Identification and analysis of recently duplicated genes in channel catfish (Ictalurus punctatus) genome

Abstract

Gene duplication is an important source of genetic innovation and structure and usually associated to the lineage-specific adaptive trait during evolution, such as genes related to immunity, development and reproduction. Channel catfish (Ictalurus punctatus) is the primary aquaculture species in the United States, which represents 70% of the total aquaculture production. However, the set size of duplicated genes and duplication pattern in channel catfish are still less well understood. In this study, a total of 2,130 duplicated gene sets were identified by using predicted mRNA in channel catfish. Similar overall distribution patterns of duplication size were observed among catfish and model fish species (zebrafish, medaka, stickle and Tetraodon) under comparison, significant differences were noted, with catfish harboring the highest percentage (69.4%) of duplicated gene sets with only two copies. A total of 1,128 duplication sets can be characterized with their duplication types with Intra-chromosomal duplications accounting for most proportion. The large number of duplicated genes with low Ks indicated that most of duplicated genes predicted in this study were recently duplicated genes. GO enrichment analysis indicated that GO terms associated to various metabolic and catabolic processes, response to stimuli and signal transduction were over-represented in duplicated genes. When compared with the four model fish species, a total of 239 catfish specific duplicated genes were identified, with 71.1% of duplication sets containing 2 copies and 59.4% of duplicated genes (pairwise) had small Ks values of ≤ 1. These results suggested that catfish species-specific duplicated genes were mostly recent. The catfish species-specific duplicated genes included a set of genes related to immune and stress responses suggesting a mechanism for catfish to adapt to its environment. This study is the first study on surveying genome-wide duplicated genes in channel catfish. This research is not only useful for further catfish whole genome annotation, but also useful for understanding environmental adaption in channel catfish.