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Wolbachia pipientis  is possibly the most widespread endosymbiont of arthropods and nematodes. While all  Wolbachia  strains have historically been defined as a single species, 16 monophyletic clusters of diversity (called supergroups) have been described. Different supergroups have distinct host ranges and symbiotic relationships, ranging from mutualism to reproductive manipulation. In filarial nematodes, which include parasites responsible for major diseases of humans (such as  Onchocerca volvulus , agent of river blindness) and companion animals ( Dirofilaria immitis,  the dog heartworm),  Wolbachia  has an obligate mutualist role and is the target of new treatment regimens. Here, we compare the genomes of eight  Wolbachia  strains, spanning the diversity of the major supergroups (A–F), analysing synteny, transposable element content, GC skew and gene loss or gain. We detected genomic features that differ between  Wolbachia  supergroups, most notably in the C and D clades from filarial nematodes. In particular, strains from supergroup C (symbionts of  O. volvulus  and  D. immitis ) present a pattern of GC skew, conserved synteny and lack of transposable elements, unique in the  Wolbachia  genus. These features could be the consequence of a distinct symbiotic relationship between C  Wolbachia  strains and their hosts, highlighting underappreciated differences between the mutualistic supergroups found within filarial nematodes.

Supergroup C Wolbachia , mutualist symbionts of filarial nematodes, have a distinct genome structure