Journal
TRENDS IN PLANT SCIENCE
Volume 19, Issue 10, Pages 672-680Publisher
ELSEVIER SCIENCE LONDON
DOI: 10.1016/j.tplants.2014.05.008
Keywords
Chlamydomonas; algae; nomenclature; gene symbols; Phytozome; annotation
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Funding
- National Institutes of Health (NIH) [R24 GM092473, R37 GM030626]
- NIH [T32ES015457, GM100753]
- Office of Science of the US Department of Energy [DE-AC02-05CH11231]
- Direct For Biological Sciences
- Div Of Molecular and Cellular Bioscience [0951094] Funding Source: National Science Foundation
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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.
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