Catfish genomic studies: Progress and perspectives

Catfish is the primary aquaculture species in the United States. Its genome research has been conducted for almost two decades, with the ultimate goal to enhance genetic improvement programs, and better understand the biological characteristics of catfish and evolution. Major progress has been made including development of large-scale molecular markers, construction of high-density genetic maps, BAC-based physical maps, and integration of genetic maps with physical maps. Large-scale expressed sequence tags have been generated from both channel catfish and blue catfish. Microarray platforms have been developed for the analysis of genome expression. Large numbers of BAC end sequences have been generated. Repeat structures in the catfish genome have been characterized. Rapid progress in high-throughput sequencing technology and the simultaneous development of bioinformatics tools facilitated the progress of catfish genome studies. Based on such considerable tools and resources, we have completed a high-quality reference genome sequence of channel catfish and its genome annotation. This reference genome sequence is a historical landmark of catfish research as it opens the real first step of the long march toward genetic enhancement. Followed by this great achievement, the research community needs to focus on aquaculture performance and production traits, taking advantage of the unprecedented genome resources and technology to make real progress toward genetic improvements of aquaculture brood stocks.