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

Abstract

Mitochondrial DNA (mtDNA) regions corresponding to two major tRNA gene clusters were amplified and sequenced for the Japanese pit viper, himehabu. In one of these clusters, which in most vertebrates characterized to date contains three tightly connected genes for tRNA(Ile), and tRNA(Gln), and tRNA(Met), a sequence of approximately 1.3 kb was found to be inserted between the genes for tRNA(Ile) and tRNA(Gln). The insert consists of a control-region-like sequence possessing some conserved sequence blocks, and short flanking sequences which may be folded into tRNA(Pro), tRNA(Phe), and tRNA(Leu) genes. Several other snakes belonging to different families were also found to possess a control-region-like sequence and tRNA(Leu) gene between the tRNA(Ile)and tRNA(Gln) genes. We also sequenced a region surrounded by genes for cytochrome b and 12S rRNA, where the control region and genes for tRNA(Pro) and tRNA(Phe) are normally located in the mtDNAs of most vertebrates. In this region of three examined snakes, a control-region-like sequence exists that is almost completely identical to the one found between the tRNA(Ile) and tRNA(Gln) genes. The mtDNAs of these snakes thus possess two nearly identical control-region-like sequences which are otherwise divergent to a large extent between the species. These results suggest that the duplicate state of the control-region-like sequences has long persisted in snake mtDNAs, possibly since the original insertion of the control-region-like sequence and tRNA(Leu) gene into the tRNA gene cluster, which occurred in the early stage of the divergence of snakes. It is also suggested that the duplicated control-region-like sequences at two distant locations of mtDNA have evolved concertedly by a mechanism such as frequent gene conversion. The secondary structures of the determined tRNA genes point to the operation of simplification pressure on the T psi C arm of snake mitochondrial tRNAs.

Molecular phylogeography of endangered sharp-snouted pitviper (Deinagkistrodon acutus; Reptilia, Viperidae) in Mainland China

“…The ND2 gene region was amplified from the total DNA extracts using the polymerase chain reaction (PCR) with one primer pair. The forward primer was L4437c (5 0 -CAG CTA AAT AAG CTA TCG GGC CCA TAC C-3 0 ) according to Kumazawa et al (1996) with slight modification, and the reverse primer was tRNA-trpR' (5 0 -GGC TTT GAA GGC TYC TAG TTT-3 0 ) according to Ashton and de Queiroz (2001) with slight modification. The PCR contained approximately 100 ng of template DNA, 1 lL of each primer, 5 lL of 10· reaction buffer, 2 lL dNTPs (each 2.5 mM), and 2.0 U of Taq DNA polymerase in total 50 lL volume.…”

The complete mitochondrial DNA sequence and the phylogenetic position of Achalinus meiguensis (Reptilia: Squamata)

“…A pseudogene for tRNA Pro exists in the 5′ vicinity of control region II in some snakes' mtDNAs [2,4,6,23,24] , but it is not found in A. meiguensis. Comparing the snakes' sequences, we discovered that the pseudogene for tRNA Pro was only found in most of the Caenophidia, but not in the Scolecophidia, the Henophidia, and some primitive species of the Caenophidia.…”

“…Snake is shorter than vertebrate in the length of tRNA, which is one of the characteristics of snake mtDNA sequences [2,4] , and Kumazawa [2] suggested the truncation of the TΨC arm should be responsible for this. Our result is congruent with that of Kumazawa, but we also found that the truncation of "DHU" arm in snakes, which is similar to other vertebrates [3,59] , is another important reason.…”

“…Several studies showed that the gross structure of mitochondrial genome in snakes was similar to these of the other vertebrates, which was characterized as: double-stranded, circular DNAs of 16-18 kb, and encodes genes for 13 proteins, 2 rRNAs and 22 tRNAs, as well as having a major noncoding or control region that contains signals for replicating the heavy strand of mtDNA and for transcription [3] . Some unique characteristics in snake mtDNA complete sequences have been clarified previously, including duplicated control regions, a compact size, an elevated evolutionary rate and truncated tRNAs, and other shortened [1,[4][5][6] . Based on morphological studies, the genus Achalinus (Peters, 1869) was put under Xenodermatinae in Colubridae [7,8] .…”

Molecular phylogeography of the asp viper Vipera aspis (Linnaeus, 1758) in Italy: Evidence for introgressive hybridization and mitochondrial DNA capture

“…H690 GTTGAGGCTTGCATGTATA CR Kumazawa et al (1996) L4437b CAGCTAAAA AAGCTATCGGGCCCATACC ND2 Kumazawa et al (1996); Ashton and de Quieroz (2001) HtRNA-Trp GGCTTTGAAGGCTMCTAGTTT ND2 Kumazawa et al (1996); Ashton and de Quieroz (2001) The primers used for each mtDNA marker are reported together with their reference 41 …”