ArticleThe Plant cell2021
Single-cell RNA sequencing of batch Chlamydomonas cultures reveals heterogeneity in their diurnal cycle phase.
Article in The Plant cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 38 citations in OpenAlex.
- Predictive Algal Systems Biology: Integrating Omics, Genome-Scale Metabolic Models, and Machine Learning.Bioengineering (Basel, Switzerland) · 2026Review
- Phenotypic heterogeneity in a batch culture of Chlamydomonas reinhardtii with different light tolerances.PloS one · 2026Article
- Preparation, maintenance and propagation of synchronous cultures of photoactive Chlamydomonas cells.Nature protocols · 2025Review
- Applications and techniques of single-cell RNA sequencing across diverse species.Briefings in bioinformatics · 2025Review
- Cellular heterogeneity in metabolism and associated microbiome of a non-model phytoflagellate.The ISME journal · 2025Article
- Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics.The Plant cell · 2024Article
- Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton.PloS one · 2024Article
- scPrisma infers, filters and enhances topological signals in single-cell data using spectral template matching.Nature biotechnology · 2023Article
- Protoplast Preparation for Algal Single-Cell Omics Sequencing.Microorganisms · 2023Review
- A potential EARLY FLOWERING 3 homolog in Chlamydomonas is involved in the red/violet and blue light signaling pathways for the degradation of RHYTHM OF CHLOROPLAST 15.PLoS genetics · 2022Article
- Cell-Type-Specific Profiling of theMembranes · 2022Article
- Systems-wide analysis revealed shared and unique responses to moderate and acute high temperatures in the green alga Chlamydomonas reinhardtii.Communications biology · 2022Article
- Single-cell genomics revolutionizes plant development studies across scales.Development (Cambridge, England) · 2022Article
- The biology of time: dynamic responses of cell types to developmental, circadian and environmental cues.The Plant journal : for cell and molecular biology · 2022Review
- One Cell at a Time: Advances in Single-Cell Methods and Instrumentation for Discovery in Aquatic Microbiology.Frontiers in microbiology · 2022Article
- Transcription Factor-Based Genetic Engineering in Microalgae.Plants (Basel, Switzerland) · 2021Review
- Focus on the biology of plant genomes.The Plant cell · 2021Article
- Single-cell genomics goes greener.The Plant cell · 2021Article
- Co-expression networks in Chlamydomonas reveal significant rhythmicity in batch cultures and empower gene function discovery.The Plant cell · 2021Article
- Microbial Single-Cell Analysis: What Can We Learn From Mammalian?Frontiers in cell and developmental biology · 2021Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The photosynthetic unicellular alga Chlamydomonas (Chlamydomonas reinhardtii) is a versatile reference for algal biology because of its ease of culture in the laboratory. Genomic and systems biology approaches have previously described transcriptome responses to environmental changes using bulk data, thus representing the average behavior from pools of cells. Here, we apply single-cell RNA sequencing (scRNA-seq) to probe the heterogeneity of Chlamydomonas cell populations under three environments and in two genotypes differing by the presence of a cell wall. First, we determined that RNA can be extracted from single algal cells with or without a cell wall, offering the possibility to sample natural algal communities. Second, scRNA-seq successfully separated single cells into nonoverlapping cell clusters according to their growth conditions. Cells exposed to iron or nitrogen deficiency were easily distinguished despite a shared tendency to arrest photosynthesis and cell division to economize resources. Notably, these groups of cells not only recapitulated known patterns observed with bulk RNA-seq but also revealed their inherent heterogeneity. A substantial source of variation between cells originated from their endogenous diurnal phase, although cultures were grown in constant light. We exploited this result to show that circadian iron responses may be conserved from algae to land plants. We document experimentally that bulk RNA-seq data represent an average of typically hidden heterogeneity in the population.
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