The Chlamydomonas genome project: a decade on

Ian K Blaby; Crysten E Blaby-Haas; Nicolas Tourasse; Erik F Y Hom; David Lopez; Munevver Aksoy; Arthur Grossman; James Umen; Susan Dutcher; Mary Porter; Stephen King; George B Witman; Mario Stanke; Elizabeth H Harris; David Goodstein; Jane Grimwood; Jeremy Schmutz; Olivier Vallon; Sabeeha S Merchant; Simon Prochnik

doi:10.1016/j.tplants.2014.05.008

The Chlamydomonas genome project: a decade on

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

Authors

Ian K Blaby¹, Crysten E Blaby-Haas¹, Nicolas Tourasse², Erik F Y Hom³, David Lopez⁴, Munevver Aksoy⁵, Arthur Grossman⁵, James Umen⁶, Susan Dutcher⁷, Mary Porter⁸, Stephen King⁹, George B Witman¹⁰, Mario Stanke¹¹, Elizabeth H Harris¹², David Goodstein¹³, Jane Grimwood¹⁴, Jeremy Schmutz¹⁴, Olivier Vallon¹⁵, Sabeeha S Merchant¹⁶, Simon Prochnik¹⁷

Affiliations

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Review

MeSH terms

Alternative Splicing
Chlamydomonas reinhardtii / genetics*
Chromosomes, Plant / genetics*
Genetic Loci
Genome, Plant / genetics*
Genomics*
Models, Genetic
Photosynthesis / genetics
Sequence Analysis, RNA
Transcriptome

Abstract

Publication types

MeSH terms

Grants and funding