Light is a key environmental regulator in all photosynthetic organisms. Many studies focused on the physiologic response to changes in light availability of species from the Zygnematophyceae, but the impact of the absence of light and the molecular acclimation process on the other side have been poorly understood. Here we present transcriptomic analyses of Cosmarium crenatum from a polar habitat exposed to darkness. The algae were cultured in dark for one week; cell number and quantum yield of photosystem II (Fv/Fm) were monitored. Cell number was stable, but the Fv/Fm decreased in both groups, darkness-treated and control. Gene expression analysis revealed a strong repression of transcripts associated with photosynthesis, photorespiration and cell wall development. General carbohydrate and lipid metabolism were differentially regulated, but starch is shown to be the primary energy source in these conditions. Additionally, C. crenatum induced mRNA responsible for epigenetic modifications which may be a specific response to an adaption and acclimation to polar conditions. Our study sheds light on the molecular acclimation process to darkness and provides ecological implications for new perspectives in this specialized group of green algae.

High quality RNA is a crucial requirement in a variety of analyses including next generation sequencing, microarray, and gene expression studies. A number of protocols for the extraction of ribonucleic acids from algae are currently in use, but different reagents interfere with buffer capacities and therefore lower the success of the isolations. The diversity of microalgae is reflected in a large variety of biomolecules and so far no standard protocol for the extraction of RNA from these highly divergent groups has been assessed. With this study, 11 conventional protocols are compared and an alternative standardized protocol for the isolation of high quality total RNA is proposed. Furthermore, the extraction method is applied on four different microalgae species of the Chlorophyta, Charophyta, Rhodophyta, and a dinoflagellate. We present an optimized RNA extraction method, yielding total RNA of high purity and integrity from all the investigated protists. The protocol provided in this study is cost‐effective and can assist in future functional genomics, covering an essential step when working with RNA from non‐model microorganisms.