Genomic Amplification and Ovary-Specific Expression of Zona Pellucida Genes in Channel Catfish and Blue Catfish

Channel catfish (Ictalurus punctatus) is the most important aquaculture species in the United States, with the interspecific hybrid made from mating female channel catfish with male blue catfish (I. furcatus) being the predominant genotype for the catfish industry. While studying the mechanisms of their reproductive isolation, we determined zona pellucida (ZP) genes in both species. While ZP genes are well known for their ovary-specific expression in higher vertebrates such as mammals, the site of their expression in fish varies depending on species. In this study, we annotated the ZP genes in channel catfish and blue catfish and conducted phylogenetic analysis. We found that ZP genes are highly amplified in the catfish genomes, with ZP3- and ZP4-like genes being the most abundant in the genomes, derived from tandem and segmental duplications. A total of 39 and 49 ZP genes (including 4 and 5 pseudogenes) in the blue catfish genome and channel catfish genome were identified, respectively. Expression analysis using RNA-Seq revealed ovary-specific expression in females, with no expression in the gonadal tissues of males, nor in any other tissues of either males or females. RT-PCR analysis indicated that the ZP genes were not expressed until 90 days post fertilization, consistent with the timing of oogenesis of the developing gonad. Single-nucleus RNA-seq (snRNA-Seq) confirmed expression of ZP genes only in oocytes. Future studies are warranted to determine the molecular mechanisms of sex-, tissue-, and time-specific expression of ZP genes, especially in relation to various taxa within teleost fish.