Fig. 1: ‘Ca. Endonucleobacter’ infectious cycle and phylogenomic analysis.

A single ‘Ca. Endonucleobacter’ infects the mussel nucleus (early infection stage), grows through elongation and division (mid-infection stage), and finally divides through septation of the elongated cells to as many as 80,000 cells (late infection stage). In the final infection stage, the nucleus is enlarged by as much as 50-fold in volume, the host cell bursts and the parasites are released to the environment. a, ‘Ca. Endonucleobacter’ infectious cycle in the early, mid and late stages of infection, shown in the left, middle and right columns, respectively, of the top row (middle row, FISH images of ‘Ca. E. puteoserpentis’; bottom row, TEM images of ‘Ca. E. childressi’). FISH with specific probes shows the parasite (in yellow) inside mussel nuclei (DAPI-stained DNA in blue) and neighbouring symbiont-containing cells (indicated with dotted lines) with sulfur-oxidizing symbionts (in green) and methane-oxidizing symbionts (in pink) (sequences of all FISH probes are listed in Supplementary Table 6). e, ‘Ca. Endonucleobacter’ cell; c, chromatin; ne, nuclear envelope. The results are representative of five independent experiments. Scale bars, 1 μm. b, Phylogenomic analysis using 172 conserved marker genes shared between the two ‘Ca. Endonucleobacter’ genomes and those of 42 closely related Endozoicomonaceae. Genes were identified and aligned with the GToTree pipeline, the tree was calculated with IQ-TREE and branch support (1,000 replicates) was calculated with both SH-aLRT and UFBoot. Six Oceanospirillum genomes were used to root the tree. Scale bars indicate substitutions per site. Key genome characteristics are listed at the right. A full tree with all bootstrap values is shown in Supplementary Fig. 3.