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Additional file 2.

Genomic dataset for the endolithic green alga Ostreobium. Ostreobium699_1D.cds.fasta - CDS sequences Ostreobium699_1D.function.tsv - Gene function annotation (Best hit Uniprot and KEGG) Ostreobium699_1D.gff - Gene model in gff3 format Ostreobium699_1D.genome.fasta - Genome scaffold sequences Ostreobium699_1D.protein.faa - Protein sequences, Ostreobium quekettii genome data updated in December 2020., {"references":["Cintia Iha, Katherine E. Dougan, Javier A. Varela, Viridiana Avila, Christopher J. Jackson, Kenny A. Bogaert, Yibi Chen, Louise M. Judd, Ryan Wick, Kathryn E. Holt, Marisa M. Pasella, Francesco Ricci, Sonja I. Repetti, Mónica Medina, Vanessa R. Marcelino, Cheong Xin Chan, Heroen Verbruggen (2021) Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium, Current Biology, in press."]}

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.