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Comparative transcriptome analysis of catfish swimbladder reveals expression signatures in chamber formation and their response to low oxygen stress




Yang, Yujia

Type of Degree

PhD Dissertation


Fisheries and Allied Aquacultures


The swimbladder is an internal gas-filled organ in teleosts. Its major function is to regulate buoyancy. Swimbladder exhibits great variations in size, shape, number of compartments or chambers among teleosts. However, the genomic control of swimbladder variations is unknown. Channel catfish (Ictalurus punctatus), blue catfish (Ictalurus furcatus), and their F1 hybrids of female channel catfish x male blue catfish (C×B hybrid catfish) provide a good model to investigate the swimbladder morphology, because channel catfish possess a single-chambered swimbladder whereas blue catfish possess a bi-chambered swimbladder; and C×B hybrid catfish possess a bi-chambered swimbladder but with significantly reduced posterior chamber. In Chapter 2, we determined the transcriptional profiles of swimbladder from channel catfish, blue catfish, and C×B hybrid catfish. We examined their transcriptomes at both the fingerling and adult stages. Through comparative transcriptome analysis, approximately 4,000 differentially expressed genes (DEGs) were identified. Among these DEGs, members of the Wnt signaling pathway (wnt1, wnt2, nfatc1, rac2), Hedgehog signaling pathway (shh), and growth factors (fgf10, igf-1) were identified. As these genes were known to be important for branching morphogenesis of mammalian lung and of mammary glands, their association with budding of posterior chamber primordium and progressive development of bi-chambered swimbladder in fish suggested that these branching morphogenesis related genes and their functions in branching are evolutionarily conserved across a broad spectrum of species. Channel catfish is the leading aquaculture species in the US, and one of the reasons for its application in aquaculture is its relatively high tolerance against hypoxia. However, hypoxia can still cause huge economic losses to the catfish industry. Studies on hypoxia tolerance, therefore, are important for aquaculture. Fish swimbladder has been considered as an accessory respiration organ surrounded by a dense capillary countercurrent exchange system. In this regard, we conducted RNA-Seq analysis with swimbladder samples of catfish under hypoxic and normal conditions to determine if swimbladder was responsive to low oxygen treatment, and to reveal genes, their expression patterns and pathways involved in hypoxia responses in catfish. A total of 155 differentially expressed genes (DEGs) were identified from swimbladder of adult catfish, whereas a total of 2,127 DEGs were identified from swimbladder of fingerling catfish, under hypoxic condition as compared to untreated controls. Subsequent pathway analysis revealed that many DEGs under hypoxia were involved in HIF signaling pathway (nos2, eno2, camk2d2, prkcb, cdkn1a, eno1, and tfrc), MAPK signaling pathway (voltage-dependent calcium channel subunit genes), PI3K/Akt/mTOR signaling pathway (itga6, g6pc, and cdkn1a), Ras signaling pathway (efna3 and ksr2), and signaling by VEGF (fn1, wasf3, and hspb1) in catfish swimbladder. This study provided insights into regulation of gene expression and their involved gene pathways in catfish swimbladder in response to low oxygen stresses.