201
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Oliveira C, Gaiotto F, Costa M, Martinez R. Molecular genetic analysis of the yellow-breasted capuchin monkey: recommendations for ex situ conservation. GENETICS AND MOLECULAR RESEARCH 2011; 10:1471-8. [DOI: 10.4238/vol10-3gmr1115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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202
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Complete sequence of the Tibetan Mastiff mitochondrial genome and its phylogenetic relationship with other Canids (Canis, Canidae). Animal 2011; 5:18-25. [DOI: 10.1017/s1751731110001370] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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203
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The complete mitochondrial genome of bighead croaker, Collichthys niveatus (Perciformes, Sciaenidae): structure of control region and phylogenetic considerations. Mol Biol Rep 2010; 38:4673-85. [DOI: 10.1007/s11033-010-0602-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2010] [Accepted: 11/22/2010] [Indexed: 11/26/2022]
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204
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Zhang H, Chen L. The complete mitochondrial genome of dhole Cuon alpinus: phylogenetic analysis and dating evolutionary divergence within Canidae. Mol Biol Rep 2010; 38:1651-60. [PMID: 20859694 DOI: 10.1007/s11033-010-0276-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Accepted: 09/02/2010] [Indexed: 01/20/2023]
Abstract
The dhole (Cuon alpinus) is the only existent species in the genus Cuon (Carnivora: Canidae). In the present study, the complete mitochondrial genome of the dhole was sequenced. The total length is 16672 base pairs which is the shortest in Canidae. Sequence analysis revealed that most mitochondrial genomic functional regions were highly consistent among canid animals except the CSB domain of the control region. The difference in length among the Canidae mitochondrial genome sequences is mainly due to the number of short segments of tandem repeated in the CSB domain. Phylogenetic analysis was progressed based on the concatenated data set of 14 mitochondrial genes of 8 canid animals by using maximum parsimony (MP), maximum likelihood (ML) and Bayesian (BI) inference methods. The genera Vulpes and Nyctereutes formed a sister group and split first within Canidae, followed by that in the Cuon. The divergence in the genus Canis was the latest. The divarication of domestic dogs after that of the Canis lupus laniger is completely supported by all the three topologies. Pairwise sequence divergence data of different mitochondrial genes among canid animals were also determined. Except for the synonymous substitutions in protein-coding genes, the control region exhibits the highest sequence divergences. The synonymous rates are approximately two to six times higher than those of the non-synonymous sites except for a slightly higher rate in the non-synonymous substitution between Cuon alpinus and Vulpes vulpes. 16S rRNA genes have a slightly faster sequence divergence than 12S rRNA and tRNA genes. Based on nucleotide substitutions of tRNA genes and rRNA genes, the times since divergence between dhole and other canid animals, and between domestic dogs and three subspecies of wolves were evaluated. The result indicates that Vulpes and Nyctereutes have a close phylogenetic relationship and the divergence of Nyctereutes is a little earlier. The Tibetan wolf may be an archaic pedigree within wolf subspecies. The genetic distance between wolves and domestic dogs is less than that among different subspecies of wolves. The domestication of dogs was about 1.56-1.92 million years ago or even earlier.
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Affiliation(s)
- Honghai Zhang
- College of Life Science, Qufu Normal University, Qufu 273165, China.
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205
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González-Ittig RE, Salazar-Bravo J, Barquez RM, Gardenal CN. Phylogenetic relationships among species of the genus Oligoryzomys (Rodentia, Cricetidae) from Central and South America. ZOOL SCR 2010. [DOI: 10.1111/j.1463-6409.2010.00446.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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206
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Comparison research and phylogenetic implications of mitochondrial control regions in four soft-shelled turtles of Trionychia (Reptilia, Testudinata). Genes Genomics 2010. [DOI: 10.1007/s13258-010-0015-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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207
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Jang KH, Hwang UW. Complete mitochondrial genome of the Korean goralNaemorhaedus caudatus(Ruminantia, Bovidae, Antilopinae) and conserved domains in the control region of Caprini. ACTA ACUST UNITED AC 2010; 21:62-4. [DOI: 10.3109/19401736.2010.490833] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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208
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Jang KH, Hwang UW. Mitochondrial genome of the Korean musk deerMoschus moschiferus(Artiodactyla, Ruminantia, Moschidae). ACTA ACUST UNITED AC 2010; 21:65-7. [DOI: 10.3109/19401736.2010.490834] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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209
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210
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Eda M, Kuro-o M, Higuchi H, Hasegawa H, Koike H. Mosaic gene conversion after a tandem duplication of mtDNA sequence in Diomedeidae (albatrosses). Genes Genet Syst 2010; 85:129-39. [PMID: 20558899 DOI: 10.1266/ggs.85.129] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
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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Affiliation(s)
- Masaki Eda
- Graduate School of Social and Cultural Studies, Kyusyu University.
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211
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Organization and variation of the mitochondrial DNA control region in five Caprinae species. Genes Genomics 2010. [DOI: 10.1007/s13258-010-0023-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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212
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Kan XZ, Li XF, Zhang LQ, Chen L, Qian CJ, Zhang XW, Wang L. Characterization of the complete mitochondrial genome of the Rock pigeon, Columba livia (Columbiformes: Columbidae). GENETICS AND MOLECULAR RESEARCH 2010; 9:1234-49. [PMID: 20603809 DOI: 10.4238/vol9-2gmr853] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The rock pigeon (Columba livia), or Rock dove, is a member of the bird family Columbidae. We mapped the complete mitochondrial genome of the Rock pigeon. The mitochondrial genome of this species is a circular molecule of 17,229 bp in length, encoding a standard set of 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes, plus a putative control region, demonstrating a structure very similar to that of other birds. As found in other vertebrates, most of these genes are coded on the H-strand, except for NADH dehydrogenase subunit 6 (nad6) and eight tRNA genes (Gln, Ala, Asn, Cys, Tyr, Ser(UCN), Pro, Glu). The AT skew and GC skew of the whole genome, protein-coding genes, tRNA, rRNA, and the control region were calculated for the complete mitochondrial genomes of 30 avian species, representing 29 orders. All protein-coding genes initiated with ATG, except for cox1 and nad5, which began with GTG. One extra nucleotide 'C' was present in NADH dehydrogenase subunit 3 (nad3). All tRNA gene sequences have the potential to fold into typical cloverleaf secondary structures. Within the control region, conserved sequences were identified in three domains. Although the conserved blocks, such as ETAS1, ETAS2, CSB1, CSB1-like, and boxes C, D, E, and F, are readily identifiable in the C. livia control region, the typical origin of H-strand replication (O(H)), CSB2 and CSB3 could not be detected. These results provide basic information for phylogenetic analyses of birds, especially Columbiformes species.
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Affiliation(s)
- X Z Kan
- The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu, China
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213
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Kan XZ, Li XF, Lei ZP, Wang M, Chen L, Gao H, Yang ZY. Complete mitochondrial genome of Cabot's tragopan, Tragopan caboti (Galliformes: Phasianidae). GENETICS AND MOLECULAR RESEARCH 2010; 9:1204-16. [PMID: 20589618 DOI: 10.4238/vol9-2gmr820] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Cabot's tragopan, Tragopan caboti, is a globally threatened pheasant endemic to southeast China. The complete mitochondrial genome of Cabot's tragopan was sequenced. The circular genome contains 16,727 bp, encoding a standard set of 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes, plus the putative control region, a structure very similar to that of other Galliformes. As found in other vertebrates, most of these genes code on the H-strand, except for the NADH dehydrogenase subunit 6 (nad6) and eight tRNA genes (Gln, Ala, Asn, Cys, Tyr, Ser(UCN), Pro, Glu). All protein-coding genes initiated with ATG, except for cox1, which began with GTG, and had a strong skew of C vs G (GC skew = -0.29 to -0.73). One extra 'C' nucleotide was found in the NADH dehydrogenase subunit 3 (nad3). All the tRNA gene sequences have the potential to fold into typical cloverleaf secondary structures. Conserved sequences in three domains were identified within the control region (D-loop). These results provide basic information for phylogenetic analyses among Galliform birds, and especially Tragopan species.
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Affiliation(s)
- X Z Kan
- The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu, China.
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214
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Freyer C, Park CB, Ekstrand MI, Shi Y, Khvorostova J, Wibom R, Falkenberg M, Gustafsson CM, Larsson NG. Maintenance of respiratory chain function in mouse hearts with severely impaired mtDNA transcription. Nucleic Acids Res 2010; 38:6577-88. [PMID: 20566479 PMCID: PMC2965244 DOI: 10.1093/nar/gkq527] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The basal mitochondrial transcription machinery is essential for biogenesis of the respiratory chain and consists of mitochondrial RNA polymerase, mitochondrial transcription factor A (TFAM) and mitochondrial transcription factor B2. This triad of proteins is sufficient and necessary for mtDNA transcription initiation. Abolished mtDNA transcription caused by tissue-specific knockout of TFAM in the mouse heart leads to early onset of a severe mitochondrial cardiomyopathy with lethality within the first post-natal weeks. Here, we describe a mouse model expressing human TFAM instead of the endogenous mouse TFAM in heart. These rescue mice have severe reduction in mtDNA transcription initiation, but, surprisingly, are healthy at the age of 52 weeks with near-normal steady-state levels of transcripts. In addition, we demonstrate that heavy-strand mtDNA transcription normally terminates at the termination-associated sequence in the control region. This termination is abolished in rescue animals resulting in heavy (H)-strand transcription of the entire control region. In conclusion, we demonstrate here the existence of an unexpected mtDNA transcript stabilization mechanism that almost completely compensates for the severely reduced transcription initiation in rescue hearts. Future elucidation of the underlying molecular mechanism may provide a novel pathway to treat mitochondrial dysfunction in human pathology.
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Affiliation(s)
- Christoph Freyer
- Department of Laboratory Medicine, Karolinska Institutet, Retzius väg 8, 171 65 Solna, Sweden
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215
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Complete sequence and gene organization of the mitochondrial genome for Hubbard's sportive lemur (Lepilemur hubbardorum). Gene 2010; 464:44-9. [PMID: 20547216 DOI: 10.1016/j.gene.2010.06.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 06/02/2010] [Accepted: 06/03/2010] [Indexed: 11/24/2022]
Abstract
The complete mitochondrial DNA (mtDNA) genome of Hubbard's or Zombitse sportive lemur (Lepilemur hubbardorum) was generated by polymerase chain reaction (PCR) amplification, primer-walking sequencing and fragment cloning. Comparative analyses of Hubbard's sportive lemur were conducted with available complete mitochondrial genome sequences from eight other lemur species. The mitochondrial genome of Hubbard's sportive lemur is 16,854 base pairs (bp) and contains 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one control region. Three rare start codons were found, in which GTG is the start codon for the ATPase 6 subunit gene (ATP), ATC for the NADH dehydrogenase (ND) 2 subunit gene, and ATT for the ND5 subunit gene. In the control region, sequence analysis found one repetitive unit between conserved sequence blocks (CSB)-1 and CSB-2 for L. hubbardorum. Comparative analysis of eight other lemur species showed different repetitive units between and outside of these two blocks. According to the phylogenetic analysis of the 12 heavy-strand encoded protein-coding genes, all nine lemur species representative of four lemuriformes families were monophyletic. This template and the newly designed primers described in this study will allow scientists to generate comparative sequences for all sportive lemurs to validate phylogenetic discrepancies in the genus Lepilemur and to evaluate evolutionary and biogeographic models.
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216
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Di Rocco F, Zambelli A, Maté L, Vidal-Rioja L. The complete mitochondrial DNA sequence of the guanaco (Lama guanicoe): comparative analysis with the vicuña (Vicugna vicugna) genome. Genetica 2010; 138:813-8. [PMID: 20524143 DOI: 10.1007/s10709-010-9465-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Accepted: 05/20/2010] [Indexed: 11/29/2022]
Abstract
South American camelids comprise the guanaco (Lama guanicoe) and the vicuña (Vicugna vicugna), which are wild species, and the domestic llama (Lama glama) and alpaca (Lama pacos). This paper presents the first complete mitochondrial (mt) genome of the guanaco and the mt coding sequence of the vicuña. The guanaco mtDNA is 16,649 nt long and its composition and organization are similar to the mitochondrial genome of other mammals. Excluding the control region, comparison of the complete guanaco and vicuña mtDNA showed 4.4% sequence divergence. Nucleotide differences in peptide coding genes varied from 1.9% in ATP6 to 6.4% in Cyt b. These values are compatible with the close relatedness of both species identified by other authors. Based on the differences between the control region sequence here reported and that previously described, we also discuss the occurrence of NUMTs in the genome of South American camelids.
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Affiliation(s)
- Florencia Di Rocco
- Instituto Multidisciplinario de Biología Celular (IMBICE), CCT CONICET La Plata-CICPBA, C.C. 403, 1900 La Plata, Argentina.
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217
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Yan J, Liu L, Liu S, Guo X, Liu Y. Comparative analysis of mitochondrial control region in polyploid hybrids of red crucian carp (Carassius auratus) x blunt snout bream (Megalobrama amblycephala). FISH PHYSIOLOGY AND BIOCHEMISTRY 2010; 36:263-272. [PMID: 18815893 DOI: 10.1007/s10695-008-9251-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Accepted: 07/21/2008] [Indexed: 05/26/2023]
Abstract
The entire sequences of the mitochondrial (mt)DNA control region (CR) and portions of its flanking genes in the red crucian carp (RC) and blunt snout bream (BSB) as well as their polyploid hybrids (3nRB, 4nRB and 5nRB) were determined and subjected to a comparative analysis. The mtDNA-CRs of these five fish species ranged from 923 to 937 bp in length, they had the same flanking gene arrangement as other vertebrates and the pattern of nucleotide substitution bias was also similar to that in other vertebrates. Our data are consistent with the viewpoint of three domains [extended terminal associated sequence (ETAS domain), central conserved sequence block domain and conserved sequence block (CSB) domain] within the mtDNA-CR of mammals. On the basis our comparative analysis of the mtDNA-CRs of these five fish species, we were able to identify the consensus sequences of functional conserved units, including the ETAS, CSB-F, CSB-D, CSB-E, CSB1, CSB2 and CSB3 and putative promoter. The percentage of variable nucleotide positions (41.98%) in the central domain was lower than those in the ETAS and conserved domain (71.70 and 47.12%, respectively), suggesting that the central domain was the most conserved part of the mtDNA-CR. These results provide useful and important information for the further study of mtDNA-CR structure in fish. The sequence similarities of mtDNA-CR among the 3nRB, 4nRB, 5nRB hybrids and their respective female parents were higher than those among the 3nRB, 4nRB, 5nRB hybrids and their respective male parents, providing the direct evidence of stringent maternal inheritance of mtDNA-CR in the 3nRB, 4nRB and 5nRB hybrids.
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Affiliation(s)
- Jinpeng Yan
- College of Life Science, Hunan Normal University, Changsha 410081, Hunan, People's Republic of China
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218
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Kornienko IV, Vodolazhsky DI. Patterns of single nucleotide polymorphism distribution in hypervariable regions of the D-loop of human mitochondrial DNA. Mol Biol 2010. [DOI: 10.1134/s0026893310030052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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219
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Chen W, Liu S, Liu Y, Hao H, Zeng B, Chen S, Peng H, Yue B, Zhang X. Phylogeography of the Large White-Bellied RatNiviventer excelsiorSuggests the Influence of Pleistocene Glaciations in the Hengduan Mountains. Zoolog Sci 2010; 27:487-93. [DOI: 10.2108/zsj.27.487] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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220
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Okajima Y, Kumazawa Y. Mitochondrial genomes of acrodont lizards: timing of gene rearrangements and phylogenetic and biogeographic implications. BMC Evol Biol 2010; 10:141. [PMID: 20465814 PMCID: PMC2889956 DOI: 10.1186/1471-2148-10-141] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Accepted: 05/13/2010] [Indexed: 11/28/2022] Open
Abstract
Background Acrodonta consists of Agamidae and Chamaeleonidae that have the characteristic acrodont dentition. These two families and Iguanidae sensu lato are members of infraorder Iguania. Phylogenetic relationships and historical biogeography of iguanian lizards still remain to be elucidated in spite of a number of morphological and molecular studies. This issue was addressed by sequencing complete mitochondrial genomes from 10 species that represent major lineages of acrodont lizards. This study also provided a good opportunity to compare molecular evolutionary modes of mitogenomes among different iguanian lineages. Results Acrodontan mitogenomes were found to be less conservative than iguanid counterparts with respect to gene arrangement features and rates of sequence evolution. Phylogenetic relationships were constructed with the mitogenomic sequence data and timing of gene rearrangements was inferred on it. The result suggested highly lineage-specific occurrence of several gene rearrangements, except for the translocation of the tRNAPro gene from the 5' to 3' side of the control region, which likely occurred independently in both agamine and chamaeleonid lineages. Phylogenetic analyses strongly suggested the monophyly of Agamidae in relation to Chamaeleonidae and the non-monophyly of traditional genus Chamaeleo within Chamaeleonidae. Uromastyx and Brookesia were suggested to be the earliest shoot-off of Agamidae and Chamaeleonidae, respectively. Together with the results of relaxed-clock dating analyses, our molecular phylogeny was used to infer the origin of Acrodonta and historical biogeography of its descendant lineages. Our molecular data favored Gondwanan origin of Acrodonta, vicariant divergence of Agamidae and Chamaeleonidae in the drifting India-Madagascar landmass, and migration of the Agamidae to Eurasia with the Indian subcontinent, although Laurasian origin of Acrodonta was not strictly ruled out. Conclusions We detected distinct modes of mitogenomic evolution among iguanian families. Agamidae was highlighted in including a number of lineage-specific mitochondrial gene rearrangements. The mitogenomic data provided a certain level of resolution in reconstructing acrodontan phylogeny, although there still remain ambiguous relationships. Our biogeographic implications shed a light on the previous hypothesis of Gondwanan origin of Acrodonta by adding some new evidence and concreteness.
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Affiliation(s)
- Yasuhisa Okajima
- Department of Information and Biological Sciences, Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Mizuho-cho, Mizuho-ku, Nagoya 467-8501, Japan
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221
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Jondeung A, Karinthanyakit W. The complete mitochondrial DNA sequence of the short mackerel (Rastrelliger brachysoma), and its phylogenetic position within Scombroidei, Perciformes. ACTA ACUST UNITED AC 2010; 21:36-47. [PMID: 20331328 DOI: 10.3109/19401731003622529] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In order to support studies of short mackerel population genetic structure in the Gulf of Thailand and phylogenetic relationships, the mitochondrial genome of the short mackerel, Rastrelliger brachysoma, has recently been determined by a partial cloning technique, long PCR with three pairs of newly designed primers and primer walking sequencing. The complete mitochondrial genome is 16,539 bp in length and contains 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes) and a control region (CR) as in other bony fishes. Within the 845-bp CR, we identified several conserved motifs. The phylogeny obtained by Bayesian analyses based on two nucleotide datasets corresponding to the cytb and nd2 mitochondrial genes strongly support the inclusion of R. brachysoma within the monophyletic tribe of Scombrini in the family Scombridae. The obtained phylogeny also reveals high-statistical support for the existence of two distinct groups indicating that Scombroidei and Xiphioidei are two separate suborders.
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Affiliation(s)
- Amnuay Jondeung
- Department of Genetics, Kasetsart University, Bangkok, Thailand.
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222
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Liu Y, Cui Z. The complete mitochondrial genome of the mantid shrimp Oratosquilla oratoria (Crustacea: Malacostraca: Stomatopoda): Novel non-coding regions features and phylogenetic implications of the Stomatopoda. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2010; 5:190-8. [PMID: 20510661 DOI: 10.1016/j.cbd.2010.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Revised: 04/02/2010] [Accepted: 04/06/2010] [Indexed: 12/18/2022]
Abstract
The complete mitochondrial (mt) genome sequence of Oratosquilla oratoria (Crustacea: Malacostraca: Stomatopoda) was determined; a circular molecule of 15,783 bp in length. The gene content and arrangement are consistent with the pancrustacean ground pattern. The mt control region of O. oratoria is characterized by no GA-block near the 3' end and different position of [TA(A)]n-blocks compared with other reported Stomatopoda species. The sequence of the second hairpin structure is relative conserved which suggests this region may be a synapomorphic character for the Stomatopoda. In addition, a relative large intergenic spacer (101 bp) with higher A+T content than that in control region was identified between the tRNA(Glu) and tRNA(Phe) genes. Phylogenetic analyses based on the current dataset of complete mt genomes strongly support the Stomatopoda is closely related to Euphausiacea. They in turn cluster with Penaeoidea and Caridea clades while other decapods form a separate group, which rejects the monophyly of Decapoda. This challenges the suitability of Stomatopoda as an outgroup of Decapoda in phylogenetic analyses. The basal position of Stomatopoda within Eumalacostraca according to the morphological characters is also questioned.
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Affiliation(s)
- Yuan Liu
- EMBL, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
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223
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Phylogeography of the armadillo Chaetophractus villosus (Dasypodidae Xenarthra): Post-glacial range expansion from Pampas to Patagonia (Argentina). Mol Phylogenet Evol 2010; 55:38-46. [DOI: 10.1016/j.ympev.2009.12.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Revised: 12/15/2009] [Accepted: 12/21/2009] [Indexed: 11/21/2022]
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224
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Centeno-Cuadros A, Godoy JA. Structure, organization and nucleotide diversity of the mitochondrial control region and cytochromebof southern water vole (Arvicola sapidus). ACTA ACUST UNITED AC 2010; 21:48-53. [DOI: 10.3109/19401731003681103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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225
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MitoZoa: A curated mitochondrial genome database of metazoans for comparative genomics studies. Mitochondrion 2010; 10:192-9. [DOI: 10.1016/j.mito.2010.01.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Revised: 12/14/2009] [Accepted: 01/08/2010] [Indexed: 11/23/2022]
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226
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Nilsson MA. The structure of the Australian and South American marsupial mitochondrial control region. ACTA ACUST UNITED AC 2010; 20:126-38. [PMID: 19900062 DOI: 10.3109/19401730903180112] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND AND AIMS The mitochondrial control region (CR) was studied across five marsupialian orders, in order to give a detailed overview of its features. RESULTS The CR is organised into three domains similar to the CR of placental mammals. However, the conservation of different features among the marsupial orders is in general more strict. In the first domain, two conserved blocks extended termination-associated sequences (ETAS 1 and ETAS 2) are present in all marsupial orders. In the third domain, the three conserved sequence blocks (CSB 1, CSB 2 and CSB 3) are present and complete, with CSB 1 being duplicated in four of five marsupial orders. CONCLUSIONS The nucleotide frequency and secondary structures of the repeats were typical for marsupial species. The repeats are generally AT-rich except in Dasyuridae and Paucituberculata, which show a significant increase in GC content.
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Affiliation(s)
- Maria A Nilsson
- Institute for Experimental Pathology/ZMBE, University of Münster, Münster, Germany.
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227
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Cho HJ, Eda M, Nishida S, Yasukochi Y, Chong JR, Koike H. Tandem duplication of mitochondrial DNA in the black-faced spoonbill, Platalea minor. Genes Genet Syst 2010; 84:297-305. [PMID: 20057167 DOI: 10.1266/ggs.84.297] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Mitochondrial (mt) heteroplasmy in the control region (CR) of the black-faced spoonbill was investigated using LA-PCR. To avoid amplification of transpositioned nuclear genome fragment from mtDNA (numt), PCR product of the almost-complete mitochondrial genome was amplified using primers designed to anneal on the COIII gene. Then nested LA-PCR product was amplified between the cyt b and 12S rRNA genes using the almost-complete mitochondrial genome PCR product as a template. Nucleotide sequencing revealed tandem duplication composed of two units. The first contains cyt b-1, tRNA(Thr)-1, tRNA(Pro)-1, ND6-1, tRNA(Glu)-1 and CR1, and the second consists of cyt b-2, tRNA(Thr)-2, tRNA(Pro)-2, ND6-2, tRNA(Glu)-2 and CR2, followed by tRNA(Phe) and 12S rRNA. The duplicated cyt b-2 sequence coincided with 499 bp at the 3' end of cyt b-1. With the exception of the CR, the other genes in the duplicated sequence were identical to the original corresponding gene. Even though both CR1 and CR2 contain functional blocks, such as a poly-C site, a goose hairpin and a TAS structure in Domain I, the 3' end of CR1 was followed by a 112 bp sequence (non-coding region) that was not found in CR2 or in sequence homology analysis of similar genes. Meanwhile, CR2 ended in a complicated repeat sequence. The 5' franking region in the Domain I (Region A) and the 3' franking region in the Domain I (Region B) of the two CRs evolve in quite different manners: Region A was highly variable between CR1 and CR2 in the same individuals, while Region B was almost identical between them, which indicates concerted evolution.
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Affiliation(s)
- Hyong-Ju Cho
- Laboratory of Biodiversity, Department Environmental Changes, SCS, Kyushu University, Fukuoka City 819-0395, Japan
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228
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Catanese G, Manchado M, Infante C. Evolutionary relatedness of mackerels of the genus Scomber based on complete mitochondrial genomes: strong support to the recognition of Atlantic Scomber colias and Pacific Scomber japonicus as distinct species. Gene 2009; 452:35-43. [PMID: 20035845 DOI: 10.1016/j.gene.2009.12.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Revised: 12/11/2009] [Accepted: 12/12/2009] [Indexed: 11/29/2022]
Abstract
Mackerels of the genus Scomber are commercially important species, but their taxonomic status is still controversial. Although previous phylogenetic data support the recognition of Atlantic Scomber colias and Pacific Scomber japonicus as separate species, it is only based on the analysis of partial mitochondrial and nuclear DNA sequences. In an attempt to shed light on this relevant issue, we have determined the complete mitochondrial DNA sequence of S. colias, S. japonicus, and Scomber australasicus. The total length of the mitogenomes was 16,568 bp for S. colias and 16,570 bp for both S. japonicus and S. australasicus. All mitogenomes had a gene content (13 protein-coding, 2 rRNAs, and 22 tRNAs) and organization similar to that observed in Scomber scombrus and most other vertebrates. The major noncoding region (control region) ranged between 865 and 866 bp in length and showed the typical conserved blocks. Phylogenetic analyses revealed a monophyletic origin of Scomber species with regard to other scombrid fish. The major finding of this study is that S. colias and S. japonicus were significantly grouped in distinct lineages within Scomber cluster, which phylogenetically constitutes evidence that they may be considered as separate species. Additionally, molecular data here presented provide a useful tool for evolutionary as well as population genetic studies.
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Affiliation(s)
- Gaetano Catanese
- IFAPA Centro El Toruño, Junta de Andalucía, 11500 El Puerto de Santa María (Cádiz), Spain
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229
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Abhyankar A, Park HB, Tonolo G, Luthman H. Comparative sequence analysis of the non-protein-coding mitochondrial DNA of inbred rat strains. PLoS One 2009; 4:e8148. [PMID: 19997590 PMCID: PMC2781161 DOI: 10.1371/journal.pone.0008148] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Accepted: 11/08/2009] [Indexed: 11/19/2022] Open
Abstract
The proper function of mammalian mitochondria necessitates a coordinated expression of both nuclear and mitochondrial genes, most likely due to the co-evolution of nuclear and mitochondrial genomes. The non-protein coding regions of mitochondrial DNA (mtDNA) including the D-loop, tRNA and rRNA genes form a major component of this regulated expression unit. Here we present comparative analyses of the non-protein-coding regions from 27 Rattus norvegicus mtDNA sequences. There were two variable positions in 12S rRNA, 20 in 16S rRNA, eight within the tRNA genes and 13 in the D-loop. Only one of the three neutrality tests used demonstrated statistically significant evidence for selection in 16S rRNA and tRNA-Cys. Based on our analyses of conserved sequences, we propose that some of the variable nucleotide positions identified in 16S rRNA and tRNA-Cys, and the D-loop might be important for mitochondrial function and its regulation.
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Affiliation(s)
- Avinash Abhyankar
- Medical Genetics Unit, Department of Clinical Sciences-Malmö, Lund University, Malmö, Sweden.
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230
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Vanbrabant J, Goddeeris B, Martens K, Schön I. Development of primers for amplification and further research on the D-loop control region for the Common Spadefoot toad, Pelobates fuscus (Amphibia). CONSERV GENET RESOUR 2009. [DOI: 10.1007/s12686-009-9115-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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231
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Yang R, Wu X, Yan P, Su X, Yang B. Complete mitochondrial genome of Otis tarda (Gruiformes: Otididae) and phylogeny of Gruiformes inferred from mitochondrial DNA sequences. Mol Biol Rep 2009; 37:3057-66. [PMID: 19823949 DOI: 10.1007/s11033-009-9878-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2009] [Accepted: 09/30/2009] [Indexed: 01/19/2023]
Abstract
The complete nucleotide sequence of mitochondrial genome of the Great bustard (Otis tarda) was determined by using polymerase chain reaction (PCR) method. The genome is 16,849 bp in size, containing 13 protein-coding, 2 ribosomal and 22 transfer RNA genes. Sequences of the tRNA genes can be folded into canonical cloverleaf secondary structure except for tRNA-Cys and tRNA-Ser (AGY), which lose "DHU" arm. Sequence analysis showed that the O. tarda mitochondrial control region (mtCR) contained many elements in common with other avian mtCRs. A microsatellite repeat was found in the 3'-peripheral domain of the O. tarda mtCR. Based on the mitochondrial DNA sequences of 12S rRNA, 16S rRNA and tRNA-Val, a phylogenetic study of Gruiformes was performed. The result showed that Otididae was a sister group to "core Gruiformes" and Charadriiformes with strong support (97% posterior probability values) in Bayesian analysis. The taxonomic status of Rhynochetidae, Mesitornithidae, Pedionomidae and Turnicidae that traditionally belonged to Gruiformes was also discussed in this paper.
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Affiliation(s)
- Rong Yang
- College of Life Sciences, Anhui Normal University, 241000, Wuhu, Anhui Province, People's Republic of China
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232
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Zhang Y, Nie L, Huang Y, Pu Y, Zhang L. The mitochondrial DNA control region comparison studies of four hinged turtles and its phylogentic significance of the genusCuora sensu lato (Testudinata: Geoemydidae). Genes Genomics 2009. [DOI: 10.1007/bf03191253] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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233
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A comparative analysis of the complete mitochondrial genome of the Eurasian otter Lutra lutra (Carnivora; Mustelidae). Mol Biol Rep 2009; 37:1943-55. [DOI: 10.1007/s11033-009-9641-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Accepted: 07/21/2009] [Indexed: 10/20/2022]
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234
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235
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Complete nucleotide sequence and gene organization of the mitochondrial genome of Paa spinosa (Anura: Ranoidae). Gene 2009; 447:86-96. [PMID: 19631263 DOI: 10.1016/j.gene.2009.07.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Revised: 03/28/2009] [Accepted: 07/14/2009] [Indexed: 11/22/2022]
Abstract
The mt genome of Paa spinosa (Anura: Ranoidae) is a circular molecule of 18,012 bp in length, containing 38 genes (including an extra copy of tRNA-Met gene). This mt genome is characterized by three distinctive features: a cluster of rearranged tRNA genes (LTPF tRNA gene cluster), a tandem duplication of tRNA-Met gene (Met1 and Met2), and distinct repeat regions at both 5' and 3'-sides in the control region. Comparing the locations and the sequences of all tRNA-Met genes among Ranoidae, and constructing NJ tree of the nucleotide of those tRNA-Met genes, we suggested a tandem duplication of tRNA-Met gene can be regarded as a synapomorphy of Dicroglossinae. To further investigate the phylogenetic relationships of anurans, phylogenetic analyses (BI, ML and MP) based on the nucleotide dataset and the corresponding amino acid dataset of 11 protein-coding genes (except ND5 and ATP8) arrived at the similar topology.
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236
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Cadahía L, Pinsker W, Negro JJ, Pavlicev M, Urios V, Haring E. Repeated sequence homogenization between the control and pseudo-control regions in the mitochondrial genomes of the subfamily Aquilinae. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2009; 312B:171-85. [PMID: 19205013 DOI: 10.1002/jez.b.21282] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In birds, the noncoding control region (CR) and its flanking genes are the only parts of the mitochondrial (mt) genome that have been modified by intragenomic rearrangements. In raptors, two noncoding regions are present: the CR has shifted to a new position with respect to the "ancestral avian gene order," whereas the pseudo-control region (PsiCR) is located at the original genomic position of the CR. As possible mechanisms for this rearrangement, duplication and transposition have been considered. During characterization of the mt gene order in Bonelli's eagle Hieraaetus fasciatus, we detected intragenomic sequence similarity between the two regions supporting the duplication hypothesis. We performed intra- and intergenomic sequence comparisons in H. fasciatus and other falconiform species to trace the evolution of the noncoding mtDNA regions in Falconiformes. We identified sections displaying different levels of similarity between the CR and PsiCR. On the basis of phylogenetic analyses, we outline an evolutionary scenario of the underlying mutation events involving duplication and homogenization processes followed by sporadic deletions. Apparently, homogenization may easily occur if sufficient sequence similarity between the CR and PsiCR exists. Moreover, homogenization itself allows perpetuation of this continued equalization, unless this process is stopped by deletion. The Pandionidae and the Aquilinae seem to be the only two lineages of Falconiformes where homology between both regionsis still detectable, whereas in other raptors no similarity was found so far. In these two lineages, the process of sequence degeneration may have slowed down by homogenization events retaining high sequence similarity at least in some sections.
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Affiliation(s)
- Luis Cadahía
- Molecular Systematics, 1st Zoological Department, Museum of Natural History Vienna, Vienna, Austria.
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237
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Catanese G, Catanese G, Infante C, Manchado M, Catanese G, Infante C, Manchado M. Complete mitochondrial DNA sequences of the frigate tunaAuxis thazardand the bullet tunaAuxis rochei. ACTA ACUST UNITED AC 2009; 19:159-66. [DOI: 10.1080/10425170701207117] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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238
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Hwang DS, Hwang DS, Ki JS, Hwang DS, Ki JS, Jeong DH, Kim BH, Lee BK, Han SH, Lee JS. A comprehensive analysis of three Asiatic black bear mitochondrial genomes (subspeciesussuricus,formosanusandmupinensis), with emphasis on the complete mtDNA sequence ofUrsus thibetanus ussuricus(Ursidae). ACTA ACUST UNITED AC 2009. [DOI: 10.1080/19401730802389525] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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239
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He C, Han J, Ge L, Zhou Z, Gao X, Mu Y, Liu W, Cao J, Liu Z. Sequence and organization of the complete mitochondrial genomes of spotted halibut (Verasper variegatus) and barfin flounder (Verasper moseri). ACTA ACUST UNITED AC 2009; 19:246-55. [PMID: 17852351 DOI: 10.1080/10425170701563303] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
In this work, the mitochondrial genomes for spotted halibut (Verasper variegatus) and barfin flounder (Verasper moseri) were completely sequenced. The entire mitochondrial genome sequences of the spotted halibut and barfin flounder were 17,273 and 17,588 bp in length, respectively. The organization of the two mitochondrial genomes was similar to those reported from other fish mitochondrial genomes containing 37 genes (2 rRNAs, 22 tRNAs and 13 protein-coding genes) and two non-coding regions (control region (CR) and WANCY region). In the CR, the termination associated sequence (ETAS), six central conserved block (CSB-A,B,C,D,E,F), three conserved sequence blocks (CSB1-3) and a region of 61-bp tandem repeat cluster at the end of CSB-3 were identified by similarity comparison with fishes and other vertebrates. The tandem repeat sequences show polymorphism among the different individuals of the two species. The complete mitochondrial genomes of spotted halibut and barfin flounder should be useful for evolutionary studies of flatfishes and other vertebrate species.
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Affiliation(s)
- Chongbo He
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, People's Republic of China.
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240
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Guo X, Liu S, Liu Y. Evidence for maternal inheritance of mitochondrial DNA in allotetraploid. ACTA ACUST UNITED AC 2009; 18:247-56. [PMID: 17541829 DOI: 10.1080/10425170701248541] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The complete mitochondrial DNA (mtDNA) sequences of the allotetraploid and red crucian carp were determined in this paper. We compared the complete mtDNA sequences between the allotetraploid and its female parent red crucian carp, and between the allotetraploid and its male parent common carp. The results indicated that the complete mtDNA nucleotide identity (99.7%) between the allotetraploid and its female parent red crucian carp was higher than that (89.0%) between the allotetraploid and its male parent common carp. Moreover, the analysis on the start and stop codons, overlaps and spacers, and phylogeny of the mt genomes indicated the genetic relationship between the allotetraploid and its female parent red crucian carp was closer than that between the allotetraploid and its male parent common carp. Our results indicated that the allotetraploid mt genome was strictly maternally inherited. Through maternal inheritance, the mt genome in the F(11) allotetraploid displayed extremely high similarity to that in the female parent red crucian carp after 11 generations (from F(1) to F(11) hybrids). Such results indicated that the F(11) allotetraploid possessed the stable inheritance characteristic. Thus the tetraploid stocks possessed the good base to form a new tetraploid species in the future. Since the establishment of the new tetraploid stocks has the great significance in analyzing evolutionary theory of vertebrate and in improving aquaculture industry, analysis of the mt genome and the elucidation of the variation of the mt genome in the allotetraploid and its parents proved that it was a useful genetic marker to monitor the variations in the progeny of the crosses.
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Affiliation(s)
- Xinhong Guo
- College of Life Sciences, Hunan Normal University, Changsha, Hunan, People's Republic of China
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241
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Pang H, Liu W, Chen Y, Fang L, Zhang X, Cao X. Identification of complete mitochondrial genome of the tufted deer. ACTA ACUST UNITED AC 2009; 19:411-7. [PMID: 19462515 DOI: 10.1080/19401730802389517] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The tufted deer Elaphodus cephalophus are endangered animals in the world and little is understood about their mitochondrial (mt) genome. In our study, the mt genome of the tufted deer is identified--which is about 16 kb in length and contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a non-coding sequence (control region). The distinguishing feature is that GTG is the start codon of the NADH4L gene and the cyt b gene has a subterminal AAA followed by the stop codon TAG. According to 12 H strand protein-coding genes and phylogenetic analysis, Elaphodus may have a sister relationship with another deer group Muntiacus.
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Affiliation(s)
- Hong Pang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, PR China
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242
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Jönsen A, Yu X, Truedsson L, Nived O, Sturfelt G, Ibrahim S, Bengtsson A. Mitochondrial DNA polymorphisms are associated with susceptibility and phenotype of systemic lupus erythematosus. Lupus 2009; 18:309-12. [PMID: 19276298 DOI: 10.1177/0961203308097477] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The objective of this study was to investigate the possible association between mitochondrial DNA polymorphisms and systemic lupus erythematosus (SLE). A cohort from the Department of Rheumatology, Lund University Hospital, Sweden, consisting of 166 unrelated SLE patients was investigated as well as 190 unrelated healthy blood donors. Mean age at SLE diagnosis was 39 years (range 10-83) and mean follow-up time was 16 years (range 1-44). There were 87% women among the lupus patients, and the control group consisted of 98 women and 92 men from the same geographical area and with a similar age and ethnicity. The mtDNA SNP nt16189C was associated with SLE (OR = 1.98, 95% CI 1.04-3.78, P = 0.05). In addition, SNP nt13708A was associated with SLE in males (OR = 3.46, 95% CI 1.08-11.1, P = 0.04), although the number of male patients was low. Furthermore, SNP nt10398A was associated with secondary anti-phospholipid syndrome (P = 0.017, OR 8.2, 95% CI 1.1-63). In conclusion, in this study, we have for the first time investigated the possible association between SLE disease and mitochondrial DNA polymorphisms. Altogether, these novel results suggest that mtDNA polymorphisms may be associated with development of SLE and may potentially be of importance in SLE pathogenesis.
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Affiliation(s)
- A Jönsen
- Department of Clinical Sciences, Lund University Hospital, Lund University, Lund, Sweden
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243
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Lattuada L, Quaglia F, Iannelli F, Gissi C, Mantecca P, Bacchetta R, Polli M. Mitochondrial DNA sequence variations in some Italian wild boar populations. J Anim Breed Genet 2009; 126:154-63. [PMID: 19320773 DOI: 10.1111/j.1439-0388.2008.00766.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In order to investigate the relationships between Italian wild boar and major pig breeds, we studied the genetic variability of four wild boar populations in Italy (Arezzo, Pisa, Parma, Bergamo) using a 533-bp fragment of the mitochondrial control region. Sixty-nine wild boar samples were analysed, allowing the identification of 10 distinct haplotypes, which involve a total of 15 single nucleotide polymorphisms. Phylogenetic and network analyses were performed also considering several sequences of wild and domesticated forms available in the databases. The Bayesian phylogenetic tree and the Median-Joining network analyses show three main groups: the Italian (IT), European (EU) and Asian (AS) clades. The IT clade corresponds to the Maremma endemic wild boar population and also includes Sardinian individuals, while the EU and AS groups include wild boars as well as domestic pig breeds. Only two individuals from Pisa cluster in the IT group, whereas two haplotypes from Bergamo cluster in the AS group and all other samples cluster in the EU clade. These findings suggest that in Italy wild boar populations have a mixed origin, both EU and AS, and that an interbreeding between wild and domesticated strains has probably occurred. Eight of the 10 wild boars coming from the Migliarino-San Rossore-Massaciuccoli Regional Park (Pisa) belong to H2 and H3 haplotypes, and cluster into the EU clade, suggesting that this regional park is not anymore exclusive of the endemic Maremma wild boar.
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Affiliation(s)
- L Lattuada
- Dipartimento di Biologia, Università degli Studi di Milano, Milano, Italy
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244
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Bourlat SJ, Rota-Stabelli O, Lanfear R, Telford MJ. The mitochondrial genome structure of Xenoturbella bocki (phylum Xenoturbellida) is ancestral within the deuterostomes. BMC Evol Biol 2009; 9:107. [PMID: 19450249 PMCID: PMC2697986 DOI: 10.1186/1471-2148-9-107] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Accepted: 05/18/2009] [Indexed: 11/14/2022] Open
Abstract
Background Mitochondrial genome comparisons contribute in multiple ways when inferring animal relationships. As well as primary sequence data, rare genomic changes such as gene order, shared gene boundaries and genetic code changes, which are unlikely to have arisen through convergent evolution, are useful tools in resolving deep phylogenies. Xenoturbella bocki is a morphologically simple benthic marine worm recently found to belong among the deuterostomes. Here we present analyses comparing the Xenoturbella bocki mitochondrial gene order, genetic code and control region to those of other metazoan groups. Results The complete mitochondrial genome sequence of Xenoturbella bocki was determined. The gene order is most similar to that of the chordates and the hemichordates, indicating that this conserved mitochondrial gene order might be ancestral to the deuterostome clade. Using data from all phyla of deuterostomes, we infer the ancestral mitochondrial gene order for this clade. Using inversion and breakpoint analyses of metazoan mitochondrial genomes, we test conflicting hypotheses for the phylogenetic placement of Xenoturbella and find a closer affinity to the hemichordates than to other metazoan groups. Comparative analyses of the control region reveal similarities in the transcription initiation and termination sites and origin of replication of Xenoturbella with those of the vertebrates. Phylogenetic analyses of the mitochondrial sequence indicate a weakly supported placement as a basal deuterostome, a result that may be the effect of compositional bias. Conclusion The mitochondrial genome of Xenoturbella bocki has a very conserved gene arrangement in the deuterostome group, strikingly similar to that of the hemichordates and the chordates, and thus to the ancestral deuterostome gene order. Similarity to the hemichordates in particular is suggested by inversion and breakpoint analysis. Finally, while phylogenetic analyses of the mitochondrial sequences support a basal deuterostome placement, support for this decreases with the use of more sophisticated models of sequence evolution.
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Affiliation(s)
- Sarah J Bourlat
- Department of Invertebrate Zoology, Swedish Museum of Natural History, Stockholm, Sweden.
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245
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Peng H, Liu S, Zeng B, Zou F, Zhang X, Yue B. The complete mitochondrial genome and phylogenetic analysis of forest musk deer (Moschus berezovskii). J NAT HIST 2009. [DOI: 10.1080/00222930902767458] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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246
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Rotskaya UN, Rogozin IB, Vasyunina EA, Kolosova NG, Malyarchuk BA, Nevinsky GA, Sinitsyna OI. Analysis of mitochondrial DNA somatic mutations in OXYS and Wistar strain rats. BIOCHEMISTRY (MOSCOW) 2009; 74:430-7. [DOI: 10.1134/s0006297909040117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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247
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Xiao B, Ma F, Sun Y, Li QW. Comparative analysis of complete mitochondrial DNA control region of four species of Strigiformes. ACTA ACUST UNITED AC 2009; 33:965-74. [PMID: 17112967 DOI: 10.1016/s0379-4172(06)60131-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2006] [Accepted: 07/17/2006] [Indexed: 11/30/2022]
Abstract
The sequence of the whole mitochondrial (mt) DNA control region (CR) of four species of Strigiformes was obtained. Length of the CR was 3,290 bp, 2,848 bp, 2,444 bp, and 1,771 bp for Asio flammeus, Asio otus, Athene noctua, and Strix aluco, respectively. Interestingly, the length of the control region was maximum in Asio flammeus among all the avian mtDNA control regions sequenced thus far. In addition, the base composition and organization of mtDNA CR of Asio flammeus were identical to those reported for other birds. On the basis of the differential frequencies of base substitutions, the CR may be divided two variable domains, I and III, and a central conserved domain, II. The 3' end of the CR contained many tandem repeats of varying lengths and repeat numbers. In Asio flammeus, the repeated sequences consisted of a 126 bp sequence that was repeated seven times and a 78 bp sequence that was repeated 14 times. In Asio otus, there were also two repeated sequences, namely a 127 bp sequence that was repeated eight times and a 78 bp sequence that was repeated six times. The control region of Athene noctua contained three sets of repeats: a 89 bp sequence that was repeated three times, a 77 bp sequence that was repeated four times, and a 71 bp sequence that was repeated six times. Strix aluco, however, had only one repeated sequence, a 78 bp sequence that was repeated five times. The results of this study seem to indicate that these tandem repeats may have resulted from slipped-strand mispairing during mtDNA replication. Moreover, there are many conserved motifs within the repeated units. These sequences could form stable stem-loop secondary structures, which suggests that these repeated sequences play an important role in regulating transcription and replication of the mitochondrial genome.
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Affiliation(s)
- Bing Xiao
- College of Life Sciences, Liaoning Normal University, Dalian 116029, China
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