ArticlePlant communications2023
A gap-free genome assembly of Chlamydomonas reinhardtii and detection of translocations induced by CRISPR-mediated mutagenesis.
Article in Plant communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 33 citations in OpenAlex.
- UniSplicer: A deep-learning framework for accurate splice-site prediction and splice-altering mutation detection across diverse taxa.Plant communications · 2026Article
- Identification of a Novel Rice Chromosomal Translocation Line that Could Cause the Heterozygote Semi-Sterility and be Overcome by Genomic Duplication.Rice (New York, N.Y.) · 2025Article
- Cryptic infection of a giant virus in a unicellular green alga.Science (New York, N.Y.) · 2025Article
- Long and Accurate: How HiFi Sequencing is Transforming Genomics.Genomics, proteomics & bioinformatics · 2025Review
- Genome editing in the green alga Chlamydomonas: past, present practice and future prospects.The Plant journal : for cell and molecular biology · 2025Review
- Elevated accumulation of lutein and zeaxanthin in a novel high-biomass yielding strain Dunaliella sp. ZP-1 obtained through EMS mutagenesis.Biotechnology for biofuels and bioproducts · 2025Article
- Article
- Telomere-to-telomere genome of common bean (Phaseolus vulgaris L., YP4).GigaScience · 2025Article
- Protofilament-specific nanopatterns of tubulin post-translational modifications regulate the mechanics of ciliary beating.Current biology : CB · 2024Article
- Latent infection of an active giant endogenous virus in a unicellular green alga.bioRxiv : the preprint server for biology · 2024Article
- Long-Read-Based Hybrid Genome Assembly and Annotation of Snow Algal Strain CCCryo 101-99 (cf. Sphaerocystis sp., Chlamydomonadales).Genome biology and evolution · 2024Article
- Near telomere-to-telomere genome assemblies of two Chlorella species unveil the composition and evolution of centromeres in green algae.BMC genomics · 2024Article
- Gene dosage of independent dynein arm motor preassembly factors influences cilia assembly in Chlamydomonas reinhardtii.PLoS genetics · 2024Article
- Near telomere-to-telomere genome of the model plant Physcomitrium patens.Nature plants · 2024Article
- Extraction and selection of high-molecular-weight DNA for long-read sequencing from Chlamydomonas reinhardtii.PloS one · 2024Article
- Telomerase-independent survival leads to a mosaic of complex subtelomere rearrangements inGenome research · 2023Article
- The Chlamydomonas Genome Project, version 6: Reference assemblies for mating-type plus and minus strains reveal extensive structural mutation in the laboratory.The Plant cell · 2023Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Genomic assemblies of the unicellular green alga Chlamydomonas reinhardtii have provided important resources for researchers. However, assembly errors, large gaps, and unplaced scaffolds as well as strain-specific variants currently impede many types of analysis. By combining PacBio HiFi and Oxford Nanopore long-read technologies, we generated a de novo genome assembly for strain CC-5816, derived from crosses of strains CC-125 and CC-124. Multiple methods of evaluating genome completeness and base-pair error rate suggest that the final telomere-to-telomere assembly is highly accurate. The CC-5816 assembly enabled previously difficult analyses that include characterization of the 17 centromeres, rDNA arrays on three chromosomes, and 56 insertions of organellar DNA into the nuclear genome. Using Nanopore sequencing, we identified sites of cytosine (CpG) methylation, which are enriched at centromeres. We analyzed CRISPR-Cas9 insertional mutants in the PF23 gene. Two of the three alleles produced progeny that displayed patterns of meiotic inviability that suggested the presence of a chromosomal aberration. Mapping Nanopore reads from pf23-2 and pf23-3 onto the CC-5816 genome showed that these two strains each carry a translocation that was initiated at the PF23 gene locus on chromosome 11 and joined with chromosomes 5 or 3, respectively. The translocations were verified by demonstrating linkage between loci on the two translocated chromosomes in meiotic progeny. The three pf23 alleles display the expected short-cilia phenotype, and immunoblotting showed that pf23-2 lacks the PF23 protein. Our CC-5816 genome assembly will undoubtedly provide an important tool for the Chlamydomonas research community.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.