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Background  Harmful algal blooms (HABs) caused by the dinoflagellate  Cochlodinium polykrikoides  lead to severe environmental impacts in oceans worldwide followed by huge economic losses. Algicide agent copper sulfate (CuSO 4 ) is regard as an economical and effective agent for HABs mitigation; its biochemical and physiological effects were revealed in  C. polykrikoides . However, molecular mechanisms of CuSO 4  effect on the  C. polykrikoides , even other HAB species, have not been investigated. The present study investigated the transcriptional response of  C. polykrikoides  against CuSO 4  treatments, with the aim of providing certain molecular mechanism of CuSO 4  effect on the  C. polykrikoides  blooms.    Results  RNA-seq generated 173 million reads, which were further assembled to 191,212 contigs. 43.3 %, 33.9 %, and 15.6 % of contigs were annotated with NCBI NR, GO, and KEGG database, respectively. Transcriptomic analysis revealed 20.6 % differential expressed contigs, which grouped into 8 clusters according to  K -means clustering analysis, responding to CuSO 4 ; 848 contigs were up-regulated and 746 contigs were down-regulated more than 2-fold changes from 12 h to 48 h exposure. KEGG pathway analysis of eukaryotic homologous genes revealed the differentially expressed genes (DEGs) were involved in diverse pathway; amongst, the genes involved in the translation, spliceosome, and/or signal transduction genes were highly regulated. Most of photosystem related genes were down-regulated and most of mitochondria related genes were up-regulated. In addition, the genes involved in the copper ion binding or transporting and antioxidant systems were identified. Measurement of chlorophyll fluorescence showed that photosynthesis was significantly inhibited by CuSO 4  exposure.    Conclusions  This study reported the first transcriptome of the  C. polykrikoides . The widely differential expressed photosystem genes suggested photosynthetic machinery were severely affected, and may further contribute to the cell death. Furthermore, gene translation and transcription processes may be disrupted, inhibiting cell growth and proliferation, and possibly accelerating cell death. However, antioxidant systems resistant to CuSO 4  caused stress; mitochondrion may compensate for photosynthesis efficiency decreasing caused energy deficiency. In addition, various signal transduction pathways may be involved in the CuSO 4  induced regulation network in the  C. polykrikoides . These data provide the potential transcriptomic mechanism to explain the algicide CuSO 4  effect on the harmful dinoflagellate  C. polykrikoides .    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-2341-3) contains supplementary material, which is available to authorized users.

bmc genomics

Transcriptomic profiles reveal the genome-wide responses of the harmful dinoflagellate Cochlodinium polykrikoides when exposed to the algicide copper sulfate