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

Abstract

BackgroundHarmful 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 (CuSO4) 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 CuSO4 effect on the C. polykrikoides, even other HAB species, have not been investigated. The present study investigated the transcriptional response of C. polykrikoides against CuSO4 treatments, with the aim of providing certain molecular mechanism of CuSO4 effect on the C. polykrikoides blooms.ResultsRNA-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 CuSO4; 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 CuSO4 exposure.ConclusionsThis 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 CuSO4 caused stress; mitochondrion may compensate for photosynthesis efficiency decreasing caused energy deficiency. In addition, various signal transduction pathways may be involved in the CuSO4 induced regulation network in the C. polykrikoides. These data provide the potential transcriptomic mechanism to explain the algicide CuSO4 effect on the harmful dinoflagellate C. polykrikoides.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2341-3) contains supplementary material, which is available to authorized users.

Genome-wide analysis of transcription and photosynthesis inhibition in the harmful dinoflagellate Prorocentrum minimum in response to the biocide copper sulfate

“…Only two antioxidant genes were identified in the present study. This may due to the limited number of gene included in the microarray analysis or the ROS scavenging system of P. minimum may have been damaged by the high concentration of copper; however, many antioxidant genes, especially thioredoxin system genes, have been identified from the dinoflagellate Cochlodinium polykrikoides after CuSO 4 stress (Guo et al, 2016). These results suggest that these antioxidant genes function in the oxidative stress response of P. minimum.…”

Current Knowledge and Recent Advances in Marine Dinoflagellate Transcriptomic Research

“…Recently, high throughput sequencing of the Cochlodinium polykrikoides transcriptome revealed that exposure to the algaecide copper sulfate caused genes related to the photosystem to be downregulated, while most of the mitochondria related genes were upregulated [11]. Prorocentrum minimum also showed low expression of photosynthesis-related genes when exposed to biocide copper sulfate.…”

“…Thus, copper stress on dinoflagellates reduces the efficiency of photosynthesis and leads to a lower growth rate and may induce cells' death. However, Guo et al [11] suggested that upregulation of mitochondria-related genes may serve as a strategy for dinoflagellates to increase the probability of cell survival by boosting the oxidative phosphorylation process.…”

“…Their lifestyle ranges from mixotrophic through to heterotrophic and autotrophic [7][8][9]. They also have been reported to be the major cause of the harmful algae blooms (HABs), sometimes referred to as 'red tide' events in the ocean, and may result in death of marine mammals and affect human health due to the accumulative effect of toxins moving throughout the food chain when contaminated seafood is consumed [10,11].…”

RNA-Seq as an Emerging Tool for Marine Dinoflagellate Transcriptome Analysis: Process and Challenges

“…However, to annotate each of the transcripts as completely as possible requires a powerful computational tool or else the value of generated data will be minimal. In dinoflagellates transcriptomics study, the contig usually annotated by Blast alignment against NCBI non-redundant protein (NR) and nucleotide (NT), Kyoto Encyclopedia of Genes and Genomes (KEGG), SwissProt and InterPro database [34,69,70]. Blast2go is a powerful computational tool for high-throughput functional annotation of RNA sequences and data mining based on Gene Ontology (GO), for a non-model organism with a user-friendly interface and is less labor intensive [71].…”