ArticleThe Plant journal : for cell and molecular biology2018
High-throughput sequencing of the chloroplast and mitochondrion of Chlamydomonas reinhardtii to generate improved de novo assemblies, analyze expression patterns and transcript speciation, and evaluate diversity among laboratory strains and wild isolates.
Article in The Plant journal : for cell and molecular biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed, 135 citations in OpenAlex.
- Chloroplast-encoded small subunit extensions reshape the Chlamydomonas chlororibosome.Nature plants · 2026Article
- ChloroScan: Recovering Plastid Genome Bins From Metagenomic Data.Molecular ecology resources · 2026Article
- Searching for α-solenoid proteins involved in organellar gene expression.BMC genomics · 2026Article
- Integrative chloroplast genomics of Polygonaceae: evolutionary dynamics, codon optimization, and phylogenetic resolution.BMC plant biology · 2026Article
- Chloroplast-encoded small subunit extensions reshape the Chlamydomonas chlororibosome.bioRxiv : the preprint server for biology · 2026Article
- Article
- Genome-Wide Characterization and Expression Analysis ofBiology · 2025Article
- Mitochondrial mRNA oligocitydylation occurs in Chlorophyceae and Ulvales but not Bryopsidales or Trebouxiophyceae.Journal of phycology · 2025Article
- Global identification of AGO3-RNA interactions reveals targets of small RNA-mediated gene regulation in Chlamydomonas reinhardtii.Plant & cell physiology · 2025Article
- Mitochondrial support of high rates of photosynthesis.Plant communications · 2025Article
- Regulation of nucleus-encoded trans-acting factors allows orthogonal fine-tuning of multiple transgenes in the chloroplast of Chlamydomonas reinhardtii.Plant biotechnology journal · 2025Article
- Developing a media formulation to sustainFrontiers in bioengineering and biotechnology · 2025Article
- Heterologous Gene Expression in Chlamydomonas reinhardtii Chloroplast by Heterologous Promoters and Terminators, Intercistronic Expression Elements and Minichromosome.Microbial biotechnology · 2024Article
- Protocol to isolate nuclei from Chlamydomonas reinhardtii for ATAC sequencing.STAR protocols · 2024Article
- Assembly and Repair of Photosystem II inPlants (Basel, Switzerland) · 2024Review
- Preferential phosphatidylglycerol synthesis via phosphorus supply through rRNA degradation in the cyanobacterium,Frontiers in plant science · 2024Article
- Article
- Pumping iron: A multi-omics analysis of two extremophilic algae reveals iron economy management.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Current Nuclear Engineering Strategies in the Green MicroalgaLife (Basel, Switzerland) · 2023Review
- A gap-free genome assembly of Chlamydomonas reinhardtii and detection of translocations induced by CRISPR-mediated mutagenesis.Plant communications · 2023Article
2 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Chlamydomonas reinhardtii is a unicellular chlorophyte alga that is widely studied as a reference organism for understanding photosynthesis, sensory and motile cilia, and for development of an algal-based platform for producing biofuels and bio-products. Its highly repetitive, ~205-kbp circular chloroplast genome and ~15.8-kbp linear mitochondrial genome were sequenced prior to the advent of high-throughput sequencing technologies. Here, high coverage shotgun sequencing was used to assemble both organellar genomes de novo. These new genomes correct dozens of errors in the prior genome sequences and annotations. Genome sequencing coverage indicates that each cell contains on average 83 copies of the chloroplast genome and 130 copies of the mitochondrial genome. Using protocols and analyses optimized for organellar transcripts, RNA-Seq was used to quantify their relative abundances across 12 different growth conditions. Forty-six percent of total cellular mRNA is attributable to high expression from a few dozen chloroplast genes. RNA-Seq data were used to guide gene annotation, to demonstrate polycistronic gene expression, and to quantify splicing of psaA and psbA introns. In contrast to a conclusion from a recent study, we found that chloroplast transcripts are not edited. Unexpectedly, cytosine-rich polynucleotide tails were observed at the 3'-end of all mitochondrial transcripts. A comparative genomics analysis of eight laboratory strains and 11 wild isolates of C. reinhardtii identified 2658 variants in the organellar genomes, which is 1/10th as much genetic diversity as is found in the nucleus.
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