Transcriptome Analysis of Tra Catfish (Pangasianodon hypophthalmus) Early Development Provides Novel Insights for the Terrestrial Adaptation

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. Profile of transcriptome-wide gene expression levels in seven early development stages of Pangasianodon hypophthalmus