Access to the Chlamydomonas reinhardtii genome provides the means to pursue fundamental genomics-based research of relevance to algae, land plants, and animal lineages. Of the 17,741 gene models, the function of most is only of limited knowledge, thus undermining our ability to truly understand the biology of this alga, and plants at large. Transcriptomes, proteomes, and phenomes can each provide clues by presenting a global snapshot image of the behavior of the cell under specific conditions. Herein we describe the history of functional genomics, how it is being applied to Chlamydomonas, and discuss the resources available for the experimental validation of function predictions.

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.