Comparative genomics of the sexually transmitted parasite Trichomonas vaginalis reveals relaxed and convergent evolution and genes involved in spillover from birds to humans

Abstract

Trichomonas vaginalis is the causative agent of the venereal disease trichomoniasis which infects men and women globally and is associated with serious outcomes during pregnancy and cancers of the human reproductive tract. Trichomonads parasitize a range of hosts in addition to humans including birds, livestock, and domesticated animals. Recent genetic analysis of trichomonads recovered from columbid birds has provided evidence that these parasite species undergo frequent host-switching, and that a current epoch spillover event from columbids likely gave rise to T. vaginalis in humans. We undertook a comparative evolutionary genomics study of seven trichomonad species, generating chromosome-scale reference genomes for T. vaginalis and its avian sister species Trichomonas stableri, and assemblies of five other species that infect birds and mammals. Human-infecting trichomonad lineages have undergone recent and convergent genome size expansions compared to their avian sister species, and the major contributor to their increased genome size is increased repeat expansions, especially multicopy gene families and transposable elements, with genetic drift likely a driver due to relaxed selection. Trichomonads have independently host-switched twice from birds to humans, and genes implicated in the transition to the human host include those associated with host tissue adherence and phagocytosis, extracellular vesicles, and CAZyme virulence factors.

Figure 1.. Architecture and genome features of T. vaginalis G3 across its six chromosomes.

The concentric rings, from innermost to outermost, represent: (1) chromosome size in Mb; (2) gene density (green plot) shown in 20 Kb windows; vertical blue lines represent 11 rRNA cassettes, and the vertical black line represents the 47.5 Kb block from an LGT event of the bacterium Peptoniphilus harei; (3) TE density (pink plot) shown in 20 Kb windows; (4) transcript abundance (brown plot) of all genes shown as transcripts per million in 100 Kb windows; (5) TE transcript abundance (orange plot) of annotated TE genes) in 100 Kb windows; and (6) dN/dS values (grey dots). The axes are shown next to chromosome 1.

Figure 2.. Synteny plot of human parasite T. vaginalis and its closest relative in birds T. stableri.

Each T. vaginalis chromosome is colored uniquely, and synteny blocks are indicated by ribbons connecting the species’ chromosomes. TE density (genomic sequence classified as containing TEs) is indicated by normalized density plots in 100 Kb windows at the top and bottom of the figure (blue plots). Chromosomes were reordered for visualization purposes.

Figure 3.. Genome content distribution.

A. An Upset plot displaying the intersection of orthogroups identified in OrthoFinder across seven trichomonad species. Each vertical bar represents the number of orthogroups shared at each species intersection, the set size indicates the number of orthogroups found in each species, and the connected dots represent the species in the intersection. B. Ultrametric tree from 6,226 concatenated single-copy genes. Black dots at terminal nodes are proportional to estimated genome size, and hosts are denoted by cartoons. Estimated gene family expansions / contractions from 12,345 genes are denoted as + or – values on the tree. The heat map shows the log transformed count of TE family members for each tree branch.

Figure 4.

Estimated repeat content length (blue) per estimated genome size. Genomes are shown scaled by their estimated size (Mb, in parentheses). Bracket endpoints denote inferred sister species on the phylogenetic gene tree. Icons indicate human or bird host. *T. tenax has been detected in other mammals and in birds. **P. hominis has been detected in other mammals.

Figure 5.. Analysis of orthologs across seven Trichomonas species.

A. Graphs showing count of all single-copy orthologs (SCOs; left panel) and BUSCO genes (right panel) identified by RELAX as being under relaxed, neutral, or intensified selection in the species with expanded genomes (T. vaginalis and T. tenax) for a range of P-values. B. Mean dN/dS values (plotted from 1.0 to 10.0) for SCOs inferred as under relaxed positive selection (left plot) and dN/dS values (plotted from 0.0 to 1.0) for SCOs inferred as under relaxed purifying selection (right plot) for avian-infecting species and mammalian-infecting species.

Figure 6.

GO enrichment of 140 expanded gene families in T. vaginalis. Dot size represents the number of genes with a specific GO term. Biological process (BP), cellular component (CC) and molecular function (MF) are plotted. Only significant GO enrichments after FDR correction (0.05<) are reported.

Figure 7.

A. Heatmap showing number of shared expanded orthogroups between seven trichomonad species. T. vaginalis shares its largest number of expanded orthogroups with T. tenax (n=33) and Trich sp. 2a (n=35), two non-sister species that infect humans and birds, respectively. B. GO enrichment of convergently expanded multicopy gene families in T. vaginalis and T. tenax. C. GO enrichment of convergently expanded multicopy gene families in T. vaginalis and T. sp. 2a. For both B and C: size of dot represents the number of genes with a specific GO term; biological process (BP), cellular component (CC) and molecular function (MF) are plotted; only significant GO enrichments after FDR correction (0.05<) are reported.