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The heavy metal pollution in ecosystems is of increasing global concern. The main sources of the metal toxicity are the industrial waste, mining and the use of pesticides containing heavy metals. Out of all heavy metals, mercury (Hg) is considered to be the one, easily accumulated in terrestrial plants as well as aquatic organism. Hg can induce more severe oxidative stress by triggering the production of reactive oxygen species (ROS) and damage macro-molecules. ROS serve not only as dangerous molecules that damage proteins, lipids and DNA but also as signalling molecules in the regulation of biological processes such as biotic and abiotic stress responses, growth and development. This study shows the change in the Chromera velia transcriptome due to Hg stress. C. velia is the recently discovered closest known relative of apicomplexans. Our study shows the first deep transcriptomic analysis of C. velia, specifically focusing on the expression level of the genes involved in detoxification defence systems under heavy metal stress. The results show that in total 1239 genes are differentially expressed. DEGs (Differentially expressed genes) showed overall up-regulation (1,070 genes) and only 169 up-regulated genes in cultures under Mercury stress (Cvel_mer) when compared to the control level (Cvel_cont). The qPCR expression analysis exhibited a positive correlation with the findings of RNA-seq data.