Gene rearrangements in snake mitochondrial genomes: highly concerted evolution of control-region-like sequences duplicated and inserted into a tRNA gene cluster

Mitochondrial DNA (mtDNA) regions corresponding to two major tRNA geneclusters were amplified and sequenced for the Japanese pit viper, himehabu.In one of these clusters, which in most vertebrates characterized to datecontains three tightly connected genes for tRNA(Ile), and tRNA(Gln), andtRNA(Met), a sequence of approximately 1.3 kb was found to be insertedbetween the genes for tRNA(Ile) and tRNA(Gln). The insert consists of acontrol-region-like sequence possessing some conserved sequence blocks, andshort flanking sequences which may be folded into tRNA(Pro), tRNA(Phe), andtRNA(Leu) genes. Several other snakes belonging to different families werealso found to possess a control-region-like sequence and tRNA(Leu) genebetween the tRNA(Ile)and tRNA(Gln) genes. We also sequenced a regionsurrounded by genes for cytochrome b and 12S rRNA, where the control regionand genes for tRNA(Pro) and tRNA(Phe) are normally located in the mtDNAs ofmost vertebrates. In this region of three examined snakes, acontrol-region- like sequence exists that is almost completely identical tothe one found between the tRNA(Ile) and tRNA(Gln) genes. The mtDNAs ofthese snakes thus possess two nearly identical control-region-likesequences which are otherwise divergent to a large extent between thespecies. These results suggest that the duplicate state of thecontrol-region- like sequences has long persisted in snake mtDNAs, possiblysince the original insertion of the control-region-like sequence andtRNA(Leu) gene into the tRNA gene cluster, which occurred in the earlystage of the divergence of snakes. It is also suggested that the duplicatedcontrol-region-like sequences at two distant locations of mtDNA haveevolved concertedly by a mechanism such as frequent gene conversion. Thesecondary structures of the determined tRNA genes point to the operation ofsimplification pressure on the T psi C arm of snake mitochondrial tRNAs.