Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Ictalurus punctatus Ictalurus furcatus

PROVIDER: GSE247918 | GEO | 2023/11/20

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

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

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

| PRJNA1040907 | ENA

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

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

Global assessment of the acute phase response in channel catfish after infection with a Gram negative bacterium

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

Ictalurus punctatus strain:channel catfish

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

| PRJNA319455 | ENA

Expression analysis of channel catfish anterior kidney at 48h post immersion vaccination with attenuated Edwardsiella ictaluri

2011-09-10 | GSE32046 | 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

Expression analysis of channel catfish anterior kidney at 48h post immersion vaccination with attenuated Edwardsiella ictaluri

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. A six chip study using total RNA samples including 3 control and 3 vaccinated samples. Each RNA sample used for microarray was poold fish anterior kidney samples (5 fish anterior kidney samples were pooled as one). Each chip measrues the expression level of 65,182 genes. For each sequence, 3 probes were selected. Two copies were prepared on arrays.

2011-09-09 | E-GEOD-32046 | biostudies-arrayexpress

Expression analysis of channel catfish anterior kidney at 48h post immersion challenge of vaccinated fish (28 days post vaccination with attenuated Edwardsiella ictaluri) with virulent E. ictaluri

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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data