Deep sequencing-based transcriptome profiling analysis of Chlamys farreri exposed to benzo[a]pyrene

Cai, Yuefeng; Pan, Luqing; Hu, Fengxiao; Qian, Jin; Liu, Tong

doi:10.1016/j.gene.2014.09.003

Cited by 29 publications

(11 citation statements)

References 59 publications

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“…In the light of our earlier studies, the results of this transcriptome information could improve the description of the acute toxicity of high concentrations of OA for some physiological and biochemical processes and provide directions and insights for future studies involving biotoxicity models in scallops. Moreover, in the present study, the calculation and normalization methods of both analyses are different, although they report transcript abundances as fold-changes relative to the control [ 1 ]. The RNA-seq expression values employ Reads Per Kilobase Million (RPKM) for calculation [ 33 ], while qPCR fold-change values employ the mean normalized expressions method and incorporated reference gene to calculate [ 34 ].…”

Section: Discussionmentioning

confidence: 99%

“…The NADPH oxidase is composed of six homologues of the cytochrome subunit (NOX1, NOX3, NOX4, NOX5, DUOX1, and DUOX2), and increased NOX activity also induces a series of pathologies [ 44 ]. Cai et al [ 1 ] found that benzo[a]pyrene (BaP) exposure caused the upregulation of NADPH transcript in Chlamys farreri after three days. The findings of the present study indicated a greater abundance of NOX-3 transcripts in the gills of scallops exposed to OA, suggesting that it induces the activation of the NADPH oxidases, thereby generating more ROS and even cell damage.…”

Section: Discussionmentioning

confidence: 99%

“…The detoxification and biotransformation of exogenous compounds also rests on Phase II and Phase III reactions [ 1 ]. Glutathione- S -transferase (GST), which is a kind of Phase II enzyme, could catalyse the endogenous and exogenous compounds combining with glutathione (GSH) [ 1 , 45 ]. Our previous field studies have shown that GSH levels in the haemolymph of A. irradians exposed to 500 nM OA decreased sharply at 48 hpe [ 12 ].…”

Section: Discussionmentioning

confidence: 99%

“…Bivalves are among the most important commercially exploited marine species in China, sharing 75–80% of the total output of aquatic products in recent years [ 1 ]. Owing to their filter-feeding and sessile habits, worldwide distribution, and diversity of aquatic environments, bivalves are widely used as marine pollution bioindicators [ 2 ].…”

Section: Introductionmentioning

confidence: 99%

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Detoxification- and Immune-Related Transcriptomic Analysis of Gills from Bay Scallops (Argopecten irradians) in Response to Algal Toxin Okadaic Acid

Cheng

Giri

Jun

et al. 2018

Toxins

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To reveal the molecular mechanisms triggered by okadaic acid (OA)-exposure in the detoxification and immune system of bay scallops, we studied differentially-expressed genes (DEGs) and the transcriptomic profile in bay scallop gill tissue after 48 h exposure to 500 nM of OA using the Illumina HiSeq 4000 deep-sequencing platform. De novo assembly of paired-end reads yielded 55,876 unigenes, of which 3204 and 2620 genes were found to be significantly up- or down-regulated, respectively. Gene ontology classification and enrichment analysis of the DEGs detected in bay scallops exposed to OA revealed four ontologies with particularly high functional enrichment, which were ‘cellular process’ (cellular component), ‘metabolic process’ (biological process), ‘immune system process’ (biological process), and ‘catalytic process’ (molecular function). The DEGs revealed that cyclic AMP-responsive element-binding proteins, acid phosphatase, toll-like receptors, nuclear erythroid 2-related factor, and the NADPH2 quinone reductase-related gene were upregulated. In contrast, the expression of some genes related to glutathione S-transferase 1, C-type lectin, complement C1q tumor necrosis factor-related protein, Superoxide dismutase 2 and fibrinogen C domain-containing protein, decreased. The outcomes of this study will be a valuable resource for the study of gene expression induced by marine toxins, and will help understanding of the molecular mechanisms underlying the scallops’ response to OA exposure.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Detoxification- and Immune-Related Transcriptomic Analysis of Gills from Bay Scallops (Argopecten irradians) in Response to Algal Toxin Okadaic Acid

Cheng

Giri

Jun

et al. 2018

Toxins

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show abstract

“…Raw paired-end reads for these three species were downloaded from the SRA database at NCBI ( C . farreri SRR653436 [ 38 ], A . irradians SRX470082 [ 39 ], C .…”

Section: Methodsmentioning

confidence: 99%

Comparative Analysis and Distribution of Omega-3 lcPUFA Biosynthesis Genes in Marine Molluscs

2015

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Recent research has identified marine molluscs as an excellent source of omega-3 long-chain polyunsaturated fatty acids (lcPUFAs), based on their potential for endogenous synthesis of lcPUFAs. In this study we generated a representative list of fatty acyl desaturase (Fad) and elongation of very long-chain fatty acid (Elovl) genes from major orders of Phylum Mollusca, through the interrogation of transcriptome and genome sequences, and various publicly available databases. We have identified novel and uncharacterised Fad and Elovl sequences in the following species: Anadara trapezia, Nerita albicilla, Nerita melanotragus, Crassostrea gigas, Lottia gigantea, Aplysia californica, Loligo pealeii and Chlamys farreri. Based on alignments of translated protein sequences of Fad and Elovl genes, the haeme binding motif and histidine boxes of Fad proteins, and the histidine box and seventeen important amino acids in Elovl proteins, were highly conserved. Phylogenetic analysis of aligned reference sequences was used to reconstruct the evolutionary relationships for Fad and Elovl genes separately. Multiple, well resolved clades for both the Fad and Elovl sequences were observed, suggesting that repeated rounds of gene duplication best explain the distribution of Fad and Elovl proteins across the major orders of molluscs. For Elovl sequences, one clade contained the functionally characterised Elovl5 proteins, while another clade contained proteins hypothesised to have Elovl4 function. Additional well resolved clades consisted only of uncharacterised Elovl sequences. One clade from the Fad phylogeny contained only uncharacterised proteins, while the other clade contained functionally characterised delta-5 desaturase proteins. The discovery of an uncharacterised Fad clade is particularly interesting as these divergent proteins may have novel functions. Overall, this paper presents a number of novel Fad and Elovl genes suggesting that many mollusc groups possess most of the required enzymes for the synthesis of lcPUFAs.

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

et al. 2017

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Deep sequencing-based transcriptome profiling analysis of Chlamys farreri exposed to benzo[a]pyrene

Cited by 29 publications

References 59 publications

Detoxification- and Immune-Related Transcriptomic Analysis of Gills from Bay Scallops (Argopecten irradians) in Response to Algal Toxin Okadaic Acid

Detoxification- and Immune-Related Transcriptomic Analysis of Gills from Bay Scallops (Argopecten irradians) in Response to Algal Toxin Okadaic Acid

Comparative Analysis and Distribution of Omega-3 lcPUFA Biosynthesis Genes in Marine Molluscs

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

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