Dataset Information

De novo transcriptome sequencing and analysis of male, pseudo-male and female yellow perch, Perca flavescens.

ABSTRACT: Transcriptome sequencing could facilitate discovery of sex-biased genes, biological pathways and molecular markers, which could help clarify the molecular mechanism of sex determination and sexual dimorphism, and assist with selective breeding in aquaculture. Yellow perch has unique gonad system and sexual dimorphism and is an alternative model to study mechanism of sex determination, sexual dimorphism and sexual selection. In this study, we performed the de novo assembly of yellow perch gonads and muscle transcriptomes by high throughput Illumina sequencing. A total of 212,180 contigs were obtained, ranging from 127 to 64,876 bp, and N50 of 1,066 bp. The assembly RNA-Seq contigs (?200bp) were then used for subsequent analyses, including annotation, pathway analysis, and microsatellites discovery. No female- and pseudo-male-biased genes were involved in any pathways while male-biased genes were involved in 29 pathways, and neuroactive ligand receptor interaction and enzyme of trypsin (enzyme code, EC: 3.4.21.4) was highly involved. Pyruvate kinase (enzyme code, EC: 2.7.1.40), which plays important roles in cell proliferation, was highly expressed in muscles. In addition, a total of 183,939 SNPs, 11,286 InDels and 41,479 microsatellites were identified. This study is the first report on transcriptome information in Percids, and provides rich resources for conducting further studies on understanding the molecular basis of sex determinations, sexual dimorphism, and sexual selection in fish, and for population studies and marker-assisted selection in Percids.

SUBMITTER: Li YH

PROVIDER: S-EPMC5291366 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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De novo transcriptome sequencing and analysis of male, pseudo-male and female yellow perch, Perca flavescens.

Li Yan-He YH Wang Han-Ping HP Yao Hong H O'Bryant Paul P Rapp Dean D Guo Liang L Waly Eman A EA

PloS one 20170203 2

Transcriptome sequencing could facilitate discovery of sex-biased genes, biological pathways and molecular markers, which could help clarify the molecular mechanism of sex determination and sexual dimorphism, and assist with selective breeding in aquaculture. Yellow perch has unique gonad system and sexual dimorphism and is an alternative model to study mechanism of sex determination, sexual dimorphism and sexual selection. In this study, we performed the de novo assembly of yellow perch gonads ...[more]

PMID: 28158238

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Project description:The current study assessed the effect of dietary canthaxanthin and lycopene supplementation at different concentrations on growth performance and antioxidant status in yellow perch (Perca flavescens). In this regard, fish with initial weight (32 ± 1.0 g) were divided into five groups in triplicate, and fed on carotenoid-free diet (control), canthaxanthin (CTX) (50 and 100 mg/kg diet), and lycopene (200 and 400 mg/kg diet) for 60 days. Growth parameters and antioxidant enzymes were evaluated after 30 and 60 days post feeding. Tissue liver and intestine from six fish per treatment was collected for antioxidant and digestive enzymes analysis. The results revealed a significant increase (P < 0.05) of lipid content in the group fed lycopene at a dietary level 400 mg/kg for 60 days, compared to the control. Moreover, dietary carotenoids exhibited no significant effect on growth performance; this was evidenced by no significant up-regulation of growth hormone (gh) and insulin-like growth factor 1b (igf-1b) genes after 30 and 60 days post feeding. Intestinal lipase and trypsin activities were significantly improved with dietary lycopene especially at a dose of (400 mg/kg diet) for 60 days. Malondialdehyde (MDA) level in liver was also significantly decreased with dietary lycopene (400 mg/kg diet) for 60 days. Hepatic superoxide dismutase (SOD), catalase (CAT), and Glutathione peroxidase (GSH-Px) activities were significantly decreased with dietary CTX, especially at dose (100 mg/kg diet) and lycopene at a concentration of 200 and 400 mg/kg diet after 60 days feeding. Additionally, the immune-related gene interleukin-1 beta (il-1b) mRNA expression level revealed up-regulation in groups fed on CTX at different concentrations for 30 days, and fish fed lycopene at a concentration level 400 mg/kg diet for 60 days. The obtained results concluded that dietary supplementation of canthaxanthin and lycopene could enhance immune response and maintain antioxidants defense of fish. Therefore, it considered as a functional aquafeed ingredient for yellow perch.

Project description:Our main objectives were: 1) to identify transcriptional signatures specific to the exposure to two metals: Ni and Cd; 2) to investigate the mechanisms of toxicity for these two metals; and 3) to develop a predictive tool to identify the sublethal effects of Ni and Cd contaminants in fish sampled from natural environments. The molecular mechanisms underlying nickel (Ni) and cadmium (Cd) toxicity and their specific effects on fish are poorly understood. Documenting gene transcription profiles offers a powerful approach towards identifying the molecular mechanisms affected by these metals and to discover biomarkers of their toxicity. However, confounding environmental factors can complicate the interpretation of the results and the detection of biomarkers for fish captured in their natural environment. In the present study, a 1000 candidate-gene microarray, developed from a previous RNA-seq study on a subset of individual fish from contrasting level of metal contamination, was used to investigate the transcriptional response to metal (Ni and Cd) and non metal (temperature, oxygen, and diet) stressors in yellow perch (Perca flavescens). Specifically, we aimed at 1) identifying transcriptional signatures specific to Ni and Cd exposure, 2) investigating the mechanisms of their toxicity, and 3) developing a predictive tool to identify the sublethal effects of Ni and Cd contaminants in fish sampled from natural environments. A total of 479 genes displayed significantly different transcription levels when temperature varied while 287 and 177 genes were differentially transcribed at different concentrations of Ni and Cd, respectively. These metals were found to mainly affect the transcription level of genes involved in iron metabolism, transcriptional and translational processes, vitamin metabolism, blood coagulation, and calcium transport. In addition, a linear discriminant analysis (LDA) made using gene transcription levels yielded 94% correctly reassigned samples regarding their level of metal contamination, which indicates the potential of the microarray to detect perch response to Cd or Ni effects.

Dataset Information

De novo transcriptome sequencing and analysis of male, pseudo-male and female yellow perch, Perca flavescens.

Publications

De novo transcriptome sequencing and analysis of male, pseudo-male and female yellow perch, Perca flavescens.

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