Sequence variation and structural conservation in the D-loop region and flanking genes of mitochondrial DNA from Japanese pond frogs.

Abstract

The nucleotide sequences of the D-loop region and its flanking genes of the mitochondrial DNA (mtDNA) from Japanese pond frogs were determined by the methods of PCR, cloning, and sequencing. The frogs belonged to two species, one subspecies, and one local race. The gene arrangements adjacent to the D-loop region were analyzed. The frogs shared a unique mitochondrial gene order that was found in Rana catesbeiana; i.e., cyt b -D-loop region -tRNA Leu(CUN) -tRNA Thr -tRNA Pro -tRNA Phe -12S rRNA. The arrangements of the three tRNA genes of these frogs were different from those of X. laevis, a species which has the same overall structure as in mammals. Highly repetitive sequences with repeat units (16-bp or 17-bp sequence specific for each taxon) were found in the D-loop region. The length of repetitive sequences varied from 0.6 kbp to 1.2 kbp, and caused the extensive size variation in mtDNA. Several short sequence elements such as putative TAS, OH, CSB-1, and CSB-2 were found in the D-loop region of these frogs. The sequences of these short regulatory elements were conserved in R. catesbeiana, X. laevis, and also in human. The comparison of sequence divergences of the D-loop region and its adjacent genes among various taxa revealed that the rates of nucleotide substitutions depend on genes. The nucleotide sequences of the 3'-side segment of the D-loop region were the most variable among taxa, whereas those of the tRNA and 12S rRNA genes were the most conservative.

Complete Nucleotide Sequence and Gene Rearrangement of the Mitochondrial Genome of the Japanese Pond Frog Rana nigromaculata.

“…The repetitive segment (757 bp) consisted of 40 copies of a 16-bp sequence, 3 copies of a 22-bp sequence, and 3 copies of a 17-bp sequence. The same types of large repetitive segments (600 bp ~ 1200 bp) have been reported in the sibling species R. porosa (Sumida et al, 2000b). Differences in the numbers of copies of tandem repeats caused large length variations in the D-loop regions of individual Japanese pond frogs within the R. nigromaculata group (Sumida et al, 2000b).…”

“…The complete sequence of the mitochondrial DNA genome has been determined in only two species Xenopus laevis (Roe et al, 1985) and Typhlonectes natans (Zardoya and Meyer, 2000) among amphibians, whereas partial sequences including multiple gene region of the mtDNA genome have been reported in several amphibian species (Yoneyama, 1987;Yang et al, 1994;Shaffer and McKnight, 1996;Macey et al, 1997;Feller and Hedges, 1998;Sumida et al, 1998Sumida et al, , 2000aMacey et al, 2001). Xenopus shares the conserved vertebrate gene order, whereas several Rana species include gene rearrangements in partial sequences between the control region and the 12S rRNA gene (Sumida et al, 2000b). The present study showed the whole aspects of the mitochondrial gene rearrangements in the Japanese pond frog R. nigromaculata.…”

“…In amphibians, the complete mtDNA sequences have been obtained in only two species, the clawed frog Xenopus laevis (Roe et al, 1985) and the caecilian Typhlonectes natans (Zardoya and Meyer, 2000). Partial sequence data on gene arrangements have been published in several anuran species: Rana catesbeiana (Yoneyama, 1987;Fujii et al, 1988;Nagae, 1988); Rhacophorus taipeianus (Yang et al, 1994); Rana limnocharis (Macey et al, 1997); Rana pipiens (Feller and Hedges, 1998); Rana nigromaculata and Rana porosa (Sumida et al, 2000b); Rana boylii (Macey et al, 2001). Examination of partial sequences from these Rana species mtDNAs suggests that frog mtDNA has a similar gene content but different genomic organization, and that several gene rearrangements have occurred in anurans.…”

Complete nucleotide sequence and gene rearrangement of the mitochondrial genome of the bell-ring frog, Buergeria buergeri (family Rhacophoridae)

“…The tRNA cluster upstream of the 12S rRNA gene was also identified in the Japanese pond frog, Rana nigromaculata (Sumida et al, 2001) (Fig. 3) and other known ranid frogs (Yoneyama, 1987;Macey et al, 1997;Sumida et al, 2000). However, the rearrangement of the ND5 gene has not been seen in other amphibians sequenced previously.…”

High mitochondrial diversity within and among populations of Malagasy poison frogs

“…For the population genetic part of our study, we developed variants of universal primers that succeeded amplifying a large part of the moderately variable cytochrome b gene in Mantella. Attempts of amplifying and sequencing the presumably more variable control region in Mantella were unsuccessful, probably because ranoid frogs can be characterised by important length polymorphisms of this gene (Sumida et al, 2000) and by a genomic rearrangement that led to the absence of conservative priming sites between the cytochrome b and control region genes (Macey et al, 1997;Sumida et al, 2000Sumida et al, , 2001.…”