Functional Genomics of Air Breathing in Catfish

Abstract

Channel catfish (Ictalurus punctatus), tra catfish (Pangasianodon hypophthalmus) and walking catfish (Clarias macrocephalus) all belong to order Siluriformes, but I. punctatus does not possess an air breathing organ (ABO) and thus cannot breath in air, and P. hypophthalmus is a facultative air-breather and uses the swim bladder as its air breathing organ, which can help it conduct aerial breathing in the low oxygen conditions. C. macrocephalus have both gills and modified gill structures serving as an ABO, allowing them to aerial breathing (AB). C. macrocephalus can live in muddy marshes and burrows inside the mudflat during summer periods through air-breathing. These three species serve as a great model for studying the transition of life from water to terrestrial living, as well as understanding the genes which are critical for the functioning of air breathing. In this study, seven early developmental stages in I. punctatus were selected for transcriptome analysis, 22,635 genes were covered with 590 million high-quality RNA-seq reads. Differential expression analysis between neighboring developmental timepoints revealed that the most enriched biological categories were associated with growth, development and morphogenesis. A gene co-expression network constructed using WGCNA approach identified four critical modules. Among some the candidate hub genes, GDF10, FOXA2, HCEA and SYCE3 were closely related with head formation, egg development and transverse central element of synaptonemal complexes. CK1, OAZ2, DARS1 and UBE2V2 were mainly associated with regulation of cell cycle, cell growth, brain development, differentiation and proliferation of enterocytes. IFI44L and ZIP10 were considered to regulate immune activity and control ion transport. TCK1 and TGFB1 were involved in transferring phosphate and regulating cell proliferation. All these genes play vital roles in studying the early development in channel catfish and teleost fish. Seven time points in P. hypophthalmus and C. macrocephalus were selected for RNA-Seq analysis based on their transition to a stage that could live at 0 ppm oxygen. More than 587 M clean reads were ultimately generated in P. hypophthalmus, and 504 M clean reads were retained in C. macrocephalus. A total of 21,448 and 25,239 unique genes were detected in P. hypophthalmus and C. macrocephalus, respectively. Through comparative genomic analysis with I. punctatus, 109 genes were identified to be P. hypophthalmus-specific genes, while 1,458 genes were detected to be specific in C. macrocephalus. Gene expression and network analysis were performed for these specific genes. Hypoxia challenge and microtomy experiments collectively suggested the timepoints for the functioning of air breathing in P. hypophthalmus and C. macrocephalus. Fourteen genes were detected to be important to the functioning of air breathing in P. hypophthalmus, in which, hrg, grp and cx3cl1 genes were ultimately identified to be most related to the formation of air breathing ability in P. hypophthalmus. In addition, twenty-six genes were selected to be candidate genes involved in the formation of air-breathing function in C. macrocephalus, including mb, ngb, hbae genes. This study provides a large data resource for functional genomic studies in air breathing function in P. hypophthalmus and C. macrocephalus, and sheds light on the adaption of aquatic organisms to the terrestrial environment.