Channel catfish Ictalurus punctatus
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ABSTRACT:
PROVIDER: PRJNA329560 | ENA |
REPOSITORIES: ENA
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Project description:Channel catfish and blue catfish represent two economically important freshwater aquaculture species in the United States. Our study aims to investigate the gene expression differences between these two catfish species by high-throughput RNA sequencing to understand their associated phenotypic differences in growth and disease resistant. Our transcriptomic analyses provide some insights into gene function differences between the two species and the molecular basis of channel catfish growth advantage in the tank culture environment.
2023-11-20 | GSE247918 | GEO
Project description:Seven early developmental stages in channel catfish, Ictalurus punctatus, were selected for transcriptome sequencing and analysis, Differential expression analysis and WGCNA approach was applied. The genes that play vital roles in embryogenesis and regulation of early development in channel catfish were detected. Our work reveals new insights for exploring the underlying mechanisms of channel catfish early development.
2020-08-26 | GSE152002 | GEO
Project description:The hybrid between female channel catfish (Ictalurus punctatus) and male blue catfish (Ictalurus furcatus) is superior in feed conversion, disease resistance, carcass yield, and harvestability compared to both parental species. However, heterosis and heterobeltiosis only occur in pond culture, and channel catfish grow much faster than the other genetic types in small culture units. This environment-dependent heterosis is intriguing, but the underlying genetic mechanisms are not well understood. In this study, phenotypic characterization and transcriptomic analyses were performed in the channel catfish, blue catfish, and their reciprocal F1s reared in tanks. The results showed that the channel catfish is superior in growth-related morphometrics, presumably due to significantly lower innate immune function, as investigated by reduced lysozyme activity and alternative complement activity. RNA-seq analysis revealed that genes involved in fatty acid metabolism/transport are significantly upregulated in channel catfish compared to blue catfish and hybrids, which also contributes to the growth phenotype. Interestingly, hybrids have a 40-80% elevation in blood glucose than the parental species, which can be explained by a phenomenon called transgressive expression (overexpression/underexpression in F1s than the parental species). A total of 1,140 transgressive genes were identified in F1 hybrids, indicating that 8.5% of the transcriptome displayed transgressive expression. Transgressive genes upregulated in F1s are enriched for glycan degradation function, directly related to the increase in blood glucose level. This study is the first to explore molecular mechanisms of environment-dependent hetero-sis/heterobeltiosis in a vertebrate species and sheds light on the regulation and evolution of heterosis vs. hybrid incompatibility.
2022-01-05 | GSE186603 | GEO
Project description:The acute phase response (APR) is a set of metabolic and physiological reactions occurring in the host in response to tissue infection or injury and is a crucial component of the larger innate immune response. The APR is best characterized by dramatic changes in the concentration of a group of plasma proteins known as acute phase proteins (APP) which are synthesized in the liver and which function in a wide range of immunity-related activities. Utilizing a second generation high-density in situ oligonucleotide microarray for catfish, we have surveyed for the first time the APR in channel catfish liver following infection with Edwardsiella ictaluri, a fast-acting bacterial pathogen that causes enteric septicemia of catfish. Our catfish microarray design (28K) builds upon a previous 19K channel catfish array by adding recently sequenced immune transcripts from channel catfish along with 7159 unique sequences from closely-related blue catfish. Analysis of microarray results using a traditional two-fold change in gene expression cutoff and a 10% false discovery rate revealed a well-developed APR in catfish, with particularly high up-regulation (>50-fold) of genes involved in iron homeostasis (i.e. intelectin, hemopexin, haptoglobin, ferritin, and transferrin). Other classical APP upregulated greater than two-fold included coagulation factors, proteinase inhibitors, transport proteins, and complement components. Up-regulation of the majority of the complement cascade including the membrane attack complex components and complement inhibitors was observed. A number of pathogen recognition receptors (PRRs) and chemokines were also differentially expressed in the liver following infection. Validation with real-time PCR confirmed microarray results. Keywords: Disease state analysis
2007-10-23 | GSE6105 | GEO
Project description:Ictalurus punctatus strain:channel catfish Genome sequencing and assembly
| PRJNA319455 | ENA
Project description:Frass is the by-product of the larval meal industry and includes larval waste, exoskeleton sheds, and residual feed ingredients. Experimental frass was derived from the larvae of black solder flies (Hermetia illucens) fed distillers dried grains. A 10-week study was conducted to evaluate the effect of dietary levels of frass on the global gene expression of channel catfish, Ictalurus punctatus. Three diets containing 0, 50, and 300 g frass per kg diet were fed to channel catfish (5.24 ± 0.04 g) in quadruplicate aquaria to apparent satiation twice daily. Intestine (n=12 in pools of 3) and liver (n=12 in pools of 3) tissues were taken from fish at the end of the trial and processed for high-throughput Illumina RNA sequencing (RNAseq). Pairwise comparisons identified both up- and down-regulated genes in frass diets compared to no frass controls.
2024-01-31 | GSE231874 | GEO
Project description:To determine the global gene transcriptional changes in channel catfish anterior kidney after immersion vaccination with attenuated Edwardsiella ictaluri compared to sham vaccinated catfsih control. The attenuated Edwardsiella ictaluri used for vaccination was Aquavac-ESC which was commercially available.
2011-09-10 | GSE32046 | GEO
Project description:To determine the global gene transcriptional changes in vaccinated channel catfish anterior kidney after immersion challenge with a virulent Edwardsiella ictaluri compared to sham vaccinated catfish control. The attenuated Edwardsiella ictaluri used for vaccination was Aquavac-ESC which was commercially available, the virulent strain of Edwardsiella ictaluri is the AL93-58 strain.
2011-10-05 | GSE32588 | GEO
Project description:Clonal channel catfish lymphoid cell lines and mixed lymphocyte cultures (MLC) have proven extremely useful in examining immune responses at the cellular and molecular levels. To date catfish cell cultures have been biologically and phenotypically characterized using a variety of techniques including reverse transcription PCR (RT-PCR), as well as Northern and Southern Blotting. To expand the molecular characterization of these cultures, microarray analysis was employed. Clonal B (3B11), macrophage (42TA), and cytotoxic T cell (TS32.15 and TS32.17) lines and MLC were examined using a cDNA array containing ~ 2500 probes derived from EST libraries prepared from the 42TA macrophage cell line, a MLC, and 5 - 14 day old catfish fry. Analysis showed that each cell line displayed a unique RNA expression profile that included a variety of immune-related genes. Pearson correlation analysis indicated that one cytotoxic T cell line clustered with MLC, whereas a second cytotoxic T cell line was more closely associated with B cells and macrophages The microarray experiments were performed as two biological replicates and two technical replicates. In each case, gene expression in one of the three cell lines (TS32.15, TS32.17, and 42TA) or MLCs was compared against gene expression in the cell line 3B11. Biological replicates were performed on samples that were obtained from two different cell stocks that were frozen at different times and after a different number of subcultures. Technical replicates were performed as dye swaps where the dye was swapped between the test and the control cDNA. If a biological replicate was used, the control cell line also was a biological replicate.
2008-09-20 | E-GEOD-11920 | biostudies-arrayexpress
Project description:A high-density oligonucleotide microarray for channel catfish (Ictalurus punctatus) was designed and produced with Maskless Array Synthesizer technology (MAS). The microarray contained ~379,652 24-mer oligonucleotides covering ~18,999 catfish unique sequences. The global expression profiling of the catfish spleens stimulated by lipopolysaccharide (LPS) for 2h, 4h, 8h and 24h was investigated with the microarray. In the spleen samples, 409 genes were identified to be induced or repressed greater than 2-fold by LPS treatment. Self-organizing maps (SOM) clustering analysis was applied to interpret gene expression patterns, and 84 of these genes were clustered into six expression patterns. Real-time RT-PCR was used to verify the microarray results for 9 selected genes representing different expression levels. The results from real-time RT-PCR were positively correlated (R^2 = 0.87) with the results from the microarray. Channel catfish were injected with LPS or PBS carrier. Fish were killed by anesthesia overdose at 2, 4, 8, or 24h post-injection and total RNA was isolated from spleen. The experiment contained two replicate fish per time point. Relative signal intensities for each feature were generated using the Robust Multi-Array Average algorithm and log2 transformed. Transformed data were then processed using quantile normalization, and the average and std. error for each gene were calculated from the 10 perfectly matched oligos only. After detransformation, the ratio (fold change) was calculated using PBS treated samples (control) as the baseline against LPS-treated samples.
2005-11-30 | E-GEOD-3261 | biostudies-arrayexpress