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Background  Two  Calyptogena  clam intracellular obligate symbionts,  Ca . Vesicomyosocius okutanii (Vok;  C. okutanii  symbiont) and  Ca . Ruthia magnifica (Rma;  C. magnifica  symbiont), have small genomes (1.02 and 1.16 Mb, respectively) with low G+C contents (31.6% and 34.0%, respectively) and are thought to be in an ongoing stage of reductive genome evolution (RGE). They lack  recA  and some genes for DNA repair, including  mutY . The loss of  recA  and  mutY  is thought to contribute to the stabilization of their genome architectures and GC bias, respectively. To understand how these genes were lost from the symbiont genomes, we surveyed these genes in the genomes from 10 other  Calyptogena  clam symbionts using the polymerase chain reaction (PCR).    Results  Phylogenetic trees reconstructed using concatenated 16S and 23S rRNA gene sequences showed that the symbionts formed two clades, clade I (symbionts of  C. kawamurai ,  C. laubieri ,  C. kilmeri ,  C. okutanii and C. soyoae ) and clade II (those of  C. pacifica ,  C. fausta ,  C. nautilei ,  C. stearnsii ,  C. magnifica ,  C. fossajaponica and C. phaseoliformis ).  recA  was detected by PCR with consensus primers for  recA  in the symbiont of  C. phaseoliformis . A detailed homology search revealed a remnant  recA  in the Rma genome. Using PCR with a newly designed primer set, intact  recA  or its remnant was detected in clade II symbionts. In clade I symbionts, the  recA  coding region was found to be mostly deleted.  In the Rma genome, a pseudogene of  mutY  was found. Using PCR with newly designed primer sets,  mutY  was not found in clade I symbionts but was found in clade II symbionts. The G+C content of 16S and 23S rRNA genes in symbionts lacking  mutY  was significantly lower than in those with  mutY .    Conclusions  The extant  Calyptogena  clam symbionts in clade II were shown to have  recA  and  mutY  or their remnants, while those in clade I did not. The present results indicate that the extant symbionts are losing these genes in RGE, and that the loss of  mutY  contributed to the GC bias of the genomes during their evolution.

Loss of genes for DNA recombination and repair in the reductive genome evolution of thioautotrophic symbionts of Calyptogena clams