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

Sumida, Masayuki; Kanamori, Yasushi; Kaneda, Hideki; Kato, Yoji; Nishioka, Midori; Hasegawa, Masami; Yonekawa, Hiromichi

doi:10.1266/ggs.76.311

Cited by 101 publications

(84 citation statements)

References 77 publications

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“…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.…”

Section: Dna Sequencingmentioning

confidence: 99%

High mitochondrial diversity within and among populations of Malagasy poison frogs

Vences¹,

Chiari²,

Raharivololoniaina³

et al. 2004

Molecular Phylogenetics and Evolution

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The diurnal, brightly colored, and toxic frogs of the genus Mantella are among the most prominent representatives of the endemic anuran fauna of Madagascar. Especially three closely related species, M. aurantiaca, M. crocea, and M. milotympanum, are intensively collected for the pet trade, although basic data on their natural history and genetic diversity are still lacking. Our phylogenetic analyses based on 2.8 kbp of partial 16S rRNA, 12S rRNA, cytochrome b, and rhodopsin DNA sequences confirmed that these species belong to one of the five major clades in Mantella, the M. madagascariensis group. A haplotype network constructed using 830 bp of cytochrome b in 49 individuals from seven populations revealed that M. milotympanum and M. crocea have largely similar haplotypes sharing, confirming doubts about the species validity of M. milotympanum and indicating independent evolution of bright orange pattern in M. milotympanum and M. aurantiaca. Further, clustering of four individuals of M. aurantiaca from Andranomena with M. crocea suggests incomplete lineage sorting or introgression resulting from secondary contact of refugial populations. AMOVA confirmed significant intrapopulation nucleotide diversity (>20%). These diversity patterns and our field observations indicate relatively large population sizes. Hence, overcollecting is probably a minor problem and conservation efforts should rather focus on saving some large populations from habitat destruction through logging and forest fires.

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Section: Dna Sequencingmentioning

confidence: 99%

High mitochondrial diversity within and among populations of Malagasy poison frogs

Vences¹,

Chiari²,

Raharivololoniaina³

et al. 2004

Molecular Phylogenetics and Evolution

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“…Mt gene rearrangement was reported in marsupials (Pääbo et al, 1991), birds (Mindell et al, 1998;Quinn and Wilson, 1993), reptiles (Kumazawa and Endo, 2004;Macey et al, 1997;Quinn and Mindell, 1996), lampreys (Lee and Kocher, 1995), and fishes (Mabuchi et al, 2004;Inoue et al, 2003;Miya et al, 2001); therefore, mtDNA can be used as a prospective phylogenetic marker (Boore and Brown, 1995;Macey et al, 2000). In anurans, the arrangement of mt genes in basal Archeobatrachia was found to be identical to that observed in typical vertebrates (Roe et al, 1985;San Mauro et al, 2004), whereas in the phylogenetically nested Neobatrachia group, the arrangement of mt genes deviates from the classic vertebrate type (Sumida et al, 2001). Recently, a large number of mt genomes have been reported from the neobatrachian taxon Natatanura (including families of Dicroglossidae, Mantellidae, and Rachophoridae with Nyctibatrachidae and Ranidae; Frost et al, 2006).…”

Section: Introductionmentioning

confidence: 97%

“…Recently, a large number of mt genomes have been reported from the neobatrachian taxon Natatanura (including families of Dicroglossidae, Mantellidae, and Rachophoridae with Nyctibatrachidae and Ranidae; Frost et al, 2006). In Natatanurans, four tRNA mt genes are commonly rearranged from the classic type and these tRNAs form the LTPF tRNA cluster (Sumida et al, 2001;Zhang et al, 2005;Kurabayashi et al, 2006). Further gene rearrangements have been identified in Natatanurans; Rachophoridae and Mantellidae mt genes are highly rearranged, and a large number of rachophorid and mantellid mt genes contain duplicated or triplicated control regions and tRNA genes (Sano et al, 2004(Sano et al, , 2005Kurabayashi et al, 2006Kurabayashi et al, , 2008.…”

Section: Introductionmentioning

confidence: 99%

Complete mitochondrial genomes and novel gene rearrangements in two dicroglossid frogs, Hoplobatrachus tigerinus and Euphlyctis hexadactylus, from Bangladesh

et al. 2010

Self Cite

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We determined the complete nucleotide sequences of mitochondrial (mt) genomes from two dicroglossid frogs, Hoplobatrachus tigerinus (Indian Bullfrog) and Euphlyctis hexadactylus (Indian Green frog). The genome sizes are 20462 bp in H. tigerinus and 20280 bp in E. hexadactylus. Although both genomes encode the typical 37 mt genes, the following unique features are observed: 1) the ND5 genes are duplicated in H. tigerinus that have completely identical sequences, whereas duplicated ND5 genes in E. hexadactylus possessed dissimilar substitutions; 2) duplicated control region (CR) in H. tigerinus has almost identical sequences whereas single control region (CR) was found in E. hexadactylus; 3) the tRNA-Leu (CUN) gene is translocated from the LTPF tRNA cluster to downstream of ND5-1 in H. tigerinus, and the tRNA-Pro gene is translocated from the LTPF tRNA cluster to downstream of CR in E. hexadactylus; 4) pseudo tRNA-Leu (CUN) and tRNA-Pro genes are observed in E. hexadactylus; and 5) two tRNA-Met genes are encoded in both species, as observed in the previously reported dicroglossid mt genomes. Almost all observed gene rearrangements in H. tigerinus and E. hexadactylus can be explained by the tandem duplication and random loss model, except translocation of tRNA-Pro in E. hexadactylus. The novel mt genomic features found in this study may be useful for future phylogenetic studies in the dicroglossid taxa. However, the mt genome with interesting features found in the present study reveal a high level of variation of gene order and gene content, inspiring more research to understand the mechanisms behind gene and genome evolution in the dicroglossid and as well as in the amphibian taxa in future studies.

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“…We did not include Rana nigromaculata (Sumida et al, 2001) in the analyses because this species has a extremely long branch that produces phylogenetic reconstruction artifacts (results not shown). An alignment of 3676 positions was produced.…”

Section: Phylogenetic Relationships Among Jawed Vertebratesmentioning

confidence: 99%

Complete nucleotide sequence of the mitochondrial genome of a salamander, Mertensiella luschani

Zardoya¹,

Málaga-Trillo²,

Veith³

et al. 2003

Gene

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The complete nucleotide sequence (16,650 bp) of the mitochondrial genome of the salamander Mertensiella luschani (Caudata, Amphibia) was determined. This molecule conforms to the consensus vertebrate mitochondrial gene order. However, it is characterized by a long non-coding intervening sequence with two 124-bp repeats between the tRNA Thr and tRNA Pro genes. The new sequence data were used to reconstruct a phylogeny of jawed vertebrates. Phylogenetic analyses of all mitochondrial protein-coding genes at the amino acid level recovered a robust vertebrate tree in which lungfishes are the closest living relatives of tetrapods, salamanders and frogs are grouped together to the exclusion of caecilians (the Batrachia hypothesis) in a monophyletic amphibian clade, turtles show diapsid affinities and are placed as sister group of crocodiles+birds, and the marsupials are grouped together with monotremes and basal to placental mammals. The deduced phylogeny was used to characterize the molecular evolution of vertebrate mitochondrial proteins. Amino acid frequencies were analyzed across the main lineages of jawed vertebrates, and leucine and cysteine were found to be the most and least abundant amino acids in mitochondrial proteins, respectively. Patterns of amino acid replacements were conserved among vertebrates. Overall, cartilaginous fishes showed the least variation in amino acid frequencies and replacements. Constancy of rates of evolution among the main lineages of jawed vertebrates was rejected. D

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

Cited by 101 publications

References 77 publications

High mitochondrial diversity within and among populations of Malagasy poison frogs

High mitochondrial diversity within and among populations of Malagasy poison frogs

Complete mitochondrial genomes and novel gene rearrangements in two dicroglossid frogs, Hoplobatrachus tigerinus and Euphlyctis hexadactylus, from Bangladesh

Complete nucleotide sequence of the mitochondrial genome of a salamander, Mertensiella luschani

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