Surprisal analysis of genome-wide transcript profiling identifies differentially expressed genes and pathways associated with four growth conditions in the microalga Chlamydomonas

• Published in: PloS one 2018, Vol.13 (4), p.e0195142-e0195142
• Main Authors: Bogaert, Kenny A, Manoharan-Basil, Sheeba S, Perez, Emilie, Levine, Raphael D, Remacle, Francoise, Remacle, Claire
• Format: Article
• Language: English
• Subjects: Algae; Aquatic microorganisms; Biology and Life Sciences; Biosynthesis; Chlamydomonas; Chlamydomonas reinhardtii; Cluster analysis; Clustering; Cultivation; Darkness; Data processing; Environmental conditions; Gene expression; Genes; Genomes; Growth conditions; Life sciences; Light; Metabolism; Methods; Microalgae; NADH; Nicotinamide adenine dinucleotide; Phenotypes; Photosynthesis; Physical chemistry; Physical Sciences; Physiology; Proteomics; Research and Analysis Methods; Ribonucleic acid; RNA; Sciences du vivant; Statistical analysis; Statistical methods; Transcription; Vector quantization
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0195142

The usual cultivation mode of the green microalga Chlamydomonas is liquid medium and light. However, the microalga can also be grown on agar plates and in darkness. Our aim is to analyze and compare gene expression of cells cultivated in these different conditions. For that purpose, RNA-seq data are obtained from Chlamydomonas samples of two different labs grown in four environmental conditions (agar@light, agar@dark, liquid@light, liquid@dark). The RNA seq data are analyzed by surprisal analysis, which allows the simultaneous meta-analysis of all the samples. First we identify a balance state, which defines a state where the expression levels are similar in all the samples irrespectively of their growth conditions, or lab origin. In addition our analysis identifies additional constraints needed to quantify the deviation with respect to the balance state. The first constraint differentiates the agar samples versus the liquid ones; the second constraint the dark samples versus the light ones. The two constraints are almost of equal importance. Pathways involved in stress responses are found in the agar phenotype while the liquid phenotype comprises ATP and NADH production pathways. Remodeling of membrane is suggested in the dark phenotype while photosynthetic pathways characterize the light phenotype. The same trends are also present when performing purely statistical analysis such as K-means clustering and differentially expressed genes.