Genome evolution and phylogenomic analysis of Candidatus Kinetoplastibacterium, the betaproteobacterial endosymbionts of Strigomonas and Angomonas

Abstract

It has been long known that insect-infecting trypanosomatid flagellates from the genera Angomonas and Strigomonas harbor bacterial endosymbionts (Candidatus Kinetoplastibacterium or TPE [trypanosomatid proteobacterial endosymbiont]) that supplement the host metabolism. Based on previous analyses of other bacterial endosymbiont genomes from other lineages, a stereotypical path of genome evolution in such bacteria over the duration of their association with the eukaryotic host has been characterized. In this work, we sequence and analyze the genomes of five TPEs, perform their metabolic reconstruction, do an extensive phylogenomic analyses with all available Betaproteobacteria, and compare the TPEs with their nearest betaproteobacterial relatives. We also identify a number of housekeeping and central metabolism genes that seem to have undergone positive selection. Our genome structure analyses show total synteny among the five TPEs despite millions of years of divergence, and that this lineage follows the common path of genome evolution observed in other endosymbionts of diverse ancestries. As previously suggested by cell biology and biochemistry experiments, Ca. Kinetoplastibacterium spp. preferentially maintain those genes necessary for the biosynthesis of compounds needed by their hosts. We have also shown that metabolic and informational genes related to the cooperation with the host are overrepresented amongst genes shown to be under positive selection. Finally, our phylogenomic analysis shows that, while being in the Alcaligenaceae family of Betaproteobacteria, the closest relatives of these endosymbionts are not in the genus Bordetella as previously reported, but more likely in the Taylorella genus.

Fig. 1.—

Genomic atlas of Candidatus Kinetoplastibacterium crithidii (A) and Ca. K. blastocrithidii (B). Tracks represent, from the outside to inside: genomic coordinates, in kbp; genes in the plus strand (defined as the strand where dnaA is located, blue); genes in the minus strand (red); rRNA genes in the plus strand; rRNA genes in the minus strand; tRNA genes in the plus strand; tRNA genes in the minus strand; GC content above or below average; GC skew.

Fig. 2.—

Maximum likelihood supermatrix phylogeny (233 concatenated orthologs) of the Betaproteobacteria class, with Alpha- and Gammaproteobacteria as outgroups. For the Betaproteobacteria, families are indicated on the right of each clade. Numbers on branches represent bootstrap support (only support of 50 or greater shown). Black circles with white numbers mark the different betaproteobacterial orders: 1, Neisseriales; 2, Nitrosomonadales; 3, Gallionellales; 4, Methylophilales; 5, Hydrogenophilales; 6, Burkholderiales; 7, Rhodocyclales. The five endosymbionts sequenced in this work are represented in bold.

Fig. 3.—

Orthologous group presence/absence display for the five Candidatus Kinetoplastibacterium genomes, in order of occurrence in the sequence after the dnaA gene. Boxes in the same column represent putative orthologs as identified by OrthoMCL. Organisms are denoted as: CKdes for Ca. K. desouzaii; CKcri for Ca. K. crithidii; CKbla for Ca. K. blastocrithidii; CKonc for Ca. K. oncopeltii; and CKgal for Ca. K. galatii. Box sizes are not proportional to gene lengths in the genome, and blocks are grouped in sets of 10 for aesthetic reasons only. Blue colour box denotes that ortholog is present in more than one organism; green, ortholog is present in one organism only; red, ortholog is present as a pseudogene; white, ortholog is absent.