The Chlamydomonas genome project: a decade on

Creative Commons License

Blaby I. K., Blaby-Haas C. E., Tourasse N., Hom E. F. Y., Lopez D., Aksoy M., ...More

TRENDS IN PLANT SCIENCE, vol.19, no.10, pp.672-680, 2014 (SCI-Expanded) identifier identifier identifier

  • Publication Type: Article / Review
  • Volume: 19 Issue: 10
  • Publication Date: 2014
  • Doi Number: 10.1016/j.tplants.2014.05.008
  • Journal Name: TRENDS IN PLANT SCIENCE
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus
  • Page Numbers: pp.672-680
  • Keywords: Chlamydomonas, algae, nomenclature, gene symbols, Phytozome, annotation, EXPRESSED SEQUENCE TAGS, UNIFORM NOMENCLATURE, PROTEOMIC ANALYSIS, ANNOTATION, DATABASE, RESOURCE, REINHARDTII, TOOL, COMPLEMENTATION, GENERATION
  • Akdeniz University Affiliated: No

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.