Cite this paper:
SHI Pengju, DONG Shihang, ZHANG Huanjun, WANG Peiliang, NIU Zhuang, FANG Yan. Transcriptome profiling analysis of Mactra veneriformis by deep sequencing after exposure to 2,2',4,4'-tetrabromodiphenyl ether[J]. HaiyangYuHuZhao, 2018, 36(2): 490-507

Transcriptome profiling analysis of Mactra veneriformis by deep sequencing after exposure to 2,2',4,4'-tetrabromodiphenyl ether

SHI Pengju1, DONG Shihang1, ZHANG Huanjun2, WANG Peiliang3, NIU Zhuang1, FANG Yan1
1 School of Agriculture, Ludong University, Yantai 264025, China;
2 Shandong Marine Resource and Environment Research Institute, Shandong Provincial Key Laboratory of Restoration for Marine Ecology, Yantai 264006, China;
3 Weihai Hongrun Marine Technology Co. Ltd., Weihai 264200, China
Abstract:
Polybrominated diphenyl ethers (PBDEs) are ubiquitous global pollutants, which are known to have immune, development, reproduction, and endocrine toxicity in aquatic organisms, including bivalves. 2,2',4,4'-Tetrabromodiphenyl ether (BDE-47) is the predominant PBDE congener detected in environmental samples and the tissues of organisms. However, the mechanism of its toxicity remains unclear. In this study, high-throughput sequencing was performed using the clam Mactra veneriformis, a good model for toxicological research, to clarify the transcriptomic response to BDE-47 and the mechanism responsible for the toxicity of BDE-47. The clams were exposed to 5 μg/L BDE-47 for 3 days and the digestive glands were sampled for high-throughput sequencing analysis. We obtained 127 648, 154 225, and 124 985 unigenes by de novo assembly of the control group reads (CG), BDE-47 group reads (BDEG), and control and BDE-47 reads (CG & BDEG), respectively. We annotated 32 176 unigenes from the CG & BDEG reads using the NR database. We categorized 24 401 unigenes into 25 functional COG clusters and 21 749 unigenes were assigned to 259 KEGG pathways. Moreover, 17 625 differentially expressed genes (DEGs) were detected, with 10 028 upregulated DEGs and 7 597 downregulated DEGs. Functional enrichment analysis showed that the DEGs were involved with detoxification, antioxidant defense, immune response, apoptosis, and other functions. The mRNA expression levels of 26 DEGs were verified by quantitative real-time PCR, which demonstrated the high agreement between the two methods. These results provide a good basis for future research using the M. veneriformis model into the mechanism of PBDEs toxicity and molecular biomarkers for BDE-47 pollution. The regulation and interaction of the DEGs would be studied in the future for clarifying the mechanism of PBDEs toxicity.
Key words:    transcriptomic response|Mactra veneriformis|2,2',4,4'-tetrabromodiphenyl ether   
Received: 2016-12-27   Revised:
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References:
Aarab N, Lemaire-Gony S, Unruh E, Hansen P D, Larsen B K, Andersen O K, Narbonne J F. 2006. Preliminary study of responses in mussel (Mytilus edilus) exposed to bisphenol A, diallyl phthalate and tetrabromodiphenyl ether. Aquatic Toxicology, 78(S):S86-S92.
An L H, Hu J Y, Yang M, Zheng B H, Wei A, Shang J J, Zhao X R. 2011. CYP1A mRNA expression in redeye mullets(Liza haematocheila) from Bohai Bay, China. Marine Pollution Bulletin, 62(4):718-725.
Audic S, Claverie J M. 1997. The significance of digital gene expression profiles. Genome Research, 7(10):986-995.
Barja-Fernández S, Míguez J M, Álvarez-Otero R. 2013.Histopathological effects of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) in the gills, intestine and liver of turbot(Psetta maxima). Ecotoxicology and Environmental Safety, 95:60-68.
Baršienė J, Šyvokienė J, Bjornstad A. 2006. Induction of micronuclei and other nuclear abnormalities in mussels exposed to bisphenol A, diallyl phthalate and tetrabromodiphenyl ether-47. Aquatic Toxicology, 78(S):S105-S108.
Brammell B F, McClain J S, Oris J T, Price D J, Birge W J, Elskus A A. 2010. CYP1A expression in caged rainbow trout discriminates among sites with various degrees of polychlorinated biphenyl contamination. Archives of Environmental Contamination and Toxicology, 58(3):772-782.
Breitholtz M, Wollenberger L. 2003. Effects of three PBDEs on development, reproduction and population growth rate of the harpacticoid copepod Nitocra spinipes. Aquatic Toxicology, 64(1):85-96.
Bresolin T, de Freitas Rebelo M, Bainy A C D. 2005. Expression of PXR, CYP3A and MDR1 genes in liver of zebrafish. Comparative Biochemistry and Physiology Part C:Toxicology & Pharmacology, 140(3-4):403-407.
Cai Y F, Pan L Q, Hu F X, Jin Q, Liu T. 2014. Deep sequencingbased transcriptome profiling analysis of Chlamys farreri exposed to benzo[a]pyrene. Gene, 551(2):261-270.
Chen H H, Zha J M, Liang X F, Bu J H, Wang M, Wang Z J. 2013. Sequencing and de novo assembly of the Asian Clam (Corbicula fluminea) transcriptome using the illumine GAⅡx method. Plos One, 8(11):e79516.
Chen L G, Zhu B R, Guo Y Y, Xu T, Lee J S, Qian P Y, Zhou B S. 2016. High-throughput transcriptome sequencing reveals the combined effects of key e-waste contaminants, decabromodiphenyl ether (BDE-209) and lead, in zebrafish larvae. Environmental Pollution, 214:324-333.
Conesa A, Götz S, García-Gómez J M, Terol J, Talón M, Robles M. 2005. Blast2GO:a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21(18):3 674-3 676.
Contardo-Jara V, Pflugmacher S, Nützmann G, Kloas W, Wiegand C. 2010. The β-receptor blocker metoprolol alters detoxification processes in the non-target organism Dreissena polymorpha. Environmental Pollution, 158(6):2 059-2 066.
Fang Y, Yang H S, Liu B Z, Zhang L B. 2013. Transcriptional response of lysozyme, metallothionein, and superoxide dismutase to combined exposure to heavy metals and bacteria in Mactra veneriformis. Comparative Biochemistry and Physiology Part C:Toxicology & Pharmacology, 157(1):54-62.
Fang Y, Yang H S, Wang T M, Liu B Z, Zhao H L, Chen M Y. 2010. Metallothionein and superoxide dismutase responses to sublethal cadmium exposure in the clam Mactra veneriformis. Comparative Biochemistry and Physiology Part C:Toxicology & Pharmacology, 151(3):325-333.
Fossi M C, Casini S, Bucalossi D, Marsili L. 2008. First detection of CYP1A1 and CYP2B induction in Mediterranean cetacean skin biopsies and cultured fibroblasts by Western blot analysis.MarineEnvironmental Research, 66(1):3-6.
Fossi M C, Casini S, Maltese S, Panti C, Spinsanti G, Marsili L. 2014. An "ex vivo" model to evaluate toxicological responses to mixtures of contaminants in cetaceans:integumentum biopsy slices. Environmental Toxicology, 29(10):1 107-1 121.
Frouin H, Lebeuf M, Hammill M, Masson S, Fournier M. 2010. Effects of individual polybrominated diphenyl ether(PBDE) congeners on harbour seal immune cells in vitro. Marine Pollution Bulletin, 60(2):291-298.
Geick A, Eichelbaum M, Burk O. 2001. Nuclear receptor response elements mediate induction of intestinal MDR1 by rifampin. The Journal of Biological Chemistry, 276(18):14 581-14 587.
Ghosh R, Lokman P M, Lamare M D, Metcalf V J, Burritt D J, Davison W, Hageman K J. 2013. Changes in physiological responses of an Antarctic fish, the emerald rock cod(Trematomus bernacchii), following exposure to polybrominated diphenyl ethers (PBDEs). Aquatic Toxicology, 128-129:91-100.
Giannetti M, Casini S, Marsili L, Maltese S, Campani T, Carletti L, Fossi M C. 2012. First evidence of induction of CYP1A in Caretta caretta skin biopsy slices treated with polycyclic aromatic hydrocarbons, organochlorines and polybrominated diphenyl ethers. Comparative Biochemistry and Physiology Part A:Molecular & Integrative Physiology, 163(S):S18-S19.
Grabherr M G, Haas B J, Yassour M, Levin J Z, Thompson D A, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q D, Chen Z H, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren B W, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29(7):644-652.
Hu X N, Zhang J Q, Jiang Y S, Lei Y X, Lu L G, Zhou J, Huang H Y, Fang D K, Tao G H. 2014. Effect on metabolic enzymes and thyroid receptors induced by BDE-47 by activation the pregnane X receptor in HepG2, a human hepatoma cell line. Toxicology in Vitro, 28(8):1 377-1 385.
Irato P, Piccinni E, Cassini A, Santovito G. 2007. Antioxidant responses to variations in dissolved oxygen of Scapharca inaequivalvis and Tapes philippinarum, two bivalve species from the lagoon of Venice. Marine Pollution Bulletin, 54(7):1 020-1 030.
Iseli C, Jongeneel C V, Bucher P. 1999. ESTScan:a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. In:Park M ed. Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park. p.138-148.
Ji C L, Wu H F, Wei L, Zhao J M, Yu J B. 2013. Proteomic and metabolomic analysis reveal gender-specific responses of mussel Mytilus galloprovincialis to 2,2',4,4'-tetrabromodiphenyl ether (BDE 47). Aquatic Toxicology, 140-141:449-457.
Jin J, Liu W Z, Wang Y, Tang X Y. 2008. Levels and distribution of polybrominated diphenyl ethers in plant, shellfish and sediment samples from Laizhou Bay in China.Chemosphere, 71(6):1 043-1 050.
Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y. 2008. KEGG for linking genomes to life and the environment. Nucleic Acids Research, 36(D1):D480-D484.
Law R J, Allchin C R, de Boer J, Covaci A, Herzke D, Lepom P, Morris S, Tronczynski J, de Wit C A. 2006. Levels and trends of brominated flame retardants in the European environment. Chemosphere, 64(2):187-208.
Liu B, Jiang G F, Zhang Y F, Li J L, Li X J, Yue J S, Chen F, Liu H Q, Li H J, Zhu S P. 2011. Analysis of transcriptome differences between resistant and susceptible strains of the citrus red mite Panonychus citri (Acari:Tetranychidae). PLoS One, 6(12):e28516.
Liu T, Pan L Q, Jin Q, Cai Y F. 2015. Differential gene expression analysis of benzo(a)pyrene toxicity in the clam, Ruditapes philippinarum. Ecotoxicology and Environmental Safety, 115:126-136.
Lv Q Y, Wan B, Guo L H, Zhao L X, Yang Y. 2015. In vitro immune toxicity of polybrominated diphenyl ethers on murine peritoneal macrophages:apoptosis and immune cell dysfunction. Chemosphere, 120:621-630.
Miao J J, Pan L Q, Zhang W H, Liu D, Cai Y F, Li Z. 2014.Identification of differentially expressed genes in the digestive gland of manila clam Ruditapes philippinarum exposed to BDE-47. Comparative Biochemistry and Physiology Part C:Toxicology & Pharmacology, 161:15-20.
Milan M, Matozzo V, Pauletto M, Di Camillo B, Giacomazzo M, Boffo L, Binato G, Marin M G, Patarnello T, Bargelloni L. 2016. Can ecological history influence response to pollutants? Transcriptomic analysis of Manila clam collected in different Venice lagoon areas and exposed to heavy metal. Aquatic Toxicology, 174:123-133.
Moore M N, Allen J I. 2002. A computational model of the digestive gland epithelial cell of marine mussels and its simulated responses to oil-derived aromatic hydrocarbons.Marine Environmental Research, 54(3-5):579-584.
Mortazavi A, Williams B A, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods, 5(7):621-628.
Peters A K, Sanderson J T, Bergman Å, van den Berg M. 2006.Antagonism of TCDD-induced ethoxyresorufin-Odeethylation activity by polybrominated diphenyl ethers(PBDEs) in primary cynomolgus monkey (Macaca fascicularis) hepatocytes. Toxicology Letters, 164(2):123-132.
Santovito G, Boldrin F, Irato P. 2015. Metal and metallothionein distribution in different tissues of the Mediterranean clam Venerupis philippinarum during copper treatment and detoxification. Comparative Biochemistry and Physiology Part C:Toxicology & Pharmacology, 174-175:46-53.
Santovito G, Piccinni E, Cassini A, Irato P, Albergoni V. 2005.Antioxidant responses of the Mediterranean mussel, Mytilus galloprovincialis, to environmental variability of dissolved oxygen. Comparative Biochemistry and Physiology Part C:Toxicology & Pharmacology, 140(3-4):321-329.
Schecter A, Johnson-Welch S, Tung K C, Harris T R, Päpke O, Rosen R. 2007. Polybrominated diphenyl ether (PBDE) levels in livers of U.S. human fetuses and newborns. Journal of Toxicology and Environmental Health, Part A, 70(1):1-6.
Stockholm Convention. 2015. http://chm.pops.int.com.
Veldhoen N, Lowe C J, Davis C, Mazumder A, Helbing C C. 2009. Gene expression profiling in the deep water horse mussel Modiolus modiolus (L.) located near a marine municipal wastewater outfall. Aquatic Toxicology, 93(2-3):116-124.
Watkins R E, Wisely G B, Moore L B, Collins J L, Lambert M H, Williams S P, Willson T M, Kliewer S A, Redinbo M R. 2001. The human nuclear xenobiotic receptor PXR:structural determinants of directed promiscuity. Science, 292(5525):2 329-2 333.
Wollenberger L, Dinan L, Breitholtz M. 2005. Brominated flame retardants:activities in a crustacean development test and in an ecdysteroid screening assay. Environmental Toxicology and Chemistry, 24(2):400-407.
Yang J L, Wei X M, Xu J, Yang D L, Liu X Q, Yang J M, Fang J H, Hu X K. 2012. A sigma-class glutathione S-transferase from Solen grandis that responded to microorganism glycan and organic contaminants. Fish & Shellfish Immunology, 32(6):1 198-1 204.
Ye J, Fang L, Zheng H K, Zhang Y, Chen J, Zhang Z J, Wang J, Li S T, Li R Q, Bolund L, Wang J. 2006. WEGO:a web tool for plotting GO annotations. Nucleic Acids Research, 34(S2):W293-W297.
Ye R R, Lei E N Y, Lam M H W, Chan A K Y, Bo J, van de Merwe J P, Fong A C C, Yang M M S, Lee J S, Segner H E, Wong C K C, Wu R S S, Au D W T. 2012. Genderspecific modulation of immune system complement gene expression in marine medaka Oryzias melastigma following dietary exposure of BDE-47. Environmental Science and Pollution Research, 19(7):2 477-2 487.
Yu L Q, Han Z H, Liu C S. 2015. A review on the effects of PBDEs on thyroid and reproduction systems in fish.General and Comparative Endocrinology, 219:64-73.