Parallel Evolution of Bacteroidota as Long-Term Endosymbionts of Insects

Symbiotic relationships transform diverse aspects of both symbiont and host biology. The most visible changes include a massive reduction of the endosymbiont genome and the development of novel host organs, cells, and compartments specialized for harboring the symbionts. However, many insect symbiosis studies have previously focused either on Proteo-bacteria or only on a particular symbiosis stage, limiting our broad understanding of how and why symbiont diversity arises from specific microbial clades, how the symbiont genomes erode over evolutionary time, and what the consequences of symbiosis are for diverse host-symbiont pairs. Thanks to the repeated gains and losses of nutritional symbionts, scale insects provide an ideal evolutionary playground for tracking the parallel transitions of insect symbionts that originated as independent evolutionary replicates from the same bacterial phylum. Using extensive genome sampling across the scale insect phylogeny, we recapitulated the path of Bacteroidota transitioning from recently established host-associated bacteria to highly specialized insect endosymbionts with minimal gene sets. Their genomes exhibit strikingly parallel patterns of gene loss and pseudogenization across all gene categories, with some stochastic differences in essential genes for genetic processing and amino acid biosynthesis. In addition to the genetic transition, we show with imaging methods that the symbiotic cells and organs exhibit a trend from more dispersed bacteriocytes to highly compact (and likely more specialized) bacteriomes, which are closely localized to the hosts digestive system. Our results outline at both genomic and cellular levels a recurrent path by which insect symbioses independently arise, are temporarily maintained for up to several hundred million years, and then are replaced by new symbionts that repeat the process. The gradual nature of the process implies that the outcomes of symbiosis initially depend on how professional vs. naive the host and symbiont are. Over evolutionary time, compatible host-symbiont lineages emerge from these interactions and become preferred.