Comparative genomic analysis revealed twenty-six candidate genes involved in the air-breathing function of the broadhead catfish Clarias macrocephalus
Walking catfish (Clarias macrocephalus) and channel catfish (Ictalurus punctatus) are freshwater fish species of the Siluriformes order. C. macrocephalus has both gills and modified gill structures serving as an air breathing organ (ABO) which allows them aerial breathing (AB), while I. punctatus does not possess an air-breathing organ (ABO), and thus cannot breathe in air. These two species provide an excellent model for studying the molecular basis of accessory air-breathing organ development in teleost fish. In this study, seven development stages in C. macrocephalus were selected for RNA-seq analysis to compare with channel catfish as the time when air breathing organ developed and became functional. Through comparative genetic contents analysis, 1,458 genes were identified to be present in C. macrocephalus, but absent from I. punctatus. Gene expression analysis and protein-protein intersection (PPI) analysis were performed, 26 genes were selected in C. macrocephalus, including mb, ngb, hbae genes, which are mainly associated with oxygen carrier activity, oxygen binding and heme binding activities.  Our work provides a large data resource for exploring the genomic basis of air breathing function in C. macrocephalus and offers an insight into the adaption of aquatic organisms to hypoxia and high ammonia environment. Overall design: Profile of transcriptome-wide gene expression levels in seven early development stages of Clarias macrocephalus