RNA-seq data and surprisal analysis of icl mutant and control strain of the green microalga Chlamydomonas reinhardtii during day/night cycles

The data presented in this article are associated to the research article “Surprisal analysis of the transcriptomic response of the green microalga Chlamydomonas to the addition of acetate during day/night cycles” (Willamme et al., 2018) [1]. Here the RNA-seq data of the icl mutant, a null mutant of the isocitrate lyase gene, and its control are summarized and the FPKM values are listed. The data were analysed using surprisal analysis and the genes contributing the strongest to the mutant and wild type phenotype are listed. The raw data are accessible at BioProject PRJNA437393 with SRA accession number SRP136101 (experiments SRX3824204–SRX3824249). The raw data set and expression values used for surprisal analysis are made public to enable critical or extended analyses

Surprisal analysis of the transcriptomic response of the green microalga Chlamydomonas to the addition of acetate during day/night cycles

Our study aims to find gene pathways that depend on acetate assimilation under diurnal conditions in the microalga Chlamydomonas. We compare the transcriptome of two strains, one control and one mutant deficient for the glyoxylate cycle essential in acetate metabolism, cultivated under day/night cycles with acetate. We apply surprisal analysis, an information-theoretic approach, to the RNA-seq data. Carrying out the analysis on groups of dark and light phase samples separately allows identifying constraints and gene pathways that discriminate between mutant and control samples. Carbon metabolism is the most important in the light phase for the control strain while the dark phase is enriched in cell division pathways. The mutant phenotype includes genes pathways of stress response and autophagy in the two phases. Cell division pathways are found in the light phase and catabolic pathways in the dark phase, highlighting a rewiring of the mutant transcriptome in these cyclic cultivation conditions

Advances in Genetic Engineering of Microalgae

Hallmann A. Advances in Genetic Engineering of Microalgae. In: Grand Challenges in Algae Biotechnology. Grand Challenges in Biology and Biotechnology. Cham: Springer International Publishing; 2020: 159-221