The bighead catfish (Clarias macrocephalus) and channel catfish (Ictalurus punctatus) are freshwater species in the Siluriformes order. C. macrocephalus has both gills and modified gill structures serving as an air-breathing organ (ABO), while I. punctatus does not possess such an organ, and cannot breathe in air, providing an excellent model for studying the molecular basis of ABO development in teleost fish. To investigate the critical time window for the development of air-breathing function, seven development stages were selected based on hypoxia challenge results, and RNA-seq was performed upon C. macrocephalus to compare with the non-air-breathing I. punctatus. Five-hundred million reads were generated and 25,239 expressed genes were annotated in C. macrocephalus. Among those, 8675 genes were differentially expressed across developmental stages. Comparative genomic analysis identified 1458 C. macrocephalus specific genes, which were absent in I. punctatus. Gene network and protein-protein interaction analyses identified 26 key hub genes involved in the air-breathing function. Three top candidate genes, mb, ngb, hbae, are mainly associated with oxygen carrying, oxygen binding, and heme binding activities. Our study provides a rich data set for exploring the genomic basis of air-breathing function in C. macrocephalus and offers insights into the adaption to hypoxic environments.

鳙 ( Clarias macrocephalus ) 和鲶鱼 ( Ictalurus punctatus ) 是鲶形目中的淡水物种。C. macrocephalus有鳃和改良的鳃结构作为呼吸器官（ABO），而I. punctatus没有这样的器官，不能呼吸空气，为研究 ABO 发育的分子基础提供了一个很好的模型在硬骨鱼中。为了研究呼吸功能发育的关键时间窗口，根据缺氧挑战结果选择了七个发育阶段，并对C. macrocephalus进行 RNA-seq与非呼吸I. punctatus 进行比较. 在C. macrocephalus中产生了 5 亿个读数，并注释了 25,239 个表达的基因。其中，8675 个基因在不同发育阶段差异表达。比较基因组分析确定了 1458 个C. macrocephalus特定基因，这些基因在I. punctatus中不存在。基因网络和蛋白质-蛋白质相互作用分析确定了 26 个与呼吸功能有关的关键枢纽基因。三大候选基因，MB，NGB，hbae，主要与携带氧气，氧气结合，与血红素结合活动有关。我们的研究为探索C. macrocephalus呼吸功能的基因组基础提供了丰富的数据集 并提供有关对缺氧环境的适应的见解。