ArticleThe Plant cell2023
The Chlamydomonas Genome Project, version 6: Reference assemblies for mating-type plus and minus strains reveal extensive structural mutation in the laboratory.
Article in The Plant cell, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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72 citing papers in PubMed, 106 citations in OpenAlex.
- The cold case of state transition 7 (stt7) mutants of Chlamydomonas reinhardtii, solved by whole-genome sequencing.The New phytologist · 2026Article
- A RAF-SnRK2-PP2C functional module regulates cell survival in the chlorophyte Chlamydomonas reinhardtii.The New phytologist · 2026Article
- Estimation of chloroplast macromolecular complex copy numbers and subunit stoichiometries during the Chlamydomonas reinhardtii cell cycle.The Plant journal : for cell and molecular biology · 2026Article
- Intron retention dominates alternative splicing reprogramming during anaerobic stress in Chlamydomonas reinhardtii.Planta · 2026Article
- Multiomics studies reveal how ambient temperature changes govern cellular responses of Chlamydomonas.The Plant cell · 2026Article
- CIA5 and its interacting metal-binding GTPase ZNG3 are degraded by the proteasome in Zn deficiency.The Plant journal : for cell and molecular biology · 2026Article
- Searching for α-solenoid proteins involved in organellar gene expression.BMC genomics · 2026Article
- Structure and energy transfer of a far-red-absorbing euglenophyte PSI-LhcE-LhcbM supercomplex.Nature communications · 2026Article
- Induction of collective behavior by β-1,3-glucans in microalgae.Science advances · 2026Article
- Energy metabolism and adaptation to hypoxia in the non-photosynthetic green alga Leontynka.BMC biology · 2026Article
- SAGA1 and SAGA2 localize the starch sheath to the pyrenoid inbioRxiv : the preprint server for biology · 2026Article
- Client distribution between Chlamydomonas FDX1 and FDX2 in carbon, nitrogen and sulfur assimilation.bioRxiv : the preprint server for biology · 2026Article
- Acclimation to high and low diurnal light is flexible inProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Proteomic analysis of the pyrenoid-traversing membranes of Chlamydomonas reinhardtii reveals novel components.The New phytologist · 2026Article
- Mono-mix strategy enables comparative proteomics of a cross-kingdom microbial symbiosis.PloS one · 2026Article
- Integrating co-expression network analysis and machine learning to reveal the regulatory landscape ofPeerJ · 2026Article
- Hidden diversity: Transcriptomic and photosynthetic variation among common 'wild type' Chlamydomonas strains.The Plant journal : for cell and molecular biology · 2025Article
- Article
- Targeted genetic manipulation and yeast-like evolutionary genomics in the green alga Auxenochlorella.The Plant cell · 2025Article
- Targeted genetic manipulation and yeast-like evolutionary genomics in the green algabioRxiv : the preprint server for biology · 2025Article
12 more citing papers are in PubMed but not listed here.
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Authors and funding
18 authors at 7 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Five versions of the Chlamydomonas reinhardtii reference genome have been produced over the last two decades. Here we present version 6, bringing significant advances in assembly quality and structural annotations. PacBio-based chromosome-level assemblies for two laboratory strains, CC-503 and CC-4532, provide resources for the plus and minus mating-type alleles. We corrected major misassemblies in previous versions and validated our assemblies via linkage analyses. Contiguity increased over ten-fold and >80% of filled gaps are within genes. We used Iso-Seq and deep RNA-seq datasets to improve structural annotations, and updated gene symbols and textual annotation of functionally characterized genes via extensive manual curation. We discovered that the cell wall-less classical reference strain CC-503 exhibits genomic instability potentially caused by deletion of the helicase RECQ3, with major structural mutations identified that affect >100 genes. We therefore present the CC-4532 assembly as the primary reference, although this strain also carries unique structural mutations and is experiencing rapid proliferation of a Gypsy retrotransposon. We expect all laboratory strains to harbor gene-disrupting mutations, which should be considered when interpreting and comparing experimental results. Collectively, the resources presented here herald a new era of Chlamydomonas genomics and will provide the foundation for continued research in this important reference organism.
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