A draft genome of the striped catfish, Pangasianodon hypophthalmus, for comparative analysis of genes relevant to development and a resource for aquaculture improvement

• DOI: 10.1186/s12864-018-5079-x
• Publication Date: 2018-10-05T12:16:52Z
• Authors: Oanh T. P. Kim; Phuong T. Nguyen; Eiichi Shoguchi; Kanako Hisata; Thuy T. B. Vo; Jun Inoue; Chuya Shinzato; Binh T. N. Le; Koki Nishitsuji; Miyuki Kanda; Vu H. Nguyen; Hai V. Nong; Noriyuki Satoh
• Keywords: Comparative Genomics

The striped catfish, Pangasianodon hypophthalmus, is a freshwater and benthopelagic fish common in the Mekong River delta. Catfish constitute valuable source of dietary protein. Therefore, they are cultured worldwide, P. hypophthalmus food staple area. However, genetic information about culture stock, unavailable for breeding improvement, although genetics channel Ictalurus punctatus, has been reported. To acquire genome sequence data as useful resource marker-assisted breeding, we decoded draft performed comparative analyses.Using Illumina platform, obtained both nuclear mitochondrial DNA sequences. Molecular phylogeny using confirmed that member family Pangasiidae nested within clade including families Cranoglanididae Ictaluridae. was estimated at approximately 700 Mb, assembled into 568 scaffolds with an N50 14.29 Mbp, to contain ~ 28,600 protein-coding genes, comparable those catfish zebrafish. Interestingly, zebrafish produce gadusol, but genes biosynthesis this sunscreen compound have lost from genomes. differences gene contents between these two catfishes were found vitamin D-binding protein cytosolic phospholipase A2, which only catfish. Hox cluster genomes comprised seven paralogous groups, similar zebrafish, analysis clarified lineage-specific losses A5a, B10a, A11a. Genes insulin-like growth factor (IGF) signaling conserved In addition identification MHC class I sex determination-related loci, hypothetical chromosomes by comparison demonstrated usefulness marker resource.We developed genomic resources Possible conservation development candidates comparing model fish, Danio rerio, Since constituent resembles it likely functions applicable well.