Comparative Transcriptome Analysis of the Swimbladder Reveals Expression Signatures in Response to Hypoxia in Channel Catfish, Ictalurus punctatus

Low oxygen (hypoxia) can have adverse impacts on aquaculture fish production. Catfish is the leading aquaculture species in the US. In spite of the relatively high levels of tolerance of catfish against low oxygen, hypoxia can still lead to huge economic losses due to heavy mortalities. Studies on low oxygen tolerance, therefore, are important for aquaculture.  Fish swimbladder has long been believed to be the homolog of the tetrapod lung, but the molecular evidence is still lacking. In this study, we conducted RNA-Seq analysis using swimbladder samples of catfish under low oxygen and normal conditions to determine if swimbladder was involved in respiration, and to reveal genes, their expression patterns and pathways involved in response to hypoxia in catfish.  A total of 529 million 100bp paired-end reads were generated. The short reads were assembled by Tophat and Cufflinks software into 170,838 contigs using the reference genome sequence as a guide. The average contig length was 3,215 bp and contig N50 was 6,139 bp. The differentially expression genes (DEGs) were identified with respect to oxygen levels and body size. Subsequent function analysis revealed that many DEGs under hypoxia were involved in carbon dioxide transportation, respiration metabolism, stress response, collagen, and immune responses. In addition to these genes, DEGs between fingerling and adult also included adhere junction, growth regulation and signal transduction. Taken together, these results suggested that the teleost swimbladder indeed have functions for respiration, and that the teleost swimbladder resembles in function to the tetrapod lung.