The complete DNA sequence of the mitochondrial genome of the self-fertilizing fish Rivulus marmoratus (Cyprinodontiformes, Rivulidae) and the first description of duplication of a control region in fish

Lee, Jae Seong; Miya, Masaki; Lee, Yong Sung; Kim, Chul Geun; Park, Eun Ho; Aoki, Yasunobu; Nishida, Mutsumi

doi:10.1016/s0378-1119(01)00765-x

Cited by 93 publications

(76 citation statements)

References 31 publications

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“…This evidence suggests that the duplicated control regions are undergoing concerted evolution. The existence of two control regions has been reported in the following metazoans: snakes (Kumazawa et al, 1998), Komodo dragon (Kumazawa and Endo, 2004), parrots (Eberhard et al, 2001), fishes (Lee et al, 2001, Inoue et al, 2003, sea cucumbers (Arndt and Smith, 1998), and metastriate ticks (Black and Roehrdanz, 1998). High sequence similarity between duplicated control regions has been observed in all of these cases.…”

Section: Discussionmentioning

confidence: 97%

Complete nucleotide sequence of the mitochondrial genome of Schlegel's tree frog Rhacophorus schlegelii (family Rhacophoridae): duplicated control regions and gene rearrangements

et al. 2005

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The complete nucleotide sequence (21,359 bp) of the mitochondrial DNA of the rhacophorid frog Rhacophorus schlegelii was determined. The gene content, nucleotide composition, and codon usage of this genome corresponded to those typical of vertebrates. However, the Rh. schlegelii genome was unusually large due to the inclusion of two control regions and the accumulation of lengthy repetitive sequences in these regions. The two control regions had 97% sequence similarity over 1,510 bp, suggesting the occurrence of concerted sequence evolution. Comparison of the gene organizations among anuran species revealed that the mitochondrial gene arrangement of Rh. schlegelii diverged from that of typical vertebrates but was similar to that of Buergeria buergeri. The positions of the tRNA-Leu(CUN) and tRNA-Thr genes were exchanged between Rh. schlegelii and B. buergeri . Based on parsimonious consideration and the basal phylogenetic position of B. buergeri , these genes seemed to have been rearranged in an ancestral lineage leading to Rh. schlegelii .

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Section: Discussionmentioning

confidence: 97%

Complete nucleotide sequence of the mitochondrial genome of Schlegel's tree frog Rhacophorus schlegelii (family Rhacophoridae): duplicated control regions and gene rearrangements

et al. 2005

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“…Various non-coding regions have been reported from fish mitochondrial DNAs: tandem repeats (Lunt et al 1998), duplication of CR (Lee et al 2001), intergenic spacers (Shields & Gust 1995, Bakke et al 1999, and tRNA pseudogenes (Mabuchi et al 2004). Exact alignment among nucleotide sequences of non-coding regions is rather difficult due to the limited length and high frequency of insertions, deletions, and duplications; nevertheless, it can enable us to reconstruct the population history in great detail.…”

Section: Discussionmentioning

confidence: 99%

The population history of the deep-sea demersal fish Bothrocara hollandi in the Japan Sea revealed by tandem repeat units in the mitochondrial non-coding region

Kodama

Kojima

2009

Plankton Benthos Res

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Abstract:We determined the nucleotide sequences of the non-coding region between the genes for tRNA Thr and tRNA Pro in 433 specimens of the deep-sea demersal fish Bothrocara hollandi obtained from the Japan Sea and the Okhotsk Sea. This region consisted of 1-3 copies of sequences, which originated from the duplication of the 5Ј-region of the tRNA Pro gene. All the individuals from the Okhotsk Sea have two copies and those from the Japan Sea were shown to have 1-3 copies. Of the individuals obtained from the Japan Sea, those with more than one copy and those with a single copy corresponded to Group A and Group B, respectively, which have been defined in a previous study. On the other hand, a closely related species, Bothrocara tanakae, has a single copy, and no non-coding region was detected for the congeneric species Bothrocara molle. Duplication of the unit might have occurred three times during the evolution of B. hollandi. During the last glacial maximum (LGM) when most of the Japan Sea was anoxic, ancestors of Group A would have inhabited the shallower areas of the Japan Sea which did not become anoxic while those of Group B might have survived in other refuges in the Japan Sea. Low genetic diversity of Group B suggests that a severe bottleneck might have occurred in the population size of an ancestral population of Group B during the LGM.

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“…Sequence duplications in the mt genome frequently involve the control region (CR), which is associated with the initiation of transcription and mtDNA replication. Duplicated and concertedly evolved CRs have been reported in snakes (Kumazawa et al, 1996(Kumazawa et al, , 1998, sea cucumbers (Arndt and Smith, 1998), ticks (Black and Roehrdanz, 1998;Campbell and Barker, 1999;Shao et al, 2005a), birds (Eberhard et al, 2001;Abbott et al, 2005;Jouventin et al, 2006;Gibb et al, 2007;Smith et al, 2007;Lawrence et al, 2008;Cho et al, 2009;Gomez-Diaz et al, 2009), fish (Lee et al, 2001;Tatarenkov and Avise, 2007), thrips (Shao et al, 2003), lizards (Kumazawa and Endo, 2004;Amer and Kumazawa, 2005), a sea firefly (Ogoh and Ohmiya, 2004), cephalopods (Yokobori et al, 2004), a frog (Sano et al, 2005), mites (Shao et al, 2005b(Shao et al, , 2006, and turtles (Parham et al, 2006a(Parham et al, , 2006b). Some of the duplications involve structural genes or tRNAs (Kumazawa et al, 1998;Campbell and Barker, 1999;Eberhard et al, 2001;Yokobori et al, 2004;Abbott et al, 2005;Shao et al, 2005b;Parham et al, 2006b;Gibb et al, 2007;Cho et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

Mosaic gene conversion after a tandem duplication of mtDNA sequence in Diomedeidae (albatrosses)

Eda¹,

Kuro-o

Higuchi

et al. 2010

Genes Genet. Syst.

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Although the tandem duplication of mitochondrial (mt) sequences, especially those of the control region (CR), has been detected in metazoan species, few studies have focused on the features of the duplicated sequence itself, such as the gene conversion rate, distribution patterns of the variation, and relative rates of evolution between the copies. To investigate the features of duplicated mt sequences, we partially sequenced the mt genome of 16 Phoebastria albatrosses belonging to three species (P. albatrus, P. nigripes, and P. immutabilis). More than 2,300 base pairs of tandemly-duplicated sequence were shared by all three species. The observed gene arrangement was shared in the three Phoebastria albatrosses and suggests that the duplication event occurred in the common ancestor of the three species. Most of the copies in each individual were identical or nearly identical, and were maintained through frequent gene conversions. By contrast, portions of CR domains I and III had different phylogenetic signals, suggesting that gene conversion had not occurred in those sections after the speciation of the three species. Several lines of data, including the heterogeneity of the rate of molecular evolution, nucleotide differences, and putative secondary structures, suggests that the two sequences in CR domain I are maintained through selection; however, additional studies into the mechanisms of gene conversion and mtDNA synthesis are required to confirm this hypothesis.

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The complete DNA sequence of the mitochondrial genome of the self-fertilizing fish Rivulus marmoratus (Cyprinodontiformes, Rivulidae) and the first description of duplication of a control region in fish

Cited by 93 publications

References 31 publications

Complete nucleotide sequence of the mitochondrial genome of Schlegel's tree frog Rhacophorus schlegelii (family Rhacophoridae): duplicated control regions and gene rearrangements

Complete nucleotide sequence of the mitochondrial genome of Schlegel's tree frog Rhacophorus schlegelii (family Rhacophoridae): duplicated control regions and gene rearrangements

The population history of the deep-sea demersal fish Bothrocara hollandi in the Japan Sea revealed by tandem repeat units in the mitochondrial non-coding region

Mosaic gene conversion after a tandem duplication of mtDNA sequence in Diomedeidae (albatrosses)

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