Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1066770 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27643504_1.fastq.gz | Fastqsanger.gz | |||
| SRR27643504_2.fastq.gz | Fastqsanger.gz | |||
| SRR27643505_1.fastq.gz | Fastqsanger.gz | |||
| SRR27643505_2.fastq.gz | Fastqsanger.gz | |||
| SRR27643506_1.fastq.gz | Fastqsanger.gz |
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Project description:This study examined differentially expressed (DE) gene transcripts and regulated pathways of two geographically distinct channel catfish (Ictalurus punctatus) strains and one hybrid catfish (I. punctatus x [blue catfish] I. furcatus) strain to test whether one particular catfish type handled thermal stress better. Following a six-week growth experiment, where fish were subjected to daily cycling temperatures of either 27-31M-BM-0C or 32-36M-BM-0C, mimicking pond fluctuations. We sequenced 18 cDNA libraries of liver samples to obtain 61 million reads per library. There were 5,443 DE transcripts and 41,689 regulated pathways. Northern channel catfish had the highest amount of DE transcripts (48.6%), 5 times that of southern channel catfish, and the greatest amount of transcripts with fold changes M-bM-^IM-% 2. The overall amount of temperature-induced DE transcripts between southern hybrid and southern channel catfish was fairly comparable in relation to that of northern channel catfish, however, there were more transcripts up- or downregulated with M-bM-^IM-% 2 fold changes in channel catfish strains compared to the southern hybrid catfish. Results from this study strongly suggest genetic differences between geographic catfish types affect physiological responses to thermal stress. Furthermore, a number of genes were linked to thermal stress tolerance, which may be beneficial for understanding geographic differences in thermal stress tolerance in ectotherms and for strain development of catfish. Hepatic mRNA profiles of three fingerling catfish types following a six week growth experiment of daily cycling temperatures of either 27-31M-BM-0C or 32-36M-BM-0C, mimicking pond fluctuations.
2014-04-23 | E-GEOD-56982 | biostudies-arrayexpress
Project description:This study examined differentially expressed (DE) gene transcripts and regulated pathways of two geographically distinct channel catfish (Ictalurus punctatus) strains and one hybrid catfish (I. punctatus x [blue catfish] I. furcatus) strain to test whether one particular catfish type handled thermal stress better. Following a six-week growth experiment, where fish were subjected to daily cycling temperatures of either 27-31°C or 32-36°C, mimicking pond fluctuations. We sequenced 18 cDNA libraries of liver samples to obtain 61 million reads per library. There were 5,443 DE transcripts and 41,689 regulated pathways. Northern channel catfish had the highest amount of DE transcripts (48.6%), 5 times that of southern channel catfish, and the greatest amount of transcripts with fold changes ≥ 2. The overall amount of temperature-induced DE transcripts between southern hybrid and southern channel catfish was fairly comparable in relation to that of northern channel catfish, however, there were more transcripts up- or downregulated with ≥ 2 fold changes in channel catfish strains compared to the southern hybrid catfish. Results from this study strongly suggest genetic differences between geographic catfish types affect physiological responses to thermal stress. Furthermore, a number of genes were linked to thermal stress tolerance, which may be beneficial for understanding geographic differences in thermal stress tolerance in ectotherms and for strain development of catfish.
2014-04-23 | GSE56982 | GEO
Project description:Catfish farming is the largest aquaculture industry in the U.S., where hybrid catfish produced by channel catfish, Ictalurus punctatus ♀ × blue catfish, I. furcatus ♂, represent >50% of the harvest. Typically, older blue catfish (≥5 years) are selected for artificial fertilization. However, observations at our facilities and reports from hatcheries indicate a high degree of variation in reproductive performance among individuals. Thus, it is essential to establish links between paternal age and reproductive success, as it is apparent that advanced paternal age leads to changes in reproductive performance. Since there are no prior studies regarding the changes in testis transcriptome in blue catfish males during aging, we evaluated global gene expression of testis at age 2,4,7 and 9. Significant differential expressed genes and gene ontology of pairwise comparisons between age 2 and each test age are presented and discussed.
2025-03-17 | GSE290987 | GEO
Project description:Catfish is the most important species in US aquaculture, accounting for 70% of freshwater production. The production of hybrids of female channel catfish (Ictalurus punctatus) and male blue catfish (I. furcatus) constitutes over 50% of the total harvest due to their superior production traits and enhanced disease resistance. However, hybrids cannot be produced naturally, and male must be euthanized for sperm collection. An appropriate storage condition is essential to preserve the sperm’s ability to fertilize eggs during the female spawning season. Cryopreservation is a widely used method for sperm storage. However, it has been shown to affect sperm gene expression in many vertebrate species. A high degree of individual variability among cryopreserved sperm was reported, resulting in huge variations in hatch rate. Since high-quality gametes are the prerequisites for hybrid catfish reproduction, in this study, we investigate the molecular mechanisms underlying male reproductive performance, which is critical for the accurate prediction of hatching rate and offspring performance in hatchery environments.
2025-05-16 | GSE296208 | 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:Channel catfish, Ictalurus punctatus, are the primary cultured species of the catfish industry. Significant losses in production are attributed to bacterial diseases which are challenging to control and new interventions need to be developed. To gain insight into the in situ catfish immune system, we used single-nuclei RNAseq. We produced two single-nuclei atlases from three individual catfish using flow cytometry sorted IgM+ splenic cells. Libraries were prepared using the 10X Genomics system and sequenced on an Illumina sequencer. The reads were aligned to the reference genome (Ip Coco_2.0) using Cell Ranger (v8.0.0).
2025-04-09 | GSE278995 | 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:Walking catfish (Clarias macrocephalus) and channel catfish (Ictalurus punctatus) are freshwater fish species of the Siluriformes order. C. macrocephalus has both gills and modified gill structures serving as an air breathing organ (ABO) which allows them aerial breathing (AB), while I. punctatus does not possess an air-breathing organ (ABO), and thus cannot breathe in air. These two species provide an excellent model for studying the molecular basis of accessory air-breathing organ development in teleost fish. In this study, seven development stages in C. macrocephalus were selected for RNA-seq analysis to compare with channel catfish as the time when air breathing organ developed and became functional. Through comparative genetic contents analysis, 1,458 genes were identified to be present in C. macrocephalus, but absent from I. punctatus. Gene expression analysis and protein-protein intersection (PPI) analysis were performed, 26 genes were selected in C. macrocephalus, including mb, ngb, hbae genes, which are mainly associated with oxygen carrier activity, oxygen binding and heme binding activities. Our work provides a large data resource for exploring the genomic basis of air breathing function in C. macrocephalus and offers an insight into the adaption of aquatic organisms to hypoxia and high ammonia environment.
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Project description:Stomach content of blue catfish (Ictalurus furcatus)
| PRJNA509916 | ENA