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Open research questions in Protist diversity and phylogeny

86 unresolved questions extracted from the limitations and future-work sections of 219 Protist diversity and phylogeny papers in our library. Each links back to the study that raised it.

What the literature leaves open

  • One challenge is the limited read length of short-read sequencing platforms, which constrains taxonomic assignment. Another challenge is the potential for bias in metabarcoding data due to uneven sequencing effort. The study also faces the challenge of comparing short-read and long-read sequencing approaches, which require different bioinformatic pipelines and classifier methods.

    Unveiling Protist Composition and Diversity Patterns With eDNA Metabarcoding: Comparing Short‐ and Long‐Read Approaches · 2026 · DOI

  • further comparison of SR and LR metabarcoding methods, - investigation of the effect of different bioinformatic pipelines on results

    Unveiling Protist Composition and Diversity Patterns With eDNA Metabarcoding: Comparing Short‐ and Long‐Read Approaches · 2026 · DOI

  • The cellular role of extracellular glutamate sensing in diatoms remains to be elucidated, although the ability to sense this abundant amino acid may represent a mechanism that allows unicellular eukaryotes to detect wounding of neighbouring cells within a population.

    Glutamate as an extracellular signalling molecule in unicellular protists · 2026 · DOI

  • In this study, we reconstructed the phylogeny of Copepoda using amino acid sequences of 40 orthologous genes, with particular emphasis on the previously understudied order Platycopioida.

    First genomic analysis of Platycopioida and phylogenomics across six copepod orders · 2026 · DOI

  • Moreover, adaptive evolution of angiosperm plastid genes remains poorly understood.

    Comparative plastome analysis of the sister genera Ceratocephala and Myosurus (Ranunculaceae) reveals signals of adaptive evolution to arid and aquatic environments · 2024 · DOI

  • However, little is known about whether structural variations of plastomes are associated with adaptation to or occupancy of new environments.

    Comparative plastome analysis of the sister genera Ceratocephala and Myosurus (Ranunculaceae) reveals signals of adaptive evolution to arid and aquatic environments · 2024 · DOI

  • Ichthyosporea is an underexplored group of unicellular eukaryotes closely related to animals.

    Ichthyosporea: a window into the origin of animals · 2024 · DOI

  • Although a photomorphogenesis signalosome (COP9/CSN) has been identified, the mechanism by which this large complex contributes to the pathophysiological processes in filamentous fungi remains unclear.

    Translocon Subunits of the COP9 Signalosome Complex Are a Central Hub for Regulating Multiple Photoresponsive Processes and Autophagic Flux in Magnaporthe oryzae · 2024 · DOI

  • These represent the first whole-genome resources for Solenogastres and will be valuable for future studies investigating this understudied group and molluscan evolution as a whole.

    Two draft genomes of enigmatic Solenogastres (Mollusca, Aplacophora) Epimenia babai and Neomenia megatrapezata · 2024 · DOI

  • Further investigation of the evolution of eukaryotes using fossil-testable predictions. Development of more complex models that account for additional effects. Investigation of the implications of the results for our understanding of the evolution of eukaryotes.

    Clade dynamics support an early origin of crown eukaryotes · 2026 · DOI

  • The absence of a clear timeline for eukaryogenesis leaves a critical gap in connecting biological innovations to Earth's environmental history. The molecular clock estimates for the age of LECA have produced estimates ranging from 1000 Ma to 1900 Ma, reflecting uncertainty in substitution rates and calibration points.

    Clade dynamics support an early origin of crown eukaryotes · 2026 · DOI

  • Molecular phylogeny analyses based on SSU rDNA sequence data support previous inferences that Cyclotrichium should be removed from Litostomatea; however, its final class-level affiliation remains to be investigated.

    Taxonomy and Phylogeny of the Little-Known Ciliate Genus Cyclotrichium: With Special Reference to Two New Species · 2026 · DOI

  • Further analysis of the phylogenetic signals of different metabolic functions. Investigation of the mechanisms of horizontal gene transfer between prokaryotes.

    Origins of eukaryotic metabolism · 2026 · DOI

  • The extent and sources of prokaryotic contributions to the eukaryotic proteome remain debated. The driving force behind the endosymbiotic integration is still under debate.

    Origins of eukaryotic metabolism · 2026 · DOI

  • Further study of the mechanisms of bacterial entry into mitochondria. Investigation of the metabolic exchanges between mitochondria and endosymbiotic bacteria.

    Volume electron microscopy reveals bacterial endosymbiosis within host mitochondria · 2026 · DOI

  • The approach was limited to DNA as a template. The data is not Lagrangian as the four water masses do not flow in concert.

    Taxonomy as an indicator of trophic diversity in microbial eukaryotic plankton in an Arctic outflow gateway · 2026 · DOI

  • The functional diversity and distribution of microbial eukaryotes remain incompletely understood. The study aims to address this gap by examining microbial eukaryote assemblages in the Arctic.

    Taxonomy as an indicator of trophic diversity in microbial eukaryotic plankton in an Arctic outflow gateway · 2026 · DOI

  • The study faced challenges in identifying pcox-CO oxidizers due to the lack of conserved genes. The study had to develop stringent criteria to minimize overestimation of pcox-CO oxidizer diversity.

    Diversity and geographical distribution of potential carbon monoxide oxidizers using molybdenum-containing enzymes in the ocean · 2026 · DOI

  • The study may have underestimated the diversity of pcox-CO oxidizers due to relatively low read recruitment. The study used a limited number of species clusters for absolute quantification.

    Diversity and geographical distribution of potential carbon monoxide oxidizers using molybdenum-containing enzymes in the ocean · 2026 · DOI

  • The need for a review and archiving process for digital interactions datasets. The lack of a citable version of the globalbioticinteractions/fungaltraits dataset.

    Versioned Archive and Review of Biotic Interactions and Taxon Names Found within globalbioticinteractions/fungaltraits hash://md5/3d1deb1394360f06cebca96cf7d0a3a4 · 2026 · DOI

  • The study faces challenges in annotating differentially expressed transcripts due to limited genetic resources for brown algae. The research identifies a limited number of annotated candidate genes, which may be due to annotation bias.

    Regional transcriptomic divergence reveals thermal adaptation mechanisms in the giant kelp Macrocystis pyrifera · 2026 · DOI

  • Functional genomics remains limited in brown algae, - Scarce genetic resources are available for brown algae, - Annotation bias may exist as key processes in model species are often identified by over-expression, - Few under-expressed genes were annotated in M. pyrifera

    Regional transcriptomic divergence reveals thermal adaptation mechanisms in the giant kelp Macrocystis pyrifera · 2026 · DOI

  • The responsiveness of glycosome contents to changes in kinetoplastids' extracellular environments is a major gap in knowledge. The study aims to address this gap by testing the effects of nutrient and oxygen variation on glycosome-linked enzyme levels.

    Cross-species comparisons in a unified medium suggest broadly stable glycosome-linked enzyme levels under nutrient and oxygen variation · 2026 · DOI

  • The study of symbiotic protists and their diversity is important for understanding their roles in various environments. Integrative taxonomic approaches are necessary for resolving species identities and improving the characterisation of symbiotic protists. The mobilid genus Leiotrocha is a focus of study for advancing taxonomic and biological knowledge.

    Contributions to the mobilid genus Leiotrocha Fabre-Domergue, 1888 · 2026 · DOI

  • While the involvement of some enzymes in the biogenesis and function of the 1°siRNAs is not surprising, like Dicer1, the necessity of RNA-dependent-RNA-Polymerase (RdRP) activity remains unknown. The reason for such differences remains unclear. Our findings highlight the diversity of feeding strategies in the Vampyrellida and demonstrate how much remains to be discovered about these widespread and fascinating microbes. However, the phylogenetic relationships of major groups within stramenopiles are poorly resolved, due to both lack of massive sequence data, especially for heterotrophic representatives, and lack of data on yet undescribed diversity of stramenopiles, including many predicted by metagenomic studies (e. I will discuss the open questions and main conclusions from these findings for future scenarios (global warming).

    Contributions to the mobilid genus Leiotrocha Fabre-Domergue, 1888 · 2026 · DOI

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86 open questions have been extracted from the limitations and future-work passages of 219 Protist diversity and phylogeny papers in our library. Each one below links back to the study that raised it, so you can read the original claim in context.

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