Purifying selection and molecular adaptation in the genome of Verminephrobacter, the heritable symbiotic bacteria of earthworms

While genomic erosion is common among intracellular symbionts, patterns of genome evolution in heritable extracellular endosymbionts remain elusive. We study vertically transmitted extracellular endosymbionts (Verminephrobacter, Betaproteobacteria) that form a beneficial, species-specific, and evolutionarily old (60-130 MYA) association with earthworms. We assembled a draft genome of Verminephrobacter aporrectodeae and compared it to the genomes of Verminephrobacter eiseniae and two non-symbiotic close relatives (Acidovorax). Similar to V. eiseniae, the V. aporrectodeae genome was not markedly reduced in size and showed no A-T bias. We characterized the strength of purifying selection (dN/dS) and codon usage bias in 876 orthologous genes. Symbiont genomes exhibited strong purifying selection (dN/dS = 0.09 ± 0.07), although transition to symbiosis entailed relaxation of purifying selection as evidenced by 50% higher values and less codon usage bias in symbiont compared to reference geno...