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 article

68 Citations (Scopus)

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

Fingerprint

Chlamydomonas
genome
genomics
genes
genome assembly
prediction
Chlamydomonas reinhardtii
organisms
cilia
transcriptomics
Chlorophyta
homeostasis
photosynthesis
RNA
chromosomes
loci

Keywords

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

Cite this

Blaby, I. K., Blaby-Haas, C. E., Tourasse, N., Hom, E. F. Y., Lopez, D., Aksoy, M., ... Prochnik, S. (2014). The Chlamydomonas genome project: A decade on. Trends in Plant Science, 19(10), 672-680. https://doi.org/10.1016/j.tplants.2014.05.008

The Chlamydomonas genome project : A decade on. / 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.

In: Trends in Plant Science, Vol. 19, No. 10, 01.10.2014, p. 672-680.

Research output: Contribution to journalReview article

Blaby, IK, Blaby-Haas, CE, Tourasse, N, Hom, EFY, Lopez, D, Aksoy, M, Grossman, A, Umen, J, Dutcher, S, Porter, M, King, S, Witman, GB, Stanke, M, Harris, EH, Goodstein, D, Grimwood, J, Schmutz, J, Vallon, O, Merchant, SS & Prochnik, S 2014, 'The Chlamydomonas genome project: A decade on', Trends in Plant Science, vol. 19, no. 10, pp. 672-680. https://doi.org/10.1016/j.tplants.2014.05.008
Blaby IK, Blaby-Haas CE, Tourasse N, Hom EFY, Lopez D, Aksoy M et al. The Chlamydomonas genome project: A decade on. Trends in Plant Science. 2014 Oct 1;19(10):672-680. https://doi.org/10.1016/j.tplants.2014.05.008
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. / The Chlamydomonas genome project : A decade on. In: Trends in Plant Science. 2014 ; Vol. 19, No. 10. pp. 672-680.
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