Abstract
The ABC gene family is recognized as one of the largest gene families in all kingdoms of life. Although many genes involved in the ABC superfamily have been annotated from several fish species, information on large sets of the ABC superfamily and their evolutionary characterization are still unclear. In the marine medaka Oryzias melastigma, 50 ABC transporters were identified with bioinformatics-aided in silico analyses, and their full-length cDNA sequences were characterized. Phylogenetic analysis revealed that they could be classified into the eight subfamilies (A–H) that include all members of all ABC subfamilies. Interestingly, several teleosts’ Abcg members were closely clustered with Abch members in a distinctive clade. The abch gene was also observed in the coelacanth and the spotted gar, suggesting that this gene was retained from a bilaterian ancestor and that a gene loss event recently occurred in the tetrapod lineage. In teleosts, the nomenclature of previously annotated abcg genes should be considered carefully, as they form a distinctive clade with the marine medaka abch subfamily and other teleost abch genes, but not with the members of the Abcg subfamily.
Highlights
In the zebrafish (Danio rerio) and the green spotted pufferfish (Tetraodon nigroviridis)[8] while no member of the Abch subfamily has been identified in other teleosts
Comparative evolutionary relationships of the entire ATP-binding cassette (ABC) superfamily have been intensively examined from tetrapods to teleosts (e.g. Danio rerio, Gadus morhua, Gasterosteus aculeatus, Ictalurus punctatus, Latimeria chalumnae, Oreochromis niloticus, Oryzias latipes, Takifugu rubripes, and Tetraodon nigroviridis)[8,10]
Containing reads were examined by BLASTX searches to the non-redundant (NR) database of National Center for Biotechnology Information (NCBI), and subsequently, 50 ABC transporters were identified in the genome information of O. melastigma
Summary
Identification and annotation of O. melastigma ABC transporters. In this study, all NBD-. Full-length sequences of all O. melastigma ABC genes were characterized and registered in the GenBank database (Table 1) after annotation of each gene using in silico analysis (i.e. BLAST search, amino acid similarity and identity comparison, and domain search). The length of these full-length ABC proteins ranged from 611 amino acids (aa) (Abcf2) to 4,758 aa (Abca[12]). Overall composition of the genes seems to be conserved from teleosts to mammals, greater divergence was observed in the ABCA/Abca subfamily, as the mean number of ABCA/Abca members was higher in two mammals (i.e. mouse and human) compared to teleosts (Fig. 2). Abcc[7] (AFV39711) abcc[8] (XP_005803356) abcc[9] (XP_004083272) abcc[7] (XP_004065626) abcc[9] (XP_004067574) abcd[1] (XP_004086440) abcd[2] (XP_004082884) abcd[3] (XP_004080884) abcd[4] (XP_004083921) abce[1] (XP_004079653) abcf[1] (XP_004074386) abcf[2] (XP_004081198) abcf[3] (XP_003457877) abcg[1] (XP_004086643) abcg[2] (XP_004079651) abcg[2] (XP_006787117) abcg[2] (XP_004066087) abcg[4] (XP_004076001) abcg[4] (XP_004076385) abcg[5] (XP_004077344)
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