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ABSTRACT:
PROVIDER: PRJNA839866 | ENA |
REPOSITORIES: ENA
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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 27-31°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: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:Analysis of epigenetic and genetic loci controlling sex determination in channel catfish
| PRJNA553256 | ENA
Project description:The influence of environmental factors, especially temperature, on sex ratio is of great significance to elucidate the mechanism of sex determination. However, the molecular mechanisms by which temperature affects sex determination remains unclear, although a few candidate genes have been found to play a role in the process. In this study, we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171, 1022 and 2921 differentially expressed genes (DEGs) between high temperature and normal temperature were identified at 35, 45 and 60 days post-fertilization (dpf) respectively, revealing that DNA methyltransferases (DNMTs) and heat shock proteins (HSPs) were involved in the heat-exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway that were enriched in individuals after heat treatment included Fanconi anemia pathway, cell cycle, oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat-induced masculinization, and improve our understanding the molecular mechanisms of vertebrate sex determination.
2022-06-21 | GSE201748 | 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:Channel catfish (Ictalurus punctatus) and tra catfish (Pangasianodon hypophthalmus) both belong to the order Siluriformes. Channel catfish does not possess an air-breathing organ (ABO), and thus cannot breathe in the air, while tra catfish is a facultative air-breather and use the swim bladder as its air-breathing organ, which provides for aerial breathing in low oxygen conditions. Tra and channel catfish serve as a great comparative model for studying the transition of life from water to terrestrial living, as well as for understanding genes that are crucial for development of the swim bladder and the function of air-breathing in tra catfish. We selected seven developmental stages in tra catfish for RNA-Seq analysis based on their transition to a stage that could live at 0 ppm oxygen. More than 587 million sequencing clean reads were generated in tra catfish, and a total of 21, 448 unique genes were detected. A comparative genomic analysis was conducted between channel catfish and tra catfish. Gene expression analysis was performed for these tra catfish specific genes. Hypoxia challenge and microtomy experiments collectively suggested that there are critical timepoints for the development of the air-breathing function and swim bladder development stages in tra catfish. Key genes were identified to be the best candidates of genes related to the air-breathing ability in tra catfish. This study provides a large data resource for functional genomic studies in air-breathing function in tra catfish, and sheds light on the adaption of aquatic organisms to the terrestrial environment.
2021-01-12 | GSE154904 | GEO
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:In fish, the sex determining mechanisms can broadly be classified as genotypic (GSD), temperature-dependent (TSD), or genotypic plus temperature effects (GSD+TE). For the fish species with TSD or GSD+TE, extremely high or low temperature can affect its sex determination and differentiation. For long time, the underlying changes in DNA methylation that occur during high or low temperature induced sex reversal have not been fully clarified. In this study, we used Nile tilapia as a model to perform a genome-wide survey of differences in DNA methylation in female and male gonads between control and high temperature induced groups using methylated DNA immunoprecipitation (MeDIP). We identified the high temperature induction-related differentially methylated regions (DMRs), and performed functional enrichment analysis for genes exhibiting DMR. These identified differentially methylated genes were potentially involved in the connection between environmental temperature and sex reversal in Nile tilapia. In this study, four samples (control females, CF; control males, CM; induced females, IF; induced males, IM) were analyzed.
2015-08-27 | E-GEOD-72386 | biostudies-arrayexpress
Project description:In fish, the sex determining mechanisms can broadly be classified as genotypic (GSD), temperature-dependent (TSD), or genotypic plus temperature effects (GSD+TE). For the fish species with TSD or GSD+TE, extremely high or low temperature can affect its sex determination and differentiation. For long time, the underlying changes in DNA methylation that occur during high or low temperature induced sex reversal have not been fully clarified. In this study, we used Nile tilapia as a model to perform a genome-wide survey of differences in DNA methylation in female and male gonads between control and high temperature induced groups using methylated DNA immunoprecipitation (MeDIP). We identified the high temperature induction-related differentially methylated regions (DMRs), and performed functional enrichment analysis for genes exhibiting DMR. These identified differentially methylated genes were potentially involved in the connection between environmental temperature and sex reversal in Nile tilapia.
2015-08-27 | GSE72386 | GEO