Rainbow trout mitochondrial DNA: sequence and structural characteristics of the non-coding control region and flanking tRNA genes

Abstract

We have determined the sequence of the 1003-bp control region (also referred to as the ‘displacement-loop region’) and flanking tRNA genes in the mitochondrial DNA (mtDNA) of the rainbow trout, Oncorhynchus mykiss. This region has the same overall structure (i.e., trnT- trnP-control region- trnF) as in mammalian and amphibian ( Xenopus laevis) mitochondrial (mt)DNAs. The trout control region contains apparent homologues of the conserved sequence blocks (CSB) and termination-associated sequences identified in all other vertebrate mtDNA control regions; however, it is distinguished by having an imperfect direct repeat (68/73 bp; 77% positional identity) in the right domain (proximal to the phenylalanine tRNA gene), downstream from CSB-3 in the direction of heavy-strand transcription. Within the control region, rainbow trout mtDNA shares considerable sequence similarity with the mtDNAs of Atlantic cod, Gadus morhua (Johansen et al., Nucleic Acids Res. 18 (1990) 411–419] and white sturgeon, Acipenser transmontanus (Buroker et al., Genetics 124 (1990) 157-163). The highest level of identity in pairwise comparisons is 60–70% over about 80 bp in the right domain (encompassing CSB-2 and CSB-3). About 270 bp comprising the central domain of the control region (encompassing a polypyrimidine tract) are more moderately conserved (55–60% identity in pairwise comparisons), while the left domain is highly divergent. Comparison of five trout mitochondrial tRNA sequences with their human and X. laevis homologues emphasizes the strong A+T substitution bias shown by the human sequences.