also presented for the genus, providing a new temporal framework with which to understand how genetic information moves across species and strains both at the gene and biosynthetic cluster level