Genome degradation results in nested symbiosis and endosymbiont replacement in cicadas.

Gradual genome degradation and fragmentation in primary nutritional endosymbionts have required symbiont-dependent hosts periodically to replace such symbionts over evolutionary timescales, yet the processes involved in de novo emergence of endosymbiosis and symbiont replacement are challenging to ascertain. Here we show that phylogenetic relationships of two ancient vertically-transmitted bacterial endosymbionts of cicadas, Hodgkinia and Karelsulcia, mirror host phylogeny, particularly indicating a single ancestral infection of cicadas by Hodgkinia with subsequent host-symbiont codiversification before being replaced by yeast-like fungal symbionts (YLS). We demonstrate a case of co-existence of Hodgkinia with Karelsulcia and a YLS, representing an advanced ongoing symbiont replacement process. In some individuals of the cicada Chremistica ochracea, the Hodgkinia is highly degenerated but colonizes (instead of neighboring) its partner Karelsulcia. The physical fusion of these two bacterial endosymbionts yields a nested symbiosis while the new YLS is recruited, probably preserving essential metabolic pathways necessary for host nutrition and facilitating continued vertical symbiont transmission. Such fusion may have provided refuge for the degrading bacterial endosymbiont and delayed symbiont replacement. Our study sheds light on adaptive and non-adaptive evolutionary mechanisms involved in symbiont loss and replacement, offering fresh insights into endosymbiotic origins of cellular organelles.