ArticleScientific reports2019
Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed.
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- The Earth BioGenome Project Phase II: illuminating the eukaryotic tree of life.Frontiers in science · 2025Article
- The Ribosomal Operon Database: A Full-Length rDNA Operon Database Derived From Genome Assemblies.Molecular ecology resources · 2025Article
- The first single-cell sequencing ofFrontiers in microbiology · 2025Article
- Global distribution, diversity, and ecological niche of Picozoa, a widespread and enigmatic marine protist lineage.Microbiome · 2024Article
- Lessons from Extremophiles: Functional Adaptations and Genomic Innovations across the Eukaryotic Tree of Life.Genome biology and evolution · 2024Article
- DeepMicroClass sorts metagenomic contigs into prokaryotes, eukaryotes and viruses.NAR genomics and bioinformatics · 2024Article
- Insights into freshwater ciliate diversity through high throughput DNA metabarcoding.FEMS microbes · 2024Article
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- Identification of microbial metabolic functional guilds from large genomic datasets.Frontiers in microbiology · 2023Article
- Optimization of Preservation Methods Provides Insights into Photosynthetic Picoeukaryotes in Lakes.Microbiology spectrum · 2022Article
- Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean.Cell genomics · 2022Article
- Niche adaptation promoted the evolutionary diversification of tiny ocean predators.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Genome sequencing and de novo assembly of the giant unicellular alga Acetabularia acetabulum using droplet MDA.Scientific reports · 2021Article
- Comparative genomics reveals new functional insights in uncultured MAST species.The ISME journal · 2021Article
- Single-cell genomics unveils a canonical origin of the diverse mitochondrial genomes of euglenozoans.BMC biology · 2021Article
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9 authors.
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Abstract
Marine planktonic protists are critical components of ocean ecosystems and are highly diverse. Molecular sequencing methods are being used to describe this diversity and reveal new associations and metabolisms that are important to how these ecosystems function. We describe here the use of the single cell genomics approach to sample and interrogate the diversity of the smaller (pico- and nano-sized) protists from a range of oceanic samples. We created over 900 single amplified genomes (SAGs) from 8 Tara Ocean samples across the Indian Ocean and the Mediterranean Sea. We show that flow cytometric sorting of single cells effectively distinguishes plastidic and aplastidic cell types that agree with our understanding of protist phylogeny. Yields of genomic DNA with PCR-identifiable 18S rRNA gene sequence from single cells was low (15% of aplastidic cell sorts, and 7% of plastidic sorts) and tests with alternate primers and comparisons to metabarcoding did not reveal phylogenetic bias in the major protist groups. There was little evidence of significant bias against or in favor of any phylogenetic group expected or known to be present. The four open ocean stations in the Indian Ocean had similar communities, despite ranging from 14°N to 20°S latitude, and they differed from the Mediterranean station. Single cell genomics of protists suggests that the taxonomic diversity of the dominant taxa found in only several hundreds of microliters of surface seawater is similar to that found in molecular surveys where liters of sample are filtered.
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