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

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

Genetics, Cell Biology and Development (TMED)

Research output: Contribution to journal › Review article › peer-review

118 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 language	English (US)
Pages (from-to)	672-680
Number of pages	9
Journal	Trends in Plant Science
Volume	19
Issue number	10
DOIs	https://doi.org/10.1016/j.tplants.2014.05.008
State	Published - Oct 1 2014

Bibliographical note

Publisher Copyright:
© 2014 Elsevier Ltd.

Keywords

Algae
Annotation
Chlamydomonas
Gene symbols
Nomenclature
Phytozome

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Blaby, I. K., Blaby-Haas, C. E., Tourasse, N., Hom, E. F. Y., Lopez, D., Aksoy, M., Grossman, A., Umen, J., Dutcher, S., Porter, M., King, S., Witman, G. B., Stanke, M., Harris, E. H., Goodstein, D., Grimwood, J., Schmutz, J., Vallon, O., Merchant, S. S., & 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

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

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The Chlamydomonas genome project: A decade on

Abstract

Bibliographical note

Keywords

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