The draft genome of strain cCpun from biting midges establishes Cardinium as a paraphyletic group, and reveals a novel gene family expansion in a symbiont

Background: It is estimated that 13% of arthropod species carry the heritable symbiont Cardinium hertigii. 16S rRNA and gyrB sequence divides this species into three clades, with the A group infecting a range of arthropods, the B group infecting nematode worms, and the C group infecting Culicoides biting midges. To date, genome sequence has only been available for strains from clade A and B, impeding general understanding of the evolutionary history of the radiation. We present a draft genome sequence for a C group Cardinium, motivated both by the paucity of genomic information outside of the A group, and the importance of Culicoides biting midge hosts as arbovirus vectors. Methods: We reconstructed the genome of cCpun, a Cardinium strain from group C that naturally infects Culicoides punctatus, through Illumina sequencing of infected host specimens. Results: The draft genome presented has high completeness, with BUSCO scores comparable to closed group A Cardinium genomes. Phylogenomic analysis based on concatenated single copy core proteins revealed that Cardinium, as currently considered, is paraphyletic, with strains of Ca. Paenicardinium endoni from nematodes nested within the two groups infecting arthropod hosts. Analysis of the genome of cCpun revealed expansion of a variety of gene families classically considered important in symbiosis (e.g. ankyrin domain containing genes), and one set – characterized by DUF1703 domains – not previously associated with symbiotic lifestyle. This protein group encodes putative secreted nucleases, and the cCpun genome carried at least 25 widely divergent paralogs, of which 24 had a common ancestor in the C group ancestor. The genome revealed no evidence in support of B vitamin provisioning to its haematophagous host, and indeed suggests Cardinium may be a net importer of biotin. Discussion: These data indicate Cardinium, as currently conceived, to be paraphyletic. The draft genome further produces new hypotheses as to the interaction of the symbiont with the midge host, in particular the biological role of DUF1703 nuclease proteins that are predicted as being secreted by cCpun, but in contrast provides no support for a role for the symbiont in provisioning the host with B vitamins.