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Channel catfish Ictalurus punctatus

ABSTRACT: Bacterial 16S rRNA V4 amplicons representing intestinal microbiota of channel catfish across developmental ontogeny (3, 65, 125, 193 dph), dietary changes (FM control and three alternative formulations), and/or host-genetics (three strains of blue and channel catfish). Raw sequence reads

PROVIDER: PRJNA329560 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3939140_1.fastq.gz	Fastqsanger.gz
	SRR3939140_2.fastq.gz	Fastqsanger.gz
	SRR3939150_1.fastq.gz	Fastqsanger.gz
	SRR3939150_2.fastq.gz	Fastqsanger.gz
	SRR3939160_1.fastq.gz	Fastqsanger.gz

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Environmental dependent heterosis and transgressive gene expression in reciprocal hybrids between the channel catfish Ictalurus punctatus and the blue catfish Ictalurus furcatus

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

Deep transcriptomic analysis reveals the dynamic developmental progression during early development of channel catfish (Ictalurus punctatus)

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

Ictalurus punctatus strain:channel catfish

Project description:Ictalurus punctatus strain:channel catfish Genome sequencing and assembly

| PRJNA319455 | ENA

Transcriptome analysis revealed potential mechanisms of channel catfish growth advantage over blue catfish in tank culture environment

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

Expression Profiles of Cloned Channel Catfish (Ictalurus punctatus) Lymphoid Cell Lines and a Mixed Lymphocyte Culture

2008-09-20 | GSE11920 | GEO

Expression Profiles of Cloned Channel Catfish (Ictalurus punctatus) Lymphoid Cell Lines and a Mixed Lymphocyte Culture

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

Evasion of Mucosal Defenses During Aeromonas hydrophila Infection of Channel Catfish (Ictalurus puncatus) Skin

Project description:The mucosal surfaces of fish serve as the first-line of defense against the myriad of aquatic pathogens present in the aquatic environment. The immune repertoire functioning at these interfaces is still poorly understood. The skin, in particular, must process signals from several fronts, sensing and integrating environmental, nutritional, social, and health cues. Pathogen invasion can disrupt this delicate homeostasis with profound impacts on signaling throughout the organism. Here, we investigated the transcriptional effects of virulent A. hydrophila infection in channel catfish skin, Ictalurus punctatus. We utilized an 8X60K Agilent microarray to examine gene expression profiles at critical early timepoints following challenge—2 h, 8 h, and 12 h. Expression of a total of 2,168 unique genes was significantly perturbed during at least one timepoint. We observed dysregulation of a number of genes involved in antioxidant, cytoskeletal, immune, junctional, and nervous system pathways. In particular, A. hydrophila infection rapidly altered a number potentially critical lectins, chemokines, interleukins, and other mucosal factors in a manner predicted to enhance its ability to adhere and invade the catfish host.

2015-01-01 | GSE40733 | GEO

Gene expression profiling at the single nuclei level of channel catfish spleen

Project description:Channel catfish, Ictalurus punctatus, is an important model U.S. aquaculutre species. Given its role in food production, the catfish immune response to industry-relevant pathogens has been extensively studied and has provided crucial information on innate and adaptive immune function during disease progression. To further examine the channel catfish immune system, single-nuclei RNA sequencing on whole spleens from three adult individuals was performed. Spleen cell suspensions were prepared by passing tissues through cell sieves. Single-cell RNAseq libraries were then prepared using the 10X Genomics Chromium X with the Next GEM Single Cell 3’ Reagents and sequenced 2x150bp on an Illumina sequencer. Each demultiplexed library was aligned to the CoCo_2.0 channel catfish reference assembly, filtered, and counted to generate feature-barcode matrices. Cluster analysis allowed for the identification of multiple cell types including erythrocytes, hematopoietic stem cells, B cells, T/NK cells, myeloid lineage derivatives, plasma cells and endothelial cells. The majority of cells detected were erythrocytes, which are nucleated in teleost fish.

2024-10-02 | GSE268023 | GEO

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Project description:Channel catfish sex determination

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Project description:Channel catfish Testis Transcriptome

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