Phylogenomic Analysis of Marine Protists

Marine protists constitute a vast array of unicellular eukaryotes that underpin global biogeochemical cycles, food webs and climate regulation. Phylogenomic analysis applies genome-scale sequencing and comparative methods to resolve evolutionary relationships among these organisms, many of which remain uncultured and poorly characterised. By integrating data from environmental metagenomes, single-cell genomics and transcriptomes, researchers can infer robust phylogenies, uncover cryptic lineages and map functional gene repertoires. This approach has revealed novel branches in the eukaryote tree of life, redefined major clades such as stramenopiles and Rhizaria, and traced the origins of key innovations including plastid acquisition and phagotrophic feeding. Advances in genome assembly, orthologue detection and models of sequence evolution have allowed deeper interrogation of lineage-specific adaptations, such as metabolic pathways for nutrient utilisation, mechanisms of motility and responses to environmental gradients. Phylogenomic insights into marine protists not only enhance our understanding of early eukaryote evolution but also inform predictive models of ecosystem function, guiding efforts to monitor ocean health and assess the impact of climate change on microbial diversity.

Research from Nature Portfolio

Single-cell genomics of uncultured stramenopile lineages sampled during a global ocean survey has provided high-resolution genomes for seven prevalent heterotrophic taxa. Analysis of gene content across these genomes revealed distinct suites of motility proteins, digestive enzymes and potential horizontal gene transfers, with distribution patterns linked to temperature and depth zones. These findings underscore the functional diversity of stramenopiles in nutrient cycling and trophic interactions. Complementing this, a co-assembly strategy that pools multiple single amplified genomes from closely related picoeukaryotes has markedly increased genome recovery—boosting completeness from around 20 percent to over 70 percent. This methodological advance enables reconstruction of near-complete genomes from taxa that defy cultivation, thereby opening new avenues for phylogenomic placement and exploration of evolutionary novelties in marine protist lineages.

Phylogenomic Analysis of Marine Protists publication trend

The graph below shows the total number of articles in phylogenomic analysis of marine protists across all publications each year (not limited to Nature Index journals).

Technical terms

Phylogenomics: The use of genome-scale data to infer evolutionary relationships among organisms.

Single-cell genomics: Sequencing the genome of an individual cell to capture genetic information from uncultured taxa.

Metagenomics: Analysis of collective genomic DNA recovered from environmental samples to reconstruct community diversity.

Transcriptome: The complete set of RNA transcripts expressed by a cell or community at a given time.

Heterotrophy: A mode of nutrition involving the uptake of organic molecules produced by other organisms.

Phagotrophy: A form of heterotrophy in which cells engulf particulate food items such as bacteria.

References

1. Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans. Nature Communications (2018).
2. Accessing the genomic information of unculturable oceanic picoeukaryotes by combining multiple single cells. Scientific Reports (2017).
3. Gene expression dynamics of natural assemblages of heterotrophic flagellates during bacterivory. Microbiome (2023).
4. Integrated overview of stramenopile ecology, taxonomy, and heterotrophic origin. The ISME Journal: Multidisciplinary Journal of Microbial Ecology (2024).