ArticleScientific reports2017
Accessing the genomic information of unculturable oceanic picoeukaryotes by combining multiple single cells.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed, 58 citations in OpenAlex.
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- The Earth BioGenome Project Phase II: illuminating the eukaryotic tree of life.Frontiers in science · 2025Article
- Best-practice guidance for Earth BioGenome Project sample collection and processing: progress and challenges in biodiverse reference genome creation.GigaScience · 2025Article
- Whole-genome scanning reveals environmental selection mechanisms that shape diversity in populations of the epipelagic diatom Chaetoceros.PLoS biology · 2022Article
- Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean.Cell genomics · 2022Article
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- 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
- Cell sorting reveals few novel prokaryote and photosynthetic picoeukaryote associations in the oligotrophic ocean.Environmental microbiology · 2021Article
- Predicting microbial growth dynamics in response to nutrient availability.PLoS computational biology · 2021Article
- An efficient single-cell transcriptomics workflow for microbial eukaryotes benchmarked on Giardia intestinalis cells.BMC genomics · 2020Article
- Genome Resolved Biogeography of Mamiellales.Genes · 2020Article
- Unexpected mitochondrial genome diversity revealed by targeted single-cell genomics of heterotrophic flagellated protists.Nature microbiology · 2020Article
- Combining morphology, behaviour and genomics to understand the evolution and ecology of microbial eukaryotes.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Review
- Single cell ecology.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Article
- Using single-cell transcriptomics to understand functional states and interactions in microbial eukaryotes.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Article
- Reconstruction of protein domain evolution using single-cell amplified genomes of uncultured choanoflagellates sheds light on the origin of animals.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Article
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Authors and funding
11 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pico-sized eukaryotes play key roles in the functioning of marine ecosystems, but we still have a limited knowledge on their ecology and evolution. The MAST-4 lineage is of particular interest, since it is widespread in surface oceans, presents ecotypic differentiation and has defied culturing efforts so far. Single cell genomics (SCG) are promising tools to retrieve genomic information from these uncultured organisms. However, SCG are based on whole genome amplification, which normally introduces amplification biases that limit the amount of genomic data retrieved from a single cell. Here, we increase the recovery of genomic information from two MAST-4 lineages by co-assembling short reads from multiple Single Amplified Genomes (SAGs) belonging to evolutionary closely related cells. We found that complementary genomic information is retrieved from different SAGs, generating co-assembly that features >74% of genome recovery, against about 20% when assembled individually. Even though this approach is not aimed at generating high-quality draft genomes, it allows accessing to the genomic information of microbes that would otherwise remain unreachable. Since most of the picoeukaryotes still remain uncultured, our work serves as a proof-of-concept that can be applied to other taxa in order to extract genomic data and address new ecological and evolutionary questions.
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