RNA-seq based whole transcriptome analysis of the cyclopoid copepod Paracyclopina nana focusing on xenobiotics metabolism

Lee, Bo Young; Kim, Hui Su; Choi, Beom Soon; Hwang, Dae Sik; Choi, Ah Young; Han, Jeonghoon; Won, Eun Ji; Choi, Ik Young; Lee, Seung Hwi; Son, Ae; Park, Heum Gi; Lee, Jae Seong

doi:10.1016/j.cbd.2015.04.002

Cited by 24 publications

(16 citation statements)

References 42 publications

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“…One such protein family comprises the Na V s. In arthropods and in particular copepods de novo transcriptomes, incomplete or fragmented genes are common within this family (e.g. see publicly accessible transcriptomes in the following references: [ 23 , 45 , 48 , 52 ] and NCBI Bioprojects PRJEB20069 , PRJNA231234 ). Thus, as a stringent test of transcriptome quality, we assessed the assembly of the L .…”

Section: Resultsmentioning

confidence: 99%

A deep transcriptomic resource for the copepod crustacean Labidocera madurae: A potential indicator species for assessing near shore ecosystem health

et al. 2017

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Coral reef ecosystems of many sub-tropical and tropical marine coastal environments have suffered significant degradation from anthropogenic sources. Research to inform management strategies that mitigate stressors and promote a healthy ecosystem has focused on the ecology and physiology of coral reefs and associated organisms. Few studies focus on the surrounding pelagic communities, which are equally important to ecosystem function. Zooplankton, often dominated by small crustaceans such as copepods, is an important food source for invertebrates and fishes, especially larval fishes. The reef-associated zooplankton includes a sub-neustonic copepod family that could serve as an indicator species for the community. Here, we describe the generation of a de novo transcriptome for one such copepod, Labidocera madurae, a pontellid from an intensively-studied coral reef ecosystem, Kāne‘ohe Bay, Oahu, Hawai‘i. The transcriptome was assembled using high-throughput sequence data obtained from whole organisms. It comprised 211,002 unique transcripts, including 72,391 with coding regions. It was assessed for quality and completeness using multiple workflows. Bench-marking-universal-single-copy-orthologs (BUSCO) analysis identified transcripts for 88% of expected eukaryotic core proteins. Targeted gene-discovery analyses included searches for transcripts coding full-length “giant” proteins (>4,000 amino acids), proteins and splice variants of voltage-gated sodium channels, and proteins involved in the circadian signaling pathway. Four different reference transcriptomes were generated and compared for the detection of differential gene expression between copepodites and adult females; 6,229 genes were consistently identified as differentially expressed between the two regardless of reference. Automated bioinformatics analyses and targeted manual gene curation suggest that the de novo assembled L. madurae transcriptome is of high quality and completeness. This transcriptome provides a new resource for assessing the global physiological status of a planktonic species inhabiting a coral reef ecosystem that is subjected to multiple anthropogenic stressors. The workflows provide a template for generating and assessing transcriptomes in other non-model species.

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Section: Resultsmentioning

confidence: 99%

A deep transcriptomic resource for the copepod crustacean Labidocera madurae: A potential indicator species for assessing near shore ecosystem health

et al. 2017

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“…The whole transcriptome of copepod Paracylipina nana detected transcripts involved in xenobiotic degradation and other metabolisms (Lee et al . ). Freshwater crab, Sinopotamon henanense , detects the presence of cadmium and functions as a biological indicator.…”

Section: Current Status Of Transcriptomics In Aquaculturementioning

confidence: 97%

Transcriptomics in aquaculture: current status and applications

Chandhini

Kumar

2018

Reviews in Aquaculture

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Transcriptomics is the analysis of total RNA transcript in a cell, which gives a broad idea of cellular processes that are active and dormant. Recent advancement in next-generation sequencing technologies like high-throughput mRNA sequencing (RNA-seq) facilitates in deciphering the functional complexity of the whole transcriptome of an organism. In the recent past, transcriptome profiling has been widely used in aquaculture for effective identification and expression analysis of candidate genes involved in growth, reproduction, development, immunity, disease, stress and toxicology. On the paucity of a comprehensive genome sequence, transcriptomics enables the detection of molecular markers such as simple sequence repeats and single-nucleotide polymorphism associated with the trait of interest. This review summarizes the process of transcriptome analysis and the current state of transcriptomics in aquaculture related to diseases and immunity, reproduction and development, growth and nutrition, toxicology and stress. Further, this review highlights the application of transcriptomics, including generation of genetic resources, differential gene expression, analysis of molecular pathways and development of molecular markers.

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“…50,51 To the best of our knowledge, some pesticides, including DDT and its homologues, polycyclic aromatic hydrocarbons (PAHs) and other environmental pollutants are suitable inducers for GSTs. 51,52 4.2 Immune responses of embryos exposed to DDT Similar to most bivalves, green mussel embryos have an innate immune system to defend against various stress factors. 53,54 Innate immunity is the only immunomodulation defence mechanism for marine invertebrates, 55 and circulating haemocytes play a key role.…”

Section: Functional Genes Related To Oxidative Stress and Detoxificationmentioning

confidence: 99%

Differential gene responses in the embryo of the green mussel Perna viridis exposed to dichlorodiphenyltrichloroethane (DDT)

et al. 2017

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The green-lipped mussel, , is considered to be an ideal indicator for marine environmental pollution. Dichlorodiphenyltrichloroethane (DDT), a typical persistent organic pollutant, is extensively distributed in marine environments. However, little is known about the toxic effects of DDT on the embryo of marine animals, particularly in marine bivalves. Using next-generation sequencing technology, we studied embryo after DDT stress at the transcriptome level. A total of 99 202 unigenes were obtained based on the 2383 bp of unigene N50. These differentially expressed genes (DEGs) participated in the various molecular pathways of biological effects, including oxidative stress, detoxification, innate immunity and neurobehavioral disease. Quantitative real-time PCR was performed to verify the mRNA expression of several genes identified by differential gene expression (DGE) analysis. The results indicated that DDT was in induced a dose-dependent manner in the embryo of , and most genes involved in oxidative stress and detoxification were up-regulated by DDT exposure; however, the immunity-related genes were down-regulated, except the genes involved in phagocytosis. Gene expression changes in embryo from provide a preliminary basis to better understand the molecular toxic response mechanisms of embryo to DDT.

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RNA-seq based whole transcriptome analysis of the cyclopoid copepod Paracyclopina nana focusing on xenobiotics metabolism

Cited by 24 publications

References 42 publications

A deep transcriptomic resource for the copepod crustacean Labidocera madurae: A potential indicator species for assessing near shore ecosystem health

A deep transcriptomic resource for the copepod crustacean Labidocera madurae: A potential indicator species for assessing near shore ecosystem health

Transcriptomics in aquaculture: current status and applications

Differential gene responses in the embryo of the green mussel Perna viridis exposed to dichlorodiphenyltrichloroethane (DDT)

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