The Chlamydomonas genome project: a decade on

• Published in: Trends in plant science Vol. 19; no. 10; pp. 672 - 680
• Main Authors: Blaby, Ian K., Blaby-Haas, Crysten E., Tourasse, Nicolas, Hom, Erik F.Y., Lopez, David, Aksoy, Munevver, Grossman, Arthur, Umen, James, Dutcher, Susan, Porter, Mary, King, Stephen, Witman, George B., Stanke, Mario, Harris, Elizabeth H., Goodstein, David, Grimwood, Jane, Schmutz, Jeremy, Vallon, Olivier, Merchant, Sabeeha S., Prochnik, Simon
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 01.10.2014; Elsevier
• Subjects: algae; Alternative Splicing; annotation; Chlamydomonas; Chlamydomonas reinhardtii; Chlamydomonas reinhardtii - genetics; Chromosomes, Plant - genetics; gene symbols; Genetic Loci; Genome, Plant - genetics; Genomics; Models, Genetic; nomenclature; Photosynthesis - genetics; Phytozome; Sequence Analysis, RNA; Transcriptome; annotation; nomenclature; algae; gene symbols; Chlamydomonas; Phytozome
• ISSN: 1360-1385; 1878-4372
• DOI: 10.1016/j.tplants.2014.05.008

•Chlamydomonas is a model algal system with a mature genome project.•Substantial improvements to the genome assembly and gene models have been made.•Diverse omics data are publicly available centered at Phytozome.net.•Uniform gene symbol and stable gene locus nomenclatures aid researchers. The green alga Chlamydomonas reinhardtii is a popular unicellular organism for studying photosynthesis, cilia biogenesis, and micronutrient homeostasis. Ten years since its genome project was initiated an iterative process of improvements to the genome and gene predictions has propelled this organism to the forefront of the omics era. Housed at Phytozome, the plant genomics portal of the Joint Genome Institute (JGI), the most up-to-date genomic data include a genome arranged on chromosomes and high-quality gene models with alternative splice forms supported by an abundance of whole transcriptome sequencing (RNA-Seq) data. We present here the past, present, and future of Chlamydomonas genomics. Specifically, we detail progress on genome assembly and gene model refinement, discuss resources for gene annotations, functional predictions, and locus ID mapping between versions and, importantly, outline a standardized framework for naming genes.