To better understand the mechanisms by which algae respond to light spectrum, we investigated the plasticity of pigment composition and gene expression (i.e., whether pigment composition and expression level changes) in the cryptophyte Rhodomonas salina grown in different spectral environments, expecting that R. salina would respond to maximize their capacity to capture available light. We asked the following questions: 1) How do the concentrations of pigments change in response to different spectral irradiance but equal intensity? and 2) How does gene expression vary among different spectral environments? We examined the pigment and transcriptional responses for the following spectral comparisons: blue vs. red light, green vs. red, and blue vs. green. The blue vs. red light comparison represented the widest energy difference between spectra (as one blue photon is more energetic than one red photon) and reflects distinct habitats in the natural world. Green vs. red light maximized the differences between the expected light absorption of all photosynthetic pigments, where blue vs. green light comparisons represented minimum energetic differences.</p><p>Our transcriptional responses were investigated at three different scales. First, we examined expression of transcripts that encode the peptide components of cryptophyte phycobiliproteins, predicting that they would correlate with concentration of the pigment and maximize available light capture. Second, we examined expression of 99 genes that were a priori identified as participating in light capture or photosynthesis, predicting that these loci would be most sensitive to light spectrum. Third, we examined genome-wide expression to identify molecular processes that interact with light spectrum but may not have obvious connections to light capture or photosynthesis. We further sought to link our assessment of pigment plasticity (change in pigment composition) and expression plasticity (change in expression level) by testing for correlations between the two across our entire experiment.