Résumé
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
genomes. Relaxation was not evenly distributed among functional gene
categories but was overrepresented in genes involved in signal
transduction and cell envelope biogenesis. The same gene categories also
harbored instances of positive selection in the Verminephrobacter clade.
In total, positive selection was detected in 89 genes, including also
genes involved in DNA metabolism, tRNA modification, and TonB-dependent
iron uptake, potentially highlighting functions important in symbiosis.
Our results suggest that the transition to symbiosis was accompanied by
molecular adaptation, while purifying selection was only moderately
relaxed, despite the evolutionary age and stability of the
host-association. We hypothesize that bi-parental transmission of
symbionts and rare genetic mixing during transmission can prevent genome
erosion in heritable symbionts.