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

Research output: Contribution to journalReview articlepeer-review

82 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)672-680
Number of pages9
JournalTrends in Plant Science
Volume19
Issue number10
DOIs
StatePublished - Oct 1 2014

Bibliographical note

Funding Information:
This work was supported by the National Institutes of Health (NIH) R24 GM092473 to S.M. and R37 GM030626 to G.W. I.K.B. and C.B-H. are supported by training grants from the NIH (T32ES015457 and GM100753, respectively). The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract DE-AC02-05CH11231. We thank Stefan Schmollinger, Alizée Malnoë, Patrice Salomé, and Ursula Goodenough for critical reading of the manuscript.

Keywords

  • Algae
  • Annotation
  • Chlamydomonas
  • Gene symbols
  • Nomenclature
  • Phytozome

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