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Chlamydomonas reinhardtii is a unicellular green member of the algae used as a model organism for photosynthesis and for the structure and function of eukaryotic flagella. A typical motile vegetative cell has two anterior flagella, a large cup-shaped chloroplast and a light-sensing eyespot. These features bring propulsion, light sensing and photosynthesis together in one experimentally tractable cell.^[ref]

Its flagella contain the same basic microtubule machinery as motile cilia in animals. This is an evolutionary relationship between organelles; bacterial flagella use a different construction. In the genome study published in 2007, researchers sequenced its nuclear genome and compared predicted proteins across organisms with different cellular capabilities. Genes shared by organisms with flagella, but absent from comparison organisms lacking them, supplied candidates for flagellar assembly and function. Comparisons with proteins experimentally found in flagella helped test those candidates.^[ref]

A photosynthetic alga can therefore illuminate defects in human cilia, while also providing a system for studying chloroplast biology.

Sabeeha S. Merchant studies photosynthesis, metabolism and how organisms manage essential metals. Her laboratory uses Chlamydomonas reinhardtii, a single-celled green alga, to investigate responses to limitations of iron and copper. Such limitations raise a concrete biochemical question: which essential tasks can a biological cell maintain when several proteins compete for a scarce chemical element? ^[ref]

Merchant is the first author of the 2007 report of the approximately 120-million-base-pair nuclear genome of Chlamydomonas reinhardtii. The team used comparative genomics to identify candidate genes associated with chloroplasts and flagella. The organism is revealing because it combines photosynthesis with motile flagella: comparisons with photosynthetic and nonphotosynthetic organisms can help distinguish these functional groups. Shared occurrence across species suggests candidate functions; experimental tests are still needed to establish what an individual protein does.^[ref]