Phylogenomics of novel ploeotid taxa contribute to the backbone of the euglenid tree

Phylogenomic workflow for uncultivable microbial eukaryotes using single-cell RNA sequencing - A case study with planktonic ciliates (Ciliophora, Oligotrichea)

Phylogenetic analyses increasingly rely on genomic and transcriptomic data to produce better supported inferences on the evolutionary relationships among microbial eukaryotes. Such phylogenomic analyses, however, require robust workflows, bioinformatic expertise and computational power. Microbial eukaryotes pose additional challenges given the complexity of their genomes and the presence of non-target sequences (e.g., symbionts, prey) in data obtained from single cells of uncultivable lineages. To address these challenges, we developed a phylogenomic workflow based on single-cell RNA sequencing, integrating all essential steps from cell isolation to data curation and species tree inference. We assessed our workflow by using publicly available and newly generated transcriptomes (11 and 28, respectively) from the Oligotrichea, a diverse group of marine planktonic ciliates. This group's phylogenetic relationships have been relatively well-studied based on ribosomal RNA gene markers, which we reconstructed by read mapping of transcriptome sequences and compared to our phylogenomic inferences. We also compared phylogenomic analyses based on single-copy protein-coding genes (well-curated orthologs) and multi-copy genes (including paralogs) by sequence concatenation and a coalescence approach (Asteroid), respectively. Finally, using subsets of up to 1,014 gene families (GFs), we assessed the influence of missing data in our phylogenomic inferences. All our analyses yielded similar results, and most inferred relationships were consistent and well-supported. Overall, we found that Asteroid provides robust support for species tree inferences, while simplifying curation steps, minimizing the effects of missing data and maximizing the number of GFs represented in the analyses. Our workflow can be adapted for phylogenomic analyses based on single-cell RNA sequencing of other uncultivable microbial eukaryotes.

Ultrastructure of Olkasia polycarbonata (Euglenozoa, Euglenida) demonstrates cytoskeletal innovations associated with the feeding and flagellar apparatuses

Euglenids are flagellates with diverse modes of nutrition, including the photosynthetic Euglenophyceae, which acquired plastids via secondary endosymbiosis with green algae, and a diverse assemblage of predators of bacteria and other microeukaryotes. Most heterotrophic euglenids have never been cultivated, so their morphology remains poorly characterized and limited to only a few studies. "Ploeotids" are a paraphyletic group representing much of the diversity of heterotrophic euglenids and are characterized by their feeding apparatus and a rigid pellicle of 10-12 longitudinally arranged strips. Ploeotid-like euglenids gave rise to the Spirocuta, a large clade of heterotrophic and photosynthetic euglenids defined by a flexible pellicle of helically arranged strips. Using single-cell approaches, we report the first ultrastructural characterization of Olkasia polycarbonata, a ploeotid that is consistently positioned as the sister lineage to the Spirocuta in multigene phylogenetic analyses. O. polycarbonata shares several morphological characteristics with members of Spirocuta, such as prominent swellings on the paraxonemal rods and a robust feeding apparatus consisting of rods and vanes. These morphological traits are consistent with the phylogenetic position of O. polycarbonata and demonstrate an increase in cytoskeletal complexity that occurred prior to the key strip duplication event in the most recent common ancestor of Spirocuta.

Ecology of free-living freshwater heterotrophic euglenoids: A summarizing review

This review aims to compile sparse information on the ecology of freshwater heterotrophic euglenoids and synthesize the main phenomena and hypotheses from published results. Apparently, heterotrophic euglenoids play a very important role in the nutrient flow of water ecosystems and are irreplaceable heterotrophic contributors in benthic communities, as their total biomass is by far the largest among heterotrophic flagellates. Even though they are obviously a very crucial part of the diversity of freshwater heterotrophic protists, and likely the most represented (in terms of biovolume) group of heterotrophic flagellates, there have been only a few attempts to elucidate their ecological preferences, roles, niches, and importance. They exhibit three nutrition modes-bacterivory, eukaryovory, and osmotrophy-which are strategies closely related to their taxonomical groupings and phylogenetic positions. Unfortunately, the phylogeny of the majority of the species remains unknown, similar to their autecology. There are major problems with the quantitative research methodologies, which is a big challenge for future research to improve.

Single-cell genomics revealed Candidatus Grellia alia sp. nov. as an endosymbiont of Eutreptiella sp. (Euglenophyceae)

Though endosymbioses between protists and prokaryotes are widespread, certain host lineages have received disproportionate attention what may indicate either a predisposition to such interactions or limited studies on certain protist groups due to lack of cultures. The euglenids represent one such group in spite of microscopic observations showing intracellular bacteria in some strains. Here, we perform a comprehensive molecular analysis of a previously identified endosymbiont in the Eutreptiella sp. CCMP3347 using a single cell approach and bulk culture sequencing. The genome reconstruction of this endosymbiont allowed the description of a new endosymbiont Candidatus Grellia alia sp. nov. from the family Midichloriaceae. Comparative genomics revealed a remarkably complete conjugative type IV secretion system present in three copies on the plasmid sequences of the studied endosymbiont, a feature missing in the closely related Grellia incantans. This study addresses the challenge of limited host cultures with endosymbionts by showing that the genomes of endosymbionts reconstructed from single host cells have the completeness and contiguity that matches or exceeds those coming from bulk cultures. This paves the way for further studies of endosymbionts in euglenids and other protist groups. The research also provides the opportunity to study the diversity of endosymbionts in natural populations.

Gleaning Euglenozoa-specific DNA polymerases in public single-cell transcriptome data

Multiple genes encoding family A DNA polymerases (famA DNAPs), which are evolutionary relatives of DNA polymerase I (PolI) in bacteria and phages, have been found in eukaryotic genomes, and many of these proteins are used mainly in organelles. Among members of the phylum Euglenozoa, distinct types of famA DNAP, PolIA, PolIBCD+, POP, and eugPolA, have been found. It is intriguing how the suite of famA DNAPs had been established during the evolution of Euglenozoa, but the DNAP data have not been sampled from the taxa that sufficiently represent the diversity of this phylum. In particular, little sequence data were available for basal branching species in Euglenozoa until recently. Thanks to the single-cell transcriptome data from symbiontids and phagotrophic euglenids, we have an opportunity to cover the "hole" in the repertory of famA DNAPs in the deep branches in Euglenozoa. The current study identified 16 new famA DNAP sequences in the transcriptome data from 33 phagotrophic euglenids and two symbiontids, respectively. Based on the new famA DNAP sequences, the updated diversity and evolution of famA DNAPs in Euglenozoa are discussed.

Molecular phylogenetics of sessile Dolium sedentarium, a petalomonad euglenid

The euglenids are a species-rich group of flagellates with varying modes of nutrition that can be found in diverse habitats. Phagotrophic members of this group gave rise to phototrophs and hold the key to understanding the evolution of euglenids as a whole, including the evolution of complex morphological characters like the euglenid pellicle. Yet to understand the evolution of these characters, a comprehensive sampling of molecular data is needed to correlate morphological and molecular data, and to estimate a basic phylogenetic backbone of the group. While the availability of SSU rDNA and, more recently, multigene data from phagotrophic euglenids has improved, several "orphan" taxa remain without any molecular data whatsoever. Dolium sedentarium is one such taxon: It is a rarely-observed phagotrophic euglenid that inhabits tropical benthic environments and is one of few known sessile euglenids. Based on morphological characters, it has been thought of as part of the earliest branch of euglenids, the Petalomonadida. We report the first molecular sequencing data for Dolium using single-cell transcriptomics, adding another small piece in the puzzle of euglenid evolution. Both SSU rDNA and multigene phylogenies confirm it as a solitary branch within Petalomonadida.