Format

Send to

Choose Destination
Trends Plant Sci. 2014 Oct;19(10):672-80. doi: 10.1016/j.tplants.2014.05.008. Epub 2014 Jun 17.

The Chlamydomonas genome project: a decade on.

Author information

1
Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.
2
Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 7141, Institut de Biologie Physico-Chimique, Paris, France.
3
Department of Molecular and Cellular Biology and FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA.
4
Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, USA.
5
Department of Plant Biology, Carnegie Institute for Science, 260 Panama Street, Stanford, CA, USA.
6
Donald Danforth Plant Science Center, St Louis, MO, USA.
7
Department of Genetics, Washington University School of Medicine, St Louis, MO, USA.
8
Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA.
9
Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA.
10
Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
11
lnstitut für Mikrobiologie und Genetik, Universität Göttingen, Göttingen, Germany.
12
Department of Biology, Duke University, Durham, NC 27708, USA.
13
US Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
14
HudsonAlpha Genome Sequencing Center, Huntsville, AL 35806, USA.
15
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.
16
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.
17
US Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA. Electronic address: seprochnik@lbl.gov.

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.

KEYWORDS:

Chlamydomonas; Phytozome; algae; annotation; gene symbols; nomenclature

PMID:
24950814
PMCID:
PMC4185214
DOI:
10.1016/j.tplants.2014.05.008
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Elsevier Science Icon for PubMed Central
Loading ...
Support Center