Genome sequencing and assembly of Candidatus Skilesia alterna

One of the most prominent examples of obligate symbiosis is the relationship between aphids and their bacterial endosymbiont Buchnera aphidicola (Gammaproteobacteria). Almost all aphids host the anciently acquired symbiont Buchnera, but we find that Geopemphigus species have lost Buchnera and rather contain a maternally transmitted bacterial symbiont from the phylum Bacteroidetes. In this study we characterize this new bacterial endosymbiont by sequencing the complete genome of the novel symbiont and show that the symbiont has lost many ancestral genes, resulting in a genome size intermediate between that of free-living and symbiotic Bacteroidetes species. Many of the genes retained in the Geopemphigus symbiont genome are involved in biosynthetic pathways for amino acids and vitamins, as in Buchnera and other insect symbionts. We use FISH microscopy to localize the Bacteroidetes symbiont of Geopemphigus and show symbionts housed within maternal bacteriocytes and within developing embryos. We propose the name “Candidatus Skilesia alterna” for the novel symbiont, which is evolutionarily distinct from any known bacterial species. This case of evolutionary replacement of Buchnera provides an opportunity to further understand the evolution and functional genomics of symbiosis.