E-GEOD-56982 - Comparative transcriptomics of geographic strains of catfishes exposed to chronic high temperatures

Status
Released on 23 April 2014, last updated on 2 June 2014
Organism
Ictalurus punctatus, Ictalurus punctatus x Ictalurus furcatus
Samples (18)
Protocols (3)
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. Hepatic mRNA profiles of three fingerling catfish types following a six week growth experiment of daily cycling temperatures of either 27-31°C or 32-36°C, mimicking pond fluctuations.
Experiment type
RNA-seq of coding RNA 
Contacts
Brian C Peterson, Heather A Stewart, Kurt C Showmaker, Mark Arick II, Peter J Allen
MINSEQE
Exp. designProtocolsFactorsProcessedSeq. reads
Files
Investigation descriptionE-GEOD-56982.idf.txt
Sample and data relationshipE-GEOD-56982.sdrf.txt
Links