Identification of diverse RNA viruses in Obscuromonas flagellates (Euglenozoa: Trypanosomatidae: Blastocrithidiinae)

Abstract

Trypanosomatids (Euglenozoa) are a diverse group of unicellular flagellates predominately infecting insects (monoxenous species) or circulating between insects and vertebrates or plants (dixenous species). Monoxenous trypanosomatids harbor a wide range of RNA viruses belonging to the families Narnaviridae, Totiviridae, Qinviridae, Leishbuviridae, and a putative group of tombus-like viruses. Here, we focus on the subfamily Blastocrithidiinae, a previously unexplored divergent group of monoxenous trypanosomatids comprising two related genera: Obscuromonas and Blastocrithidia. Members of the genus Blastocrithidia employ a unique genetic code, in which all three stop codons are repurposed to encode amino acids, with TAA also used to terminate translation. Obscuromonas isolates studied here bear viruses of three families: Narnaviridae, Qinviridae, and Mitoviridae. The latter viral group is documented in trypanosomatid flagellates for the first time. While other known mitoviruses replicate in the mitochondria, those of trypanosomatids appear to reside in the cytoplasm. Although no RNA viruses were detected in Blastocrithidia spp., we identified an endogenous viral element in the genome of B. triatomae indicating its past encounter(s) with tombus-like viruses.

Keywords: Blastocrithidia; Mitoviridae; Narnaviridae; Obscuromonas; Qin-like virus; dsRNA viruses.

Figure 1.

dsRNA screening in Obscuromonas spp. and Blastocrithidia spp. Leishmania guyanensis infected with Leishmania RNA virus 1 (LRV1) was used as a positive control. Molecular weight marker sizes are indicated on the right. Species names and IDs of the analyzed isolates (Table 1) are shown on top.

Figure 2.

Maximum likelihood phylogenetic trees based on viral RdRP amino acid sequences from Obscuromonas spp. (A) The tree for Narnaviridae and Mitoviridae rooted with Fiersviridae; two major clades of narnaviruses are indicated with vertical lines. (B) The tree for Qinviridae rooted with Yue-like viruses. Some clades in (A) and (B) were collapsed for simplicity. Numbers at branches represent standard bootstrap replicates and Bayesian posterior probabilities. Absolute supports (100/1) are shown with solid circles, those below 50 or 0.5 are replaced with dashes. The sequences of trypanosomatid viruses reported in this and in previous studies are highlighted in black and gray, respectively. For full trees in the Newick format, see Data S2 and S3.

Figure 3.

EVE of Blastocrithidia triatomae. (A) Maximum likelihood phylogenetic tree based on RdRP amino acid sequences of viruses and EVEs. Numbers at branches represent standard bootstrap replicates and Bayesian posterior probabilities. Absolute supports (100/1) are shown with solid circles, those below 50 or 0.5 are replaced with dashes. Blastocrithidia triatomae EVE is highlighted in black, Leptomonas pyrrhocoris EVE—in gray. For full tree in the Newick format, see Data S4. (B) Position of EVEs in genomes of B. triatomae and L. pyrrhocoris. Double wiggly lines indicate continuation of the scaffold (chromosome).