Complete mitochondrial DNA sequence of the endangered frog Odorrana ishikawae (family Ranidae) and unexpected diversity of mt gene arrangements in ranids

Atsushi Kurabayashi, Natsuhiko Yoshikawa, Naoki Sato, Yoko Hayashi, Shohei Oumi, Tamotsu Fujii, Masayuki Sumida

Research output: Contribution to journalArticle

45 Citations (Scopus)

Abstract

We determined the complete nucleotide sequence of the mitochondrial (mt) genome of an endangered Japanese frog, Odorrana ishikawae (family Ranidae). We also sequenced partial mt genomes of three other Odorrana and six ranid species to survey the diversity of genomic organizations and elucidate the phylogenetic problems remaining in this frog family. The O. ishikawae mt genome contained the 37 mt genes and single control region (CR) typically found in vertebrate mtDNAs, but the region of Light-strand replication origin (OL) was triplicated in this species. Four protein-encoding genes (atp6, nd2, nd3, and nd5) were found to have high sequence divergence and to be usable for population genetics studies on this endangered species. Among the surveyed ranids, only two species (Rana and Lithobates) manifested the typical neobatrachian-type mt gene arrangement. In contrast, relatively large gene rearrangements were found in Amolops, Babina, and Staurois species; and translocations of single tRNA genes (trns) were observed in Glandirana and Odorrana species. Though the inter-generic and interspecific relationships of ranid taxa remain to be elucidated based on 12S and 16S rrn sequence data, some of the derived mt gene orders were found to have synapomorphic features useful for solving problematic ranid phylogenies. The tandem duplication and random loss (TDRL) model, the traditional model for mt gene rearrangement, failed to easily explain several of the mt gene rearrangements observed here. Indeed, the recent recombination-based gene rearrangement models seemed to be more suitable for this purpose. The high frequency of gene translocations involving a specific trn block (trnH-trnS1) and several single tRNA genes suggest that there may be a retrotranslocation in ranid mt genomes.

Original languageEnglish
Pages (from-to)543-553
Number of pages11
JournalMolecular Phylogenetics and Evolution
Volume56
Issue number2
DOIs
Publication statusPublished - 2010 Aug 1
Externally publishedYes

Fingerprint

Ranidae
Gene Order
Mitochondrial Genes
Mitochondrial DNA
Mitochondrial Genome
frog
Anura
mitochondrial DNA
Gene Rearrangement
frogs
nucleotide sequences
Transfer RNA
gene
genes
Genes
genome
Endangered Species
Replication Origin
Population Genetics
Phylogeny

Keywords

  • Gene rearrangement
  • Mitochondrial genome
  • Odorrana
  • Ranidae

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

Cite this

Complete mitochondrial DNA sequence of the endangered frog Odorrana ishikawae (family Ranidae) and unexpected diversity of mt gene arrangements in ranids. / Kurabayashi, Atsushi; Yoshikawa, Natsuhiko; Sato, Naoki; Hayashi, Yoko; Oumi, Shohei; Fujii, Tamotsu; Sumida, Masayuki.

In: Molecular Phylogenetics and Evolution, Vol. 56, No. 2, 01.08.2010, p. 543-553.

Research output: Contribution to journalArticle

Kurabayashi, Atsushi ; Yoshikawa, Natsuhiko ; Sato, Naoki ; Hayashi, Yoko ; Oumi, Shohei ; Fujii, Tamotsu ; Sumida, Masayuki. / Complete mitochondrial DNA sequence of the endangered frog Odorrana ishikawae (family Ranidae) and unexpected diversity of mt gene arrangements in ranids. In: Molecular Phylogenetics and Evolution. 2010 ; Vol. 56, No. 2. pp. 543-553.
@article{b5349e2054a34166b71979efe030edf9,
title = "Complete mitochondrial DNA sequence of the endangered frog Odorrana ishikawae (family Ranidae) and unexpected diversity of mt gene arrangements in ranids",
abstract = "We determined the complete nucleotide sequence of the mitochondrial (mt) genome of an endangered Japanese frog, Odorrana ishikawae (family Ranidae). We also sequenced partial mt genomes of three other Odorrana and six ranid species to survey the diversity of genomic organizations and elucidate the phylogenetic problems remaining in this frog family. The O. ishikawae mt genome contained the 37 mt genes and single control region (CR) typically found in vertebrate mtDNAs, but the region of Light-strand replication origin (OL) was triplicated in this species. Four protein-encoding genes (atp6, nd2, nd3, and nd5) were found to have high sequence divergence and to be usable for population genetics studies on this endangered species. Among the surveyed ranids, only two species (Rana and Lithobates) manifested the typical neobatrachian-type mt gene arrangement. In contrast, relatively large gene rearrangements were found in Amolops, Babina, and Staurois species; and translocations of single tRNA genes (trns) were observed in Glandirana and Odorrana species. Though the inter-generic and interspecific relationships of ranid taxa remain to be elucidated based on 12S and 16S rrn sequence data, some of the derived mt gene orders were found to have synapomorphic features useful for solving problematic ranid phylogenies. The tandem duplication and random loss (TDRL) model, the traditional model for mt gene rearrangement, failed to easily explain several of the mt gene rearrangements observed here. Indeed, the recent recombination-based gene rearrangement models seemed to be more suitable for this purpose. The high frequency of gene translocations involving a specific trn block (trnH-trnS1) and several single tRNA genes suggest that there may be a retrotranslocation in ranid mt genomes.",
keywords = "Gene rearrangement, Mitochondrial genome, Odorrana, Ranidae",
author = "Atsushi Kurabayashi and Natsuhiko Yoshikawa and Naoki Sato and Yoko Hayashi and Shohei Oumi and Tamotsu Fujii and Masayuki Sumida",
year = "2010",
month = "8",
day = "1",
doi = "10.1016/j.ympev.2010.01.022",
language = "English",
volume = "56",
pages = "543--553",
journal = "Molecular Phylogenetics and Evolution",
issn = "1055-7903",
publisher = "Academic Press Inc.",
number = "2",

}

TY - JOUR

T1 - Complete mitochondrial DNA sequence of the endangered frog Odorrana ishikawae (family Ranidae) and unexpected diversity of mt gene arrangements in ranids

AU - Kurabayashi, Atsushi

AU - Yoshikawa, Natsuhiko

AU - Sato, Naoki

AU - Hayashi, Yoko

AU - Oumi, Shohei

AU - Fujii, Tamotsu

AU - Sumida, Masayuki

PY - 2010/8/1

Y1 - 2010/8/1

N2 - We determined the complete nucleotide sequence of the mitochondrial (mt) genome of an endangered Japanese frog, Odorrana ishikawae (family Ranidae). We also sequenced partial mt genomes of three other Odorrana and six ranid species to survey the diversity of genomic organizations and elucidate the phylogenetic problems remaining in this frog family. The O. ishikawae mt genome contained the 37 mt genes and single control region (CR) typically found in vertebrate mtDNAs, but the region of Light-strand replication origin (OL) was triplicated in this species. Four protein-encoding genes (atp6, nd2, nd3, and nd5) were found to have high sequence divergence and to be usable for population genetics studies on this endangered species. Among the surveyed ranids, only two species (Rana and Lithobates) manifested the typical neobatrachian-type mt gene arrangement. In contrast, relatively large gene rearrangements were found in Amolops, Babina, and Staurois species; and translocations of single tRNA genes (trns) were observed in Glandirana and Odorrana species. Though the inter-generic and interspecific relationships of ranid taxa remain to be elucidated based on 12S and 16S rrn sequence data, some of the derived mt gene orders were found to have synapomorphic features useful for solving problematic ranid phylogenies. The tandem duplication and random loss (TDRL) model, the traditional model for mt gene rearrangement, failed to easily explain several of the mt gene rearrangements observed here. Indeed, the recent recombination-based gene rearrangement models seemed to be more suitable for this purpose. The high frequency of gene translocations involving a specific trn block (trnH-trnS1) and several single tRNA genes suggest that there may be a retrotranslocation in ranid mt genomes.

AB - We determined the complete nucleotide sequence of the mitochondrial (mt) genome of an endangered Japanese frog, Odorrana ishikawae (family Ranidae). We also sequenced partial mt genomes of three other Odorrana and six ranid species to survey the diversity of genomic organizations and elucidate the phylogenetic problems remaining in this frog family. The O. ishikawae mt genome contained the 37 mt genes and single control region (CR) typically found in vertebrate mtDNAs, but the region of Light-strand replication origin (OL) was triplicated in this species. Four protein-encoding genes (atp6, nd2, nd3, and nd5) were found to have high sequence divergence and to be usable for population genetics studies on this endangered species. Among the surveyed ranids, only two species (Rana and Lithobates) manifested the typical neobatrachian-type mt gene arrangement. In contrast, relatively large gene rearrangements were found in Amolops, Babina, and Staurois species; and translocations of single tRNA genes (trns) were observed in Glandirana and Odorrana species. Though the inter-generic and interspecific relationships of ranid taxa remain to be elucidated based on 12S and 16S rrn sequence data, some of the derived mt gene orders were found to have synapomorphic features useful for solving problematic ranid phylogenies. The tandem duplication and random loss (TDRL) model, the traditional model for mt gene rearrangement, failed to easily explain several of the mt gene rearrangements observed here. Indeed, the recent recombination-based gene rearrangement models seemed to be more suitable for this purpose. The high frequency of gene translocations involving a specific trn block (trnH-trnS1) and several single tRNA genes suggest that there may be a retrotranslocation in ranid mt genomes.

KW - Gene rearrangement

KW - Mitochondrial genome

KW - Odorrana

KW - Ranidae

UR - http://www.scopus.com/inward/record.url?scp=77953139952&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77953139952&partnerID=8YFLogxK

U2 - 10.1016/j.ympev.2010.01.022

DO - 10.1016/j.ympev.2010.01.022

M3 - Article

C2 - 20102742

AN - SCOPUS:77953139952

VL - 56

SP - 543

EP - 553

JO - Molecular Phylogenetics and Evolution

JF - Molecular Phylogenetics and Evolution

SN - 1055-7903

IS - 2

ER -