Expansive pseudogenization and incipient genome degradation of an obligate fruit fly-bacterial mutualism

Abstract

Obligate microbial symbioses are often characterized by streamlined biosynthetic pathways and reduced genomes. The evolutionary process of this reduction first involves an increase in the abundance of non-functional coding genes (pseudogenes) followed by their removal. The olive fruit fly (Bactrocera oleae) harbors an extracellular symbiotic gut bacterium Candidatus Erwinia dacicola, which is crucial to its usage of fruit from the olive genus Olea as a larval food source. In this study, we combined genomics and transcriptomics of Ca. E. dacicola to investigate pathways that facilitate this mutualism. Of 4,675 genes in the Ca. E. dacicola genome, 1,783 were classified as pseudogenes. Some biochemical pathways such as amino acid pathways, biofilm regulator BssS, and 6-phospho-{beta}-glucosidase which are implicated in hydrolyzing oleuropein were complete. However, pathways connected to baseline homeostasis, which would impact cellular functions needed for a bacterium to be free-living, were heavily pseudogenized. Gene selection analyses in Ca. E. dacicola, when compared to related organisms, indicated positive selection on genes related to amino acid metabolism, carbon utilization, transport, and energy production. Our results indicate that Ca. E. dacicola is likely producing amino acids and metabolizing plant phytochemicals. These results reveal that the Ca. E. dacicola genome is undergoing incipient genome erosion in support of an unculturable obligate mutualism. ImportanceMany beneficial bacteria that live inside insects have highly reduced genomes, but little is known about the transitional stages that occur as free-living microbes evolve into obligate symbionts. We show that the olive fruit fly symbiont, Candidatus Erwinia dacicola, retains hallmarks of its plant-associated ancestry while undergoing extensive genome degradation, including the accumulation of mobile DNA elements and inactive genes. At the same time, genes involved in nutrient production, environmental persistence, and host interactions remain functional and are evolving under selection, providing a rare snapshot of how bacterial genomes are reshaped during the evolution of an obligate mutualism. These findings have implications for how obligate gut symbioses are formed and maintained in insect herbivores.