The symbiotic mechanism between the chemoautotrophic symbiotic bacteria and its host deep-sea Calyptogena clams, and the reductive genome evolution of these symbionts

Dense animal communities at hydrothermal vents and cold seeps rely on symbioses with chemoautotrophic bacteria. To reveal the symbiotic mechanism, we sequenced the genome of chemoautotrophic intracellular symbiont in deep-sea clam, Calyptogena okutanii. On the other hand, C. magnifica symbiont genome sequenced in USA. The genomes appear to have been reduced. To understand their reductive genome evolution (RGE), we compared their genomes. They have small genomes containing chemoautotrophic and intracellular symbiotic features, and lack most genes for DNA recombination and repair e.g. recA and mutY. Their genome structures were highly conserved excepting one inversion. Many deletions from small (1 kbp up to 11 kbp) sizes were detected and deletion numbers decreased exponentially with size. Densities of deletions, short-repeat density and A+T content were higher in non-coding regions than in coding regions. Because Calyptogena symbiont genomes lack recA, we deduced that deletions and the inversion occurred by RecA-independent recombination (RIR) at short-repeats with simultaneous consumption of repeats, and that short-repeats were regenerated by high rate of mutation with enhanced A+T bias in the absence of mutY. We proposed that an active RGE is ongoing by short-repeats dependent RIR with regeneration of short-repeats in extant Calyptogena symbionts.