Glissandra oviformis n. sp.: A novel predatory flagellate illuminates the character evolution within the eukaryotic clade CRuMs
Data files
Oct 13, 2025 version files 40.98 MB
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132Taxa340Genes88397AAposi.fst
11.67 MB
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340protein-dataset.zip
3.62 MB
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FastSiteRemoval.zip
25.39 MB
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README.md
3.25 KB
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SRT312_SSU_phylogeny.phy
289.98 KB
Abstract
Culturing protists offers a powerful approach to exploring eukaryotic diversity, especially for deep-branching lineages. In this study, we cultured and described a novel protist species, named Glissandra oviformis n sp., within the poorly studied and unclassified genus Glissandra. While an SSU rDNA gene phylogeny failed to resolve its phylogenetic placement in the eukaryotic tree, a phylogenomic analysis of 340 proteins indicated G. oviformis as a deep-branching member of the CRuMs clade. Prior to this study, this clade consisted of diverse heterotrophic amoeba and flagellates and lacks clear synapomorphies. Ultrastructural observations revealed that G. oviformis shares the characteristics with some CRuMs members, including the pellicle underlying the plasma membrane and an internal sleeve surrounding the central pair of the axoneme at the flagellar transitional region. Our findings suggest potential shared characteristics and synapomorphies for CRuMs and contribute to a deeper understanding of the character evolution within CRuMs.
https://doi.org/10.5061/dryad.gf1vhhn0b
Description of the data and file structure
Files and variables
File: 340protein-dataset.zip
Description: Contains raw data of protein sequences used in the 340-protein dataset.
File: SRT312_SSU_phylogeny.phy
Description: Dataset for SSU rDNA phylogenetic analysis.
File: 132Taxa340Genes88397AAposi.fst
Description: Dataset for 340-protein phylogenetic analysis.
File: FastSiteRemoval.zip
Description: Contains datasets for fast-site removal analysis.
SSU rDNA phylogenetic dataset
The SSU rDNA sequence of G. oviformis was aligned with those of 190 phylogenetically diverse eukaryotes using MAFFT v7.520 (Katoh and Standley 2013). After removing ambiguously aligned positions using BMGE v1.12 (Criscuolo and Gribaldo 2010) with default settings, 1,137 nucleotide positions remained.
340-protein dataset
To elucidate the phylogenetic position of G. oviformis, we prepared a phylogenomic alignment by updating an existing one comprising 351 proteins (Harada et al. 2024). For each protein, we added homologous sequences retrieved by BLASTp (with an E-value cut-off of 10⁻30) from the newly generated G. oviformis protein sequences (see above), as well as sequences from the provorans, anaeroamoebids, and other organisms (a total of 50 species, including G. oviformis added, described in Table S1). Individual single-protein alignments were generated using MAFFT v7.520 with the L-INS-i algorithm, followed by manual correction and automated exclusion of ambiguously aligned positions using BMGE v1.12.
Each single-protein alignment was subjected to a preliminary phylogenetic analysis using FASTTREE v2.1.11 (Price et al. 2010) under the LG + Γ model. The resulting approximately maximum-likelihood trees with SH-like local supports were examined to identify alignments with aberrant phylogenetic signals that strongly disagreed with well-established monophyletic groups in the eToL, including Opisthokonta, Amoebozoa, Alveolata, Stramenopiles, Rhizaria, Rhodophyta, Chloroplastida, Glaucophyta, Haptophyta, Cryptista, Jakobida, Euglenozoa, Heterolobosea, Diplomonadida, Parabasalia, and Malawimonadida. Eleven out of the 351 single-protein alignments were found to violate these criteria and were excluded from further phylogenomic analyses. The remaining 340 single-protein alignments were concatenated into a single phylogenomic alignment comprising 132 taxa with 88,397 unambiguously aligned amino acid positions.
Fast site removal
We evaluated the impact of fast-evolving positions within the 340-protein alignment. Substitution rates for each position were calculated on the ML tree by IQ-TREE v2.2.2.6, and four sets of sub-alignments were created from the original alignment by sequentially removing the top 20%, 40%, 60%, and 80% fastest-evolving positions. The original alignment and four sub-alignments were individually subjected to the ultra-fast bootstrapping approximation under the LG + Γ + F + C20 model using IQ-TREE v 2.2.2.6.
In this study, we cultured and described a novel protist species, Glissandra oviformis n. sp., within the poorly studied and unclassified genus Glissandra. To determine the phylogenetic position of G. oviformis, we conducted phylogenetic analyses using an SSU rDNA dataset and a 340-protein dataset. Furthermore, for the results based on the 340-protein dataset, we assessed the phylogenetic position of G. oviformis using fast-site removal analysis.