Burkholderia pseudomallei (Bp), the causative agent of melioidosis contains a large pathogen genome (7.2 Mb) with approximately 2000 genes of putative or unknown function. Interactions with potential hosts and environmental factors may induce rapid adaptations in these Bp genes, which can be discerned through evolutionary analysis of multiple Bp genomes. Here, we show that several previously-uncharacterized Bp genes bearing genetic signatures of rapid adaptation (positive selection) can induce diverse cellular phenotypes when expressed in mammalian cells. Notably, several of these phenotypes are plausibly related to virulence, including multi-nuclear giant cell formation, apoptosis, and autophagy induction. Specifically, we show that BPSS0180, a Type VI cluster-associated gene, is capable of inducing autophagy in both phagocytic and non-phagocytic mammalian cells. Following infection of macrophage cells, a Bp mutant disrupted in BPSS0180 exhibited significantly decreased colocalization with LC3 and impaired intracellular survival; these phenotypes were rescued by introduction of an intact BPSS0180 gene. The results suggest that BPSS0180 may be a novel inducer of host cell autophagy that contributes to Bp intracellular growth. More generally, our study highlights the utility of applying evolutionary principles to microbial genomes to identify novel virulence genes.