Ontology highlight
ABSTRACT:
PROVIDER: PRJNA886461 | ENA |
REPOSITORIES: ENA
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Project description:In this study, three small RNA libraries constructed from gonad tissues of XX female, XY male and YY super-male yellow catfish were sequenced by Solexa high-throughput sequencing technology to investigate the expression pattern of sex-biased microRNA. The sequencing data generated a total of 384 conserved miRNAs and 113 potential novel miRNAs, among which 23, 30 and 14 miRNAs were specifically detected in XX ovary, XY testis, and YY testis, respectively. Interestingly, more abundant piRNAs were found in ovary compared to testis in yellow catfish, which phenomenon is also observed in other fish species but opposite in mammalians. We detected a number of microRNAs differentially expressed between ovary and testis, such as miR-21, miR-462, miR-430 and -200 family. When compared the transcriptome between XY and YY testis, we observed relative lower expression of miR-141 and miR-429 in YY testis. Histological analysis indicated that YY super-males have more spermatids and less spermatocytes in spermatogenic cyst than XY males under the same age and culturing conditions. The expression level of miR-141 and 429 coincides with the progression of spermatogenesis both in yellow catfish and human. At last, The expression pattern of nine arbitrarily selected miRNAs detected by quantitative RT-PCR was consistent with the Solexa sequencing results. Our study provides a comprehensive miRNA transcriptome analysis for gonad of yellow catfish with different sex genotypes, and identifies a number of sex-biased miRNAs that are potentially involved in sex differentiation and spermatogenesis.
2016-01-24 | GSE54610 | GEO
Project description:Background: Yellow catfish (Pelteobagrus fulvidraco) is one of the important aquaculture species in China. In recent years, due to the high breeding density, the increasing frequency of feeding, and the excessive addition of feed fat, the excessive deposition of body fat in cultured yellow catfish has become more frequent. MicroRNAs (miRNAs) are an important gene expression regulatory signal molecule that regulates liver fat synthesis and transport and play an important role in fat deposition. However, there is a little research on the mechanism of fatty liver caused by excessive deposition of liver fat. Results: After 60 days of high-fat stress, the growth and feed conversion rate of hybrid yellow catfish (Pelteobagrus fuIvidraco♀×P. vachelli♂) were significantly inhibited, and hepatosomatic index, viscerosomatic index, hepatic triglyceride and cholesterol, and red lipid droplets in liver tissues were increased. Through high-throughput sequencing, we constructed miRNA libraries of high-fat stress at 60d, identified 346 conserved miRNAs and 410 novel miRNAs, among which 13 differentially expressed miRNAs were screened between high-fat diet group and normal-fat diet group. Also, we constructed mRNA transcriptome libraries after high-fat stress. Potential target genes for differentially expressed miRNAs were identified by bioinformatics analysis. Seven miRNA-mRNA pairs were screened. The expression of differential miRNA and mRNA and potential binding sites were analyzed by qRT-PCR and dual luciferase assay. Hybrid yellow catfish could promote the oxidative degradation of liver glucose, reduce fatty acid peroxidation, regulate antioxidant enzyme activity and response of immune and inflammatory to relieve fat deposition and liver stress. Conclusions: The disorders of fat metabolism in liver not only result in feed wastage, increase metabolic burden of yellow catfish, but also cause immune function damage, resulting in a variety of nutritional diseases. The development of this study is to understand the molecular mechanism of hepatic fat deposition in yellow catfish. It has important biological significance for improving protection of liver against stress and healthy culture.
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Project description:Hypoxia is an important environmental stressor in aquatic ecosystems, with increasingly impacts on global biodiversity. Yellow catfish is an economically important farmed fish in China, which has increased dramatically. We investigated the response of hybrid yellow catfish to hypoxia under experimental conditions and focused on the analysis of the differential expression patterns of specific genes associated with hypoxia response by RNA-seq and qPCR analysis. A total of 1556 genes were captured significantly differentially expressed, and were categorized into immune response and energy metabolism. Functional enrichment analysis revealed the NLR signaling pathway play pivotal roles in hypoxia tolerance and resistance. Our study provides important insights into the physiological acclimation, immune response and defense activity of hybrid yellow catfish under hypoxia challenge.
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Project description:In this study, we used next-generation sequencing technologies and tandem mass tags to characterize mRNA-seq, miRNA-seq and proteomic of Pelteobagrus fulvidraco, P. vachelli and hybrid yellow catfish Huangyou-1 (P. fulvidraco female ×P. vachelli male) livers and in doing so, offer deeper insight into the transcriptional and protein changes in heterosis uncovers key roles for miRNAs.
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Project description:Bacillus amyloliquefaciens FZB42 is a representative organism for Gram positive soil bacteria associated with plant roots and beneficial to plant growth. It is of immense importance to understand mechanisms of this class of bacteria adapting to rhizosphere. In this work employing differential RNA sequencing (RNA-seq) and Northern blot, we systematically identified transcription start sites of mRNAs as well as non-coding regulatory RNAs in FZB42. The genes regulated at different growth phases and located in polycistronic operons were also identified. A set of genes were re-annotated. In addition, a sRNA named Bas01 was identified to be involved in Bacillus sporulation and biofilm formation. The result we obtained provides valuable data for investigation of Bacillus gene expression and molecular details of rhizobacterial interaction with host plants. Examination of transcriptome profile of rhizobacterium B. amyloliquefaciens FZB42 grown under six conditions.
2015-10-28 | E-GEOD-66681 | biostudies-arrayexpress
Project description:We report the application of a high-throughput technique, RNA-seq, to study the transcriptomic response of P. chlororaphis and Bacillus amyloliquefaciens growing in co-cultures in King B solid medium
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Project description:High-density aquaculture and over-nutrition may cause fatty liver disease in hybrid yellow catfish, reduce the quality of fish products, and limit the development of the industry. In this experiment, Acanthopanax senticosus powder was used as an additive for hybrid yellow catfish feed. A control group (fed on a diet without A.senticosus) and five groups fed on diets supplemented with A.senticosus (0.5, 1, 2, 4 and 8 g A.senticosus / kg). To study the effects of A.senticosus on the growth performance and physiological parameters of hybrid yellow catfish, and to determine the effect of A.senticosus on the expression of genes related to lipid metabolism in the liver by transcriptome analysis. It was found that dietary supplementation with A.senticosus at 2-4g/kg can promote the growth of yellow catfish, reduce the levels of total cholesterol and triacylglycerol in serum, and increase the activity of fatty acid synthase involved in lipid transport in the liver. Gene expression profiles in the liver were compared between the control group and 4g/kg A.senticosus group, and 5 differentially expressed genes in these groups were identified. Annotation analyses using tools at the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases showed that these five differentially expressed genes were mainly involved in the regulation of fat metabolism. The experimental results show that adding a suitable amount of A.senticosus in the diet can reduce the expression of FADS2, ELOVL2, and PLPP3 genes in the liver and stimulate the expression of CYP24a gene, which will reduce the contents of TG and TC in the body, reduce the deposition of fat in the tissue, and promote lipid Metabolism to achieve the purpose of protecting the liver. Therefore, A.senticosus can be used as a healthy feed additive for hybrid yellow catfish, and the appropriate content in the diet is 2-4g/kg.
2020-07-23 | GSE154894 | GEO
Project description:Transcription profiling by array of Bacillus amyloliquefaciens strain FZB42 after soil extract treatment, at OD600=1.0 and OD600=3.0 respectively.
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