title: The Chlamydomonas genome project: a decade on.
abstract: 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.
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.
authors.forename: Ian K
authors.initials: IK
authors.lastname: Blaby
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.
authors.forename: Crysten E
authors.initials: CE
authors.lastname: Blaby-Haas
authors.affiliation: Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 7141, Institut de Biologie Physico-Chimique, Paris, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Tourasse
authors.affiliation: Department of Molecular and Cellular Biology and FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA.
authors.forename: Erik F Y
authors.initials: EF
authors.lastname: Hom
authors.affiliation: Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, USA.
authors.forename: David
authors.initials: D
authors.lastname: Lopez
authors.affiliation: Department of Plant Biology, Carnegie Institute for Science, 260 Panama Street, Stanford, CA, USA.
authors.forename: Munevver
authors.initials: M
authors.lastname: Aksoy
authors.affiliation: Department of Plant Biology, Carnegie Institute for Science, 260 Panama Street, Stanford, CA, USA.
authors.forename: Arthur
authors.initials: A
authors.lastname: Grossman
authors.affiliation: Donald Danforth Plant Science Center, St Louis, MO, USA.
authors.forename: James
authors.initials: J
authors.lastname: Umen
authors.affiliation: Department of Genetics, Washington University School of Medicine, St Louis, MO, USA.
authors.forename: Susan
authors.initials: S
authors.lastname: Dutcher
authors.affiliation: Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA.
authors.forename: Mary
authors.initials: M
authors.lastname: Porter
authors.affiliation: Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA.
authors.forename: Stephen
authors.initials: S
authors.lastname: King
authors.affiliation: Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
authors.forename: George B
authors.initials: GB
authors.lastname: Witman
authors.affiliation: lnstitut für Mikrobiologie und Genetik, Universität Göttingen, Göttingen, Germany.
authors.forename: Mario
authors.initials: M
authors.lastname: Stanke
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708, USA.
authors.forename: Elizabeth H
authors.initials: EH
authors.lastname: Harris
authors.affiliation: US Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors.forename: David
authors.initials: D
authors.lastname: Goodstein
authors.affiliation: HudsonAlpha Genome Sequencing Center, Huntsville, AL 35806, USA.
authors.forename: Jane
authors.initials: J
authors.lastname: Grimwood
authors.affiliation: HudsonAlpha Genome Sequencing Center, Huntsville, AL 35806, USA.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Schmutz
authors.affiliation: Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 7141, Institut de Biologie Physico-Chimique, Paris, France; Université Pierre et Marie Curie, Paris, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Vallon
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA.
authors.forename: Sabeeha S
authors.initials: SS
authors.lastname: Merchant
authors.affiliation: US Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA. Electronic address: seprochnik@lbl.gov.
authors.forename: Simon
authors.initials: S
authors.lastname: Prochnik
mesh_terms: D017398:Alternative Splicing; D016825:Chlamydomonas reinhardtii / Q000235:genetics*; D032461:Chromosomes, Plant / Q000235:genetics*; D056426:Genetic Loci; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics; D008957:Models, Genetic; D010788:Photosynthesis / Q000235:genetics; D017423:Sequence Analysis, RNA; D059467:Transcriptome
keywords: Chlamydomonas; Phytozome; algae; annotation; gene symbols; nomenclature