ArticleScientific reports2017
Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis.
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 12 papers.
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12 citing papers in PubMed.
- Small Things that Make a Big Difference: Single-Cell Transcriptomic of Nanociliates Reveals Genes Potentially Involved in Mixotrophy.Microbial ecology · 2025Article
- Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean.Cell genomics · 2022Article
- One Cell at a Time: Advances in Single-Cell Methods and Instrumentation for Discovery in Aquatic Microbiology.Frontiers in microbiology · 2022Article
- 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
- Combined Genome and Transcriptome Analyses of the Ciliate Schmidingerella arcuata (Spirotrichea) Reveal Patterns of DNA Elimination, Scrambling, and Inversion.Genome biology and evolution · 2020Article
- An efficient single-cell transcriptomics workflow for microbial eukaryotes benchmarked on Giardia intestinalis cells.BMC genomics · 2020Article
- 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
- 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 genomics yields a wide diversity of small planktonic protists across major ocean ecosystems.Scientific reports · 2019Article
- Leveraging single-cell genomics to expand the fungal tree of life.Nature microbiology · 2018Article
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6 authors.
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Abstract
Single-cell genomics (SCG) appeared as a powerful technique to get genomic information from uncultured organisms. However, SCG techniques suffer from biases at the whole genome amplification step that can lead to extremely variable numbers of genome recovery (5-100%). Thus, it is unclear how useful can SCG be to address evolutionary questions on uncultured microbial eukaryotes. To provide some insights into this, we here analysed 3 single-cell amplified genomes (SAGs) of the choanoflagellate Monosiga brevicollis, whose genome is known. Our results show that each SAG has a different, independent bias, yielding different levels of genome recovery for each cell (6-36%). Genes often appear fragmented and are split into more genes during annotation. Thus, analyses of gene gain and losses, gene architectures, synteny and other genomic features can not be addressed with a single SAG. However, the recovery of phylogenetically-informative protein domains can be up to 55%. This means SAG data can be used to perform accurate phylogenomic analyses. Finally, we also confirm that the co-assembly of several SAGs improves the general genomic recovery. Overall, our data show that, besides important current limitations, SAGs can still provide interesting and novel insights from poorly-known, uncultured organisms.
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