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Transcriptome analysis of male and female Sebastiscus marmoratus.

ABSTRACT: BACKGROUND:The rockfish Sebastiscus marmoratus, which is widely distributed in the East Sea and the South Sea of China, is a sensitive model for the toxic effects and mechanisms of marine contaminants. To gain a global view of the molecular mechanism(s) whereby gene expression may influence sexual dimorphism in S. marmoratus, and to develop a database for further toxicological studies, we performed a large-scale transcriptome study. METHODOLOGY/PRINCIPAL FINDINGS:The Illumina DNA sequencing platform was employed to obtain 27,559,578 and 25,821,126 reads from two cDNA libraries generated from adult male and female S. marmoratus, respectively. Transcriptome de novo assembly was carried out with the short reads assembling program-SOAPdenovo. The reads assembled into 78,675 unigenes, of which 38,677 showed homology to existing protein sequences. Clusters of orthologous groups, gene orthology, and the Kyoto Encyclopedia of Genes and Genomes annotations were performed to better understand the functions of these unigenes. There were 1,209 potential sex differentially expressed unigenes, with 1,049 predicted to be differentially expressed in females and 160 in males. Fifteen randomly chosen unigenes were confirmed using real-time PCR as female or male predominantly expressed genes. CONCLUSIONS/SIGNIFICANCE:This is the first report of an annotated transcriptome of S. marmoratus and identification of sex differentially expressed genes. These data will be of interest to researchers using this model. This work also provides an archive for future studies in molecular mechanisms of sexual dimorphism and evolution and can be used in comparative studies of other fish.

SUBMITTER: Sun L

PROVIDER: S-EPMC3507777 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Transcriptome analysis of male and female Sebastiscus marmoratus.

Sun Lingbin L Wang Chonggang C Huang Lixing L Wu Meifang M Zuo Zhenghong Z

PloS one 20121127 11

<h4>Background</h4>The rockfish Sebastiscus marmoratus, which is widely distributed in the East Sea and the South Sea of China, is a sensitive model for the toxic effects and mechanisms of marine contaminants. To gain a global view of the molecular mechanism(s) whereby gene expression may influence sexual dimorphism in S. marmoratus, and to develop a database for further toxicological studies, we performed a large-scale transcriptome study.<h4>Methodology/principal findings</h4>The Illumina DNA ...[more]

PMID: 23209808

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Project description:Simple Summary Changes in salinity can have an impact on the physiological processes of fish. In this study, RNA-seq sequencing was used to detect and analyze the differential gene expression of Sebastiscus marmoratus in salinity fluctuations and to explore the genes and pathways related to salinity stress. The results demonstrated that pik3r6b, cPLA2γ-like, and WSB1 were differentially expressed in all three groups. All three genes were highly expressed in the high-salt group, with wsb1 being more expressed than pik3r6b and cPLA2γ-like. The results of this study provide some basic theoretical references for the salinity adaptation mechanism of Sebastiscus marmoratus. Abstract The marbled rockfish, Sebastiscus marmoratus, belongs to the euryhaline fish and is an oviparous scleractinian fish. There are few studies on the adaptation mechanism, functional genes, and related pathways of S. marmoratus and salinity. The results showed that a total of 72.1 GB of clean reads were obtained and all clean reads annotated a total of 25,278 Unigenes, of which 2,160 were novel genes. Compared to 20‰, 479 and 520 differential genes were obtained for 35‰ and 10‰, respectively. Gene ontology (GO) enrichment analysis revealed significant enrichment in protein binding, ion binding, ATP binding, and catalytic activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that differentially expressed genes significantly expressed under salinity stress were mainly involved in the pathways of the cytochrome P450 metabolism of xenobiotics, tryptophan metabolism, cellular senescence, and calcium signaling pathways. Among them, pik3r6b, cPLA2γ-like, and WSB1 were differentially expressed in all three groups, and they were associated with apoptosis, inflammation, DNA damage, immune regulation, and other physiological processes. Six differentially expressed genes were randomly selected for qRT-PCR validation, and the results showed that the transcriptomic data were of high confidence.

Dataset Information

Transcriptome analysis of male and female Sebastiscus marmoratus.

Publications

Transcriptome analysis of male and female Sebastiscus marmoratus.

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