251
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Podnar M, Pinsker W, Mayer W. Complete mitochondrial genomes of three lizard species and the systematic position of the Lacertidae (Squamata). J ZOOL SYST EVOL RES 2009. [DOI: 10.1111/j.1439-0469.2008.00515.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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252
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Behar DM, Blue-Smith J, Soria-Hernanz DF, Tzur S, Hadid Y, Bormans C, Moen A, Tyler-Smith C, Quintana-Murci L, Wells RS. A novel 154-bp deletion in the human mitochondrial DNA control region in healthy individuals. Hum Mutat 2009; 29:1387-91. [PMID: 18629826 PMCID: PMC2697596 DOI: 10.1002/humu.20835] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The biological role of the mitochondrial DNA (mtDNA) control region in mtDNA replication remains unclear. In a worldwide survey of mtDNA variation in the general population, we have identified a novel large control region deletion spanning positions 16154 to 16307 (m.16154_16307del154). The population prevalence of this deletion is low, since it was only observed in 1 out of over 120,000 mtDNA genomes studied. The deletion is present in a nonheteroplasmic state, and was transmitted by a mother to her two sons with no apparent past or present disease conditions. The identification of this large deletion in healthy individuals challenges the current view of the control region as playing a crucial role in the regulation of mtDNA replication, and supports the existence of a more complex system of multiple or epigenetically-determined replication origins.
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Affiliation(s)
- Doron M Behar
- Molecular Medicine Laboratory, Rambam Health Care Campus, Haifa, Israel.
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253
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Li D, Fan L, Zeng B, Yin H, Zou F, Wang H, Meng Y, King E, Yue B. The complete mitochondrial genome of Macaca thibetana and a novel nuclear mitochondrial pseudogene. Gene 2009; 429:31-6. [DOI: 10.1016/j.gene.2008.10.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2008] [Revised: 10/03/2008] [Accepted: 10/04/2008] [Indexed: 10/21/2022]
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254
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Peng H, Liu S, Zou F, Zeng B, Yue B. Genetic diversity of captive forest musk deer (Moschus berezovskii) inferred from the mitochondrial DNA control region. Anim Genet 2008; 40:65-72. [PMID: 19076935 DOI: 10.1111/j.1365-2052.2008.01805.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Forest musk deer (Moschus berezovskii) were once distributed widely in China. However, wild populations have declined dramatically because of poaching and habitat loss. Captive breeding populations have been established for several decades, but the genetic backgrounds of most captive populations were unclear and the population sizes increased very slowly. To provide useful information for conservation and management of this species, we investigated the genetic diversity and population structure of forest musk deer by analysing a 582-bp fragment of the mitochondrial DNA (mtDNA) control region (CR) in three captive breeding populations in Sichuan Province, China. Ninety-four variable sites and 27 haplotypes were observed in 109 individuals, and the nucleotide and haplotype diversities were relatively high compared with those of other endangered mammals. Of the three investigated populations, the Maerkang population had the highest nucleotide diversity (pi=0.0568), haplotype diversity (h=0.836) and average intra-population genetic distance (0.062). The analysis of molecular variance demonstrated that most variation occurred within samples and that there was significant differentiation of the three populations. Estimates of gene flow indicated that there were few genetic exchanges among the three populations. Building pedigree records and increasing gene flow between populations will be helpful for conserving these populations and this species.
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Affiliation(s)
- H Peng
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
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255
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Cui Z, Liu Y, Li CP, You F, Chu KH. The complete mitochondrial genome of the large yellow croaker, Larimichthys crocea (Perciformes, Sciaenidae): unusual features of its control region and the phylogenetic position of the Sciaenidae. Gene 2008; 432:33-43. [PMID: 19100818 DOI: 10.1016/j.gene.2008.11.024] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Revised: 11/20/2008] [Accepted: 11/24/2008] [Indexed: 11/26/2022]
Abstract
To understand the systematic status of Larimichthys crocea in the Percoidei, we determined the complete mitochondrial (mt) genome sequence using 454 sequencing-by-synthesis technology. The complete mt genome is 16,466 bp in length including the typical structure of 22 tRNAs, 2 rRNAs, 13 protein-coding genes and the noncoding control region (CR). Further sequencing for the complete CR was performed using the primers Cyt b-F and 12S-R on six L. crocea individuals and two L. polyactis individuals. Interestingly, all seven CR sequences from L. crocea were identical while the three sequences from L. polyactis were distinct (including one from GenBank). Although the conserved blocks such as TAS and CSB-1, -2, and -3 are readily identifiable in the control regions of the two species, the typical central conserved blocks CSB-D, -E, and -F could not be detected, while they are found in Cynoscion acoupa of Sciaenidae and other Percoidei species. Phylogenetic analysis shows that L. crocea is a relatively recently emerged species in Sciaenidae and this family is closely related to family Pomacanthidae within the Percoidei. L. crocea, as the first species of Sciaenidae with complete mitochondrial genome available, will provide important information on the molecular evolution of the group. Moreover, the genus-specific pair of primers designed in this study for amplifying the complete mt control region will be very useful in studies on the population genetics and conservation biology of Larimichthys.
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Affiliation(s)
- Zhaoxia Cui
- EMBL, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
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256
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Pereira F, Soares P, Carneiro J, Pereira L, Richards MB, Samuels DC, Amorim A. Evidence for variable selective pressures at a large secondary structure of the human mitochondrial DNA control region. Mol Biol Evol 2008; 25:2759-70. [PMID: 18845547 DOI: 10.1093/molbev/msn225] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A combined effect of functional constraints and random mutational events is responsible for the sequence evolution of the human mitochondrial DNA (mtDNA) control region. Most studies targeting this noncoding segment usually focus on its primary sequence information disregarding other informative levels such as secondary or tertiary DNA conformations. In this work, we combined the most recent developments in DNA folding calculations with a phylogenetic comparative approach in order to investigate the formation of intrastrand secondary structures in the human mtDNA control region. Our most striking results are those regarding a new cloverleaf-like secondary structure predicted for a 93-bp stretch of the control region 5'-peripheral domain. Randomized sequences indicated that this structure has a more negative folding energy than the average of random sequences with the same nucleotide composition. In addition, a sliding window scan across the complete mitochondrial genome revealed that it stands out as having one of the highest folding potential. Moreover, we detected several lines of evidence of both negative and positive selection on this structure with high levels of conservation at the structure-relevant stem regions and the occurrence of compensatory base changes in the primate lineage. In the light of previous data, we discuss the possible involvement of this structure in mtDNA replication and/or transcription. We conclude that maintenance of this structure is responsible for the observed heterogeneity in the rate of substitution among sites in part of the human hypervariable region I and that it is a hot spot for the 3' end of human mtDNA deletions.
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Affiliation(s)
- Filipe Pereira
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.
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257
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Maximum-likelihood estimation of site-specific mutation rates in human mitochondrial DNA from partial phylogenetic classification. Genetics 2008; 180:1511-24. [PMID: 18791242 DOI: 10.1534/genetics.108.091116] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The mitochondrial DNA hypervariable segment I (HVS-I) is widely used in studies of human evolutionary genetics, and therefore accurate estimates of mutation rates among nucleotide sites in this region are essential. We have developed a novel maximum-likelihood methodology for estimating site-specific mutation rates from partial phylogenetic information, such as haplogroup association. The resulting estimation problem is a generalized linear model, with a nonstandard link function. We develop inference and bias correction tools for our estimates and a hypothesis-testing approach for site independence. We demonstrate our methodology using 16,609 HVS-I samples from the Genographic Project. Our results suggest that mutation rates among nucleotide sites in HVS-I are highly variable. The 16,400-16,500 region exhibits significantly lower rates compared to other regions, suggesting potential functional constraints. Several loci identified in the literature as possible termination-associated sequences (TAS) do not yield statistically slower rates than the rest of HVS-I, casting doubt on their functional importance. Our tests do not reject the null hypothesis of independent mutation rates among nucleotide sites, supporting the use of site-independence assumption for analyzing HVS-I. Potential extensions of our methodology include its application to estimation of mutation rates in other genetic regions, like Y chromosome short tandem repeats.
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258
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Zeng B, Xu L, Yue B, Li Z, Zou F. Molecular phylogeography and genetic differentiation of blue sheep Pseudois nayaur szechuanensis and Pseudois schaeferi in China. Mol Phylogenet Evol 2008; 48:387-95. [DOI: 10.1016/j.ympev.2008.05.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2007] [Revised: 04/02/2008] [Accepted: 05/08/2008] [Indexed: 02/02/2023]
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259
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Salvioli S, Capri M, Santoro A, Raule N, Sevini F, Lukas S, Lanzarini C, Monti D, Passarino G, Rose G, De Benedictis G, Franceschi C. The impact of mitochondrial DNA on human lifespan: a view from studies on centenarians. Biotechnol J 2008; 3:740-9. [PMID: 18548739 DOI: 10.1002/biot.200800046] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The role of inherited and somatic mutations of mitochondrial DNA (mtDNA) in aging and longevity is complex and highly controversial, owing to its peculiar genetics, including the phenomenon of heteroplasmy. Most of the data on mtDNA and longevity have been obtained on humans and particularly on centenarians, i. e., people who escaped or delayed the major age-related pathologies and reached the extreme limit of human lifespan. In this review we summarize the most recent advances in this field that suggest a consistent role in human longevity of both germ-line inherited and somatically acquired mutations. The particular case of the association with longevity of the somatic C150T mutation is extensively discussed, challenging the tenet that mtDNA mutations are basically detrimental. We also stress several limitations of our present knowledge, regarding the difficulty in extrapolating to humans the results obtained in animal models, owing to a variety of biological differences, including the very limited genetic variability of mtDNA in the strains used in laboratory experiments. The use of high-throughput technologies and the extensive analysis, possibly at the single cell level, of different tissues and cell types derived from the same individual will help in disentangling the complexity of mtDNA in aging and longevity.
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Affiliation(s)
- Stefano Salvioli
- Department of Experimental Pathology, University of Bologna, Bologna, Italy
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260
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Okajima Y, Kumazawa Y. Mitogenomic perspectives into iguanid phylogeny and biogeography: Gondwanan vicariance for the origin of Madagascan oplurines. Gene 2008; 441:28-35. [PMID: 18598742 DOI: 10.1016/j.gene.2008.06.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2008] [Revised: 05/28/2008] [Accepted: 06/03/2008] [Indexed: 10/22/2022]
Abstract
Complete or nearly complete nucleotide sequences of mitochondrial genomes (mtDNAs) were determined from eight species which, together with previous mtDNA data for two other taxa, cover most subfamilies of Iguanidae sensu lato. These iguanid mtDNAs were found to be rather conservative with respect to gene arrangements and molecular evolutionary rates, which contrasts with mtDNAs of Acrodonta (Agamidae and Chamaeleonidae) in which several gene rearrangements and highly accelerated molecular evolutionary rates have been known. Phylogenetic analyses consistently suggested the earliest shoot-off of a Malagasy subfamily Oplurinae and an affinity of Polychrotinae and Tropidurinae sensu stricto. However, even with the ample molecular characters derived from complete mtDNA sequences, phylogenetic relationships between iguanid subfamilies were poorly resolved in general, presumably due to the rapid ancient cladogenesis. Divergence time estimation without assuming the molecular clock suggested the Late Triassic/Early Jurassic divergence of Iguanidae from acrodonts and the Middle/Late Jurassic divergence of Oplurinae from the other iguanids. Together with geological and paleontological evidence, these results led us to propose Gondwanan vicariance for the origin of Malagasy oplurines without invoking a land bridge connection between South America/Antarctica and drifting Madagascar/India.
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Affiliation(s)
- Yasuhisa Okajima
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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261
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Breines R, Ursvik A, Nymark M, Johansen SD, Coucheron DH. Complete mitochondrial genome sequences of the Arctic Ocean codfishes Arctogadus glacialis and Boreogadus saida reveal oriL and tRNA gene duplications. Polar Biol 2008. [DOI: 10.1007/s00300-008-0463-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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262
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Scandura M, Iacolina L, Crestanello B, Pecchioli E, Di Benedetto MF, Russo V, Davoli R, Apollonio M, Bertorelle G. Ancient vs. recent processes as factors shaping the genetic variation of the European wild boar: are the effects of the last glaciation still detectable? Mol Ecol 2008; 17:1745-62. [PMID: 18371016 DOI: 10.1111/j.1365-294x.2008.03703.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The European wild boar is an important game species, subjected to local extinctions and translocations in the past, and currently enormously and worryingly expanding in some areas where management is urgently required. Understanding the relative roles of ancient and recent events in shaping the genetic structure of this species is therefore not only an interesting scientific issue, but it represents also the basis for addressing future management strategies. In addition, several pig breeds descend from the European wild boar, but the geographical location of the domestication area(s) and the possible introgression of pig genomes into wild populations are still open questions. Here, we analysed the genetic variation in different wild boar populations in Europe. Ten polymorphic microsatellites were typed in 252 wild boars and the mtDNA control region was sequenced in a subset of 145 individuals. Some samples from different pig breeds were also analysed. Our results, which were obtained considering also 612 published mtDNA sequences, suggest that (i) most populations are similarly differentiated, but the major discontinuity is found along the Alps; (ii) except for the Italian populations, European wild boars show the signature of a postglacial demographic expansion; (iii) Italian populations seem to preserve a high proportion of preglaciation diversity; (iv) the demographic decline which occurred in some areas in the last few centuries did not produce a noticeable reduction of genetic variation; (v) signs of human-mediated gene flow among populations are weak, although in some regions the effects of translocations are detectable and a low degree of pig introgression can be identified; (vi) the hypothesis of an independent domestication centre in Italy is not supported by our data, which in turn confirm that Central European wild boar might have represented an important source for domestic breeds. We can therefore conclude that recent human activities had a limited effect on the wild boar genetic structure. It follows that areas with high variation and differentiation represent natural reservoirs of genetic diversity to be protected avoiding translocations. In this context controlling some populations by hunting is not expected to affect significantly genetic variation in this species.
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Affiliation(s)
- M Scandura
- Dipartimento di Zoologia e Genetica Evoluzionistica, Università di Sassari, via Muroni 25, 07100 Sassari, Italy.
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263
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YAN L. Comparison of Mitochondrial Control Region Sequences Between Chelydridae and Platysternidae. Zool Res 2008. [DOI: 10.3724/sp.j.1141.2008.00127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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264
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Molecular characteristics of Tibetan antelope (Pantholops hodgsonii) mitochondrial DNA control region and phylogenetic inferences with related species. Small Rumin Res 2008. [DOI: 10.1016/j.smallrumres.2007.06.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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265
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Fajardo V, González I, Martín I, Rojas M, Hernández PE, Garcı´a T, Martín R. Differentiation of European wild boar (Sus scrofa scrofa) and domestic swine (Sus scrofa domestica) meats by PCR analysis targeting the mitochondrial D-loop and the nuclear melanocortin receptor 1 (MC1R) genes. Meat Sci 2008; 78:314-22. [DOI: 10.1016/j.meatsci.2007.06.018] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2007] [Revised: 06/20/2007] [Accepted: 06/23/2007] [Indexed: 11/28/2022]
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266
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Complete mitochondrial genome of the blackspot seabream, Pagellus bogaraveo (Perciformes: Sparidae), with high levels of length heteroplasmy in the WANCY region. Gene 2008; 409:44-52. [DOI: 10.1016/j.gene.2007.11.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2007] [Revised: 11/09/2007] [Accepted: 11/12/2007] [Indexed: 11/19/2022]
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267
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Rozhnov VV, Meschersky IG, Abramov AV. Geographical variation of the marbled polecat Vormela peregusna (Carnivora: Mustelidae): molecular genetic study. DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2008; 418:27-9. [PMID: 21249544 DOI: 10.1134/s0012496608010092] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2007] [Indexed: 11/22/2022]
Affiliation(s)
- V V Rozhnov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskii pr. 33, Moscow, 119071, Russia
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268
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VAN ZANT JEFFREYL, WOOTEN MICHAELC. Old mice, young islands and competing biogeographical hypotheses. Mol Ecol 2007; 16:5070-83. [DOI: 10.1111/j.1365-294x.2007.03582.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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269
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Igawa T, Kurabayashi A, Usuki C, Fujii T, Sumida M. Complete mitochondrial genomes of three neobatrachian anurans: a case study of divergence time estimation using different data and calibration settings. Gene 2007; 407:116-29. [PMID: 17997052 DOI: 10.1016/j.gene.2007.10.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2007] [Revised: 08/23/2007] [Accepted: 10/01/2007] [Indexed: 11/17/2022]
Abstract
We sequenced the whole mitochondrial (mt) genomes of three neobatrachian species: Japanese tree frog Hyla japonica, Japanese common toad Bufo japonicus, and narrow-mouthed toad Microhyla okinavensis. The gene arrangements of these genomes diverged from that of basal anurans (suborder Archaeobatrachia), but are the same as that of the members of derived frogs (i.e., superfamily Hyloidae and Ranoidae in suborder Neobatrachia), suggesting the one-time occurrence of a gene rearrangement event in an ancestral lineage of derived anurans. Furthermore, several distinct repeat motifs including putative termination-associated sequences (TASs) and conserved sequence blocks (CSBs) were observed in the control regions (CRs) of B. japonicus and H. japonica, while no repeat motifs were found in that of M. okinavensis. Phylogenetic analyses using both nucleotide and amino acid data of mt genes support monophyly of neobatrachians. The estimated divergence time based on amino acid data with multiple reference points suggests that the three living amphibian orders may have originated in the Carboniferous period, and that the divergences of anurans had occurred between the Permian and Tertiary periods. We also checked the influence of the data types and the settings of reference times on divergence time estimation. The resultant divergence times estimated from several datasets and reference time settings suggest that the substitution saturation of nucleotide data may lead to overestimated (i.e., older) branching times, especially for early divergent taxa. We also found a highly accelerated substitution rate in neobatrachian mt genes, and fast substitution possibly resulted in overestimation. To correct this erroneous estimation, it is efficient to apply several reference points among neobatrachians.
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Affiliation(s)
- Takeshi Igawa
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashihiroshima, Hiroshima, Japan
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270
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Assessing genetic variation and population structure of invasive North American beaver (Castor Canadensis Kuhl, 1820) in Tierra Del Fuego (Argentina). Biol Invasions 2007. [DOI: 10.1007/s10530-007-9161-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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271
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Yen NT, Lin CS, Ju CC, Wang SC, Huang MC. Mitochondrial DNA Polymorphism and Determination of Effects on Reproductive Trait in Pigs. Reprod Domest Anim 2007; 42:387-92. [PMID: 17635776 DOI: 10.1111/j.1439-0531.2006.00797.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The purposes of this study were to investigate single strand conformation polymorphisms (SSCP) in the D-loop region of pig mitochondrial DNA (mtDNA) and to determinate their association with the reproductive traits of meishan pigs. A total of four types of band patterns, designed SSCP band pattern A, B, C and D, were identified. A type of SSCP band pattern was present in all European-American breeds, but not in East Asian breeds. This result showed the diversified sequence in the D-loop region between European-American and East Asian populations. Two types of band patterns, B and C, were found in Meishan pigs. The average body weight at day 21 of piglets from B type dams was significantly heavier than the body weight of C type (p < 0.05). We also tested whether the SSCP patterns would be suitable for paternity testing in a family group and found that bands of all the offspring were derived from their maternal parent. Therefore, we conclude that SSCP may be a marker for identification of maternal ancestors.
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Affiliation(s)
- N-T Yen
- Department of Animal Science, National Chung Hsing University, Taichung, Taiwan
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272
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Fajardo V, González I, López-Calleja I, Martín I, Rojas M, García T, Hernández P, Martín R. PCR identification of meats from chamois (Rupicapra rupicapra), pyrenean ibex (Capra pyrenaica), and mouflon (Ovis ammon) targeting specific sequences from the mitochondrial D-loop region. Meat Sci 2007; 76:644-52. [DOI: 10.1016/j.meatsci.2007.02.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Revised: 11/15/2006] [Accepted: 02/02/2007] [Indexed: 10/23/2022]
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273
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Manchado M, Catanese G, Ponce M, Funes V, Infante C. The complete mitochondrial genome of the Senegal sole, Solea senegalensis Kaup. Comparative analysis of tandem repeats in the control region among soles. ACTA ACUST UNITED AC 2007; 18:169-75. [PMID: 17454000 DOI: 10.1080/10425170701308956] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The complete nucleotide sequence of the mitochondrial genome for the Senegal sole Solea senegalensis Kaup was determined. The mitochondrial DNA was 16,659 base pairs (bp) in length. Sequence features of the 13 protein-coding genes, two ribosomal RNAs and 22 transfer RNAs are described. The non-coding control region (1017 bp) was compared with those of the closely related soles Solea solea and Solea lascaris. The typical conservative blocks were identified. A cluster of 42 and 22 tandemly arrayed repeats was detected near the 3' end of control region in S. solea and S. lascaris, respectively. On the contrary, only two (93.8% of haplotypes) or three copies (6.2%) of an 8-bp repeated sequence motif was found in S. senegalensis. Phylogenetic analysis showed that 7 out of 9 of haplotypes bearing three copies grouped in a separate cluster. Possible mechanisms influencing the evolution of control region among soles are discussed.
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Affiliation(s)
- Manuel Manchado
- IFAPA centro El Toruño, 11500 El Puerto de Santa María, Cádiz, Spain.
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274
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Böhme MU, Fritzsch G, Tippmann A, Schlegel M, Berendonk TU. The complete mitochondrial genome of the Green Lizard Lacerta viridis viridis (Reptilia: Lacertidae) and its phylogenetic position within squamate reptiles. Gene 2007; 394:69-77. [PMID: 17391869 DOI: 10.1016/j.gene.2007.02.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Accepted: 02/09/2007] [Indexed: 10/23/2022]
Abstract
For the first time the complete mitochondrial genome was sequenced for a member of Lacertidae. Lacerta viridis viridis was sequenced in order to compare the phylogenetic relationships of this family to other reptilian lineages. Using the long-polymerase chain reaction (long PCR) we characterized a mitochondrial genome, 17,156 bp long showing a typical vertebrate pattern with 13 protein coding genes, 22 transfer RNAs (tRNA), two ribosomal RNAs (rRNA) and one major noncoding region. The noncoding region of L. v. viridis was characterized by a conspicuous 35 bp tandem repeat at its 5' terminus. A phylogenetic study including all currently available squamate mitochondrial sequences demonstrates the position of Lacertidae within a monophyletic squamate group. We obtained a narrow relationship of Lacertidae to Scincidae, Iguanidae, Varanidae, Anguidae, and Cordylidae. Although, the internal relationships within this group yielded only a weak resolution and low bootstrap support, the revealed relationships were more congruent with morphological studies than with recent molecular analyses.
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Affiliation(s)
- M U Böhme
- University of Leipzig, Biology II, Molecular Evolution and Animal Systematics, Talstrasse 33, 04103 Leipzig, Germany.
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275
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Feeroz MM, Hasan K, Hamada Y, Kawamoto Y. STR polymorphism of mtDNA D-loop in rhesus macaques of Bangladesh. Primates 2007; 49:69-72. [PMID: 17530354 DOI: 10.1007/s10329-007-0047-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2006] [Accepted: 03/20/2007] [Indexed: 11/24/2022]
Abstract
Molecular variation of mitochondrial DNA (mtDNA) was investigated for rhesus macaques (Macaca mulatta) of Bangladesh. A partial sequence (583-599 bp) of mtDNA containing the second variable region of the D-loop was compared for 39 individuals from five localities in the country. A total of seven haplotypes were detected with substitutional or insertion/deletion mutations. They contained a unique polymorphism of pentanucleotide STRs (short tandem repeats). There were at least four different length types, from two to five repeats of the unit nucleotide. One site of substitution and one site of single nucleotide insertion/deletion were also involved in the polymorphism. The mutation hot spots of the STR polymorphism were located between the first and second conserved sequence blocks (CSB1 and CSB2), as observed previously in some other mammals. The geographical distribution of the STR polymorphism revealed local differences; the northeastern population was polymorphic with three STR haplotypes, but other local populations were simply monomorphic with a single STR haplotype. Molecular phylogenetic analysis with reported sequences from outside Bangladesh indicated a low substitution diversity of mtDNA in Bangladesh. Clustering results suggested a close relationship to India and divergence from Laos and China.
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276
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Rivera PC, Ittig REG, Fraire HJR, Levis S, Gardenal CN. Molecular identification and phylogenetic relationships among the species of the genus Oligoryzomys (Rodentia, Cricetidae) present in Argentina, putative reservoirs of hantaviruses. ZOOL SCR 2007. [DOI: 10.1111/j.1463-6409.2007.00273.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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277
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Kim BC, Kang TW, Kim MS, Kim CB. The complete mitogenome of Rhodeus uyekii (Cypriniformes, Cyprinidae). ACTA ACUST UNITED AC 2007; 17:181-6. [PMID: 17286045 DOI: 10.1080/10425170600806928] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The complete nucleotide sequence of the mitochondrial genome from the R. uyekii with a total size of 16,817 bp has been determined by long PCR technology. Mitogenome of R. uyekii encoding 13 putative proteins, two ribosomal RNAs and 22 tRNAs shows typical teleost mitogenome structure. Nucleotide composition, amino acid composition and codon usage are in the range of values estimated from other teleost mitogenomes. In the AT rich region of R. uyekii, several conserved blocks which are identified from vertebrates are observed in the genome. R. uyekii, the Korean endemic species, belongs to cyprinid fish from which the information of nine mitogenomes is available. To understand the phylogenetic relationships of Cypriniformes from the known mitogenome information, we analysed Cypriniformes mitogenome based on protein coding gene sequences. In spite of more resolved picture of phylogenetic interrelationships in cyprinid fish in this study, the further study with comprehensive taxon sampling for mitogenome information is strongly needed.
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Affiliation(s)
- Byong-Chul Kim
- National Genome Information Centre, 52 Eoun-dong, Yusong-gu, Daejeon, South Korea
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278
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Peng R, Zeng B, Meng X, Yue B, Zhang Z, Zou F. The complete mitochondrial genome and phylogenetic analysis of the giant panda (Ailuropoda melanoleuca). Gene 2007; 397:76-83. [PMID: 17499457 DOI: 10.1016/j.gene.2007.04.009] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2007] [Revised: 04/10/2007] [Accepted: 04/10/2007] [Indexed: 10/23/2022]
Abstract
The complete mitochondrial genome sequence of the giant panda, Ailuropoda melanoleuca, was determined by the long and accurate polymerase chain reaction (LA-PCR) with conserved primers and primer walking sequence methods. The complete mitochondrial DNA is 16,805 nucleotides in length and contains two ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and one control region. The total length of the 13 protein-coding genes is longer than the American black bear, brown bear and polar bear by 3 amino acids at the end of ND5 gene. The codon usage also followed the typical vertebrate pattern except for an unusual ATT start codon, which initiates the NADH dehydrogenase subunit 5 (ND5) gene. The molecular phylogenetic analysis was performed on the sequences of 12 concatenated heavy-strand encoded protein-coding genes, and suggested that the giant panda is most closely related to bears.
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Affiliation(s)
- Rui Peng
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, PR China
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279
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Bhattacharya P. 3D model of RNA polymerase and bidirectional transcription. Biochem Biophys Res Commun 2007; 355:103-10. [PMID: 17288994 PMCID: PMC1995083 DOI: 10.1016/j.bbrc.2007.01.130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2007] [Accepted: 01/22/2007] [Indexed: 10/23/2022]
Abstract
In the in vitro mitochondrial (mt) transcription initiation system with mt RNA polymerase fraction and mt lysate, the transcription initiation products were shown to be synthesized bidirectionally from the only H-strand-promoter (HSP)/L-strand-promoter region (LSP) of the mitochondrial D-loop genome segment. These transcription products ranged between >100 and >800 bp with the purified mitochondrial RNA polymerase fraction, but were larger (>2030-4000 bp) in size with the mitochondrial lysate in both human and mouse. In this brief report, an in vitro reconstituted mitochondrial transcription system purified by affinity chromatography (heparin-Sepharose) from mouse hypotetraploid letter Ehrlich ascites tumor cell mitochondria was shown to initiate transcription bidirectionally from the mitochondrial D-loop region (HSP/LSP), as evidenced by in vitro generated transcription products. The in vitro generated transcription products were separated by sequencing gel. But this in vitro reconstituted transcription system was not studied beyond the D-loop region. A 3D model of the enzyme RNA polymerase was docked with both ATP and CTP.
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Affiliation(s)
- Pradip Bhattacharya
- Department of Biochemistry, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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280
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Matsui A, Rakotondraparany F, Hasegawa M, Horai S. Determination of a complete lemur mitochondrial genome from feces. MAMMAL STUDY 2007. [DOI: 10.3106/1348-6160(2007)32[7:doaclm]2.0.co;2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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281
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Phylogenetic analyses of complete mitochondrial genome sequences suggest a basal divergence of the enigmatic rodent Anomalurus. BMC Evol Biol 2007; 7:16. [PMID: 17288612 PMCID: PMC1802082 DOI: 10.1186/1471-2148-7-16] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2006] [Accepted: 02/08/2007] [Indexed: 11/24/2022] Open
Abstract
Background Phylogenetic relationships between Lagomorpha, Rodentia and Primates and their allies (Euarchontoglires) have long been debated. While it is now generally agreed that Rodentia constitutes a monophyletic sister-group of Lagomorpha and that this clade (Glires) is sister to Primates and Dermoptera, higher-level relationships within Rodentia remain contentious. Results We have sequenced and performed extensive evolutionary analyses on the mitochondrial genome of the scaly-tailed flying squirrel Anomalurus sp., an enigmatic rodent whose phylogenetic affinities have been obscure and extensively debated. Our phylogenetic analyses of the coding regions of available complete mitochondrial genome sequences from Euarchontoglires suggest that Anomalurus is a sister taxon to the Hystricognathi, and that this clade represents the most basal divergence among sampled Rodentia. Bayesian dating methods incorporating a relaxed molecular clock provide divergence-time estimates which are consistently in agreement with the fossil record and which indicate a rapid radiation within Glires around 60 million years ago. Conclusion Taken together, the data presented provide a working hypothesis as to the phylogenetic placement of Anomalurus, underline the utility of mitochondrial sequences in the resolution of even relatively deep divergences and go some way to explaining the difficulty of conclusively resolving higher-level relationships within Glires with available data and methodologies.
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282
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Jondeung A, Sangthong P, Zardoya R. The complete mitochondrial DNA sequence of the Mekong giant catfish (Pangasianodon gigas), and the phylogenetic relationships among Siluriformes. Gene 2007; 387:49-57. [PMID: 17067766 DOI: 10.1016/j.gene.2006.08.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2006] [Revised: 07/21/2006] [Accepted: 08/01/2006] [Indexed: 10/24/2022]
Abstract
The Mekong giant catfish (Pangasianodon gigas) is the largest scale-less freshwater fish of the world, and a critically endangered species. We determined the complete nucleotide sequence (16,533 bp) of the mitochondrial genome of the Mekong giant catfish, and conducted phylogenetic analyses based on mitochondrial protein (the combined amino acid sequences of all 13 mitochondrial protein coding genes) and rRNA (the combined nucleotide sequences of mitochondrial 12S and 16S rRNA genes) data sets in order to further clarify the relative phylogenetic position of P. gigas, and to recover phylogenetic relationships among 15 out of the 33 families of Siluriformes. Phylogenetic analyses (maximum parsimony, minimum evolution, maximum likelihood, Bayesian inference) of the protein data set were congruent with a basal split of the order into Loricarioidei and Siluroidei, and supported a closer relationship of the Mekong giant catfish (family Pangasiidae) to Siluridae than to Bagridae. The rRNA-based Bayesian phylogeny recovered Callichthyidae as the sister group of all other analyzed non-diplomystid catfish families, rendering Loricarioidei paraphyletic. In addition, Loricariidae were recovered as paraphyletic due to the inclusion of Astroblepidae. However, none of the two relationships received bootstrap support in the maximum parsimony, minimum evolution, and maximum likelihood analyses, and should be interpreted with caution. The derived position of Cetopsidae within Siluroidei, the sister group relationship of Pseudopimelodidae and Pimelodidae, and a close relationship of Doradidae and Auchenipteridae to the exclusion of Mochokidae were strongly supported. Pangasiidae was placed as a single lineage without clear affinities.
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Affiliation(s)
- Amnuay Jondeung
- Department of Genetics, Kasetsart University, Bangkok 10900, Thailand
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283
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Schlick NE, Jensen-Seaman MI, Orlebeke K, Kwitek AE, Jacob HJ, Lazar J. Sequence analysis of the complete mitochondrial DNA in 10 commonly used inbred rat strains. Am J Physiol Cell Physiol 2006; 291:C1183-92. [PMID: 16855218 DOI: 10.1152/ajpcell.00234.2006] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Rat remains a major biomedical model system for common, complex diseases. The rat continues to gain importance as a model system with the completion of its full genomic sequence. Although the genomic sequence has generated much interest, only three complete sequences of the rat mitochondria exist. Therefore, to increase the knowledge of the rat genome, the entire mitochondrial genomes (16,307–16,315 bp) from 10 inbred rat strains (that are standard laboratory models around the world) and 2 wild rat strains were sequenced. We observed a total of 195 polymorphisms, 32 of which created an amino acid change (nonsynonymous substitutions) in 12 of the 13 protein coding genes within the mitochondrial genome. There were 11 single nucleotide polymorphisms within the tRNA genes, six in the 12S rRNA, and 12 in the 16S rRNA including 3 insertions/deletions. We found 14 single nucleotide polymorphisms and 2 insertion/deletion polymorphisms in the D-loop. The inbred rat strains cluster phylogenetically into three distinct groups. The wild rat from Tokyo grouped closely with five inbred strains in the phylogeny, whereas the wild rat from Milwaukee was not closely related to any inbred strain. These data will enable investigators to rapidly assess the potential impact of the mitochondria in these rats on the physiology and the pathophysiology of phenotypes studied in these strains. Moreover, these data provide information that may be useful as new animal models, which result in novel combinations of nuclear and mitochondrial genomes, are developed.
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Affiliation(s)
- Nancy E Schlick
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226-0509, USA
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284
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Yue GH, Liew WC, Orban L. The complete mitochondrial genome of a basal teleost, the Asian arowana (Scleropages formosus, Osteoglossidae). BMC Genomics 2006; 7:242. [PMID: 16989663 PMCID: PMC1592092 DOI: 10.1186/1471-2164-7-242] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2006] [Accepted: 09/21/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondrial DNA-derived sequences have become popular markers for evolutionary studies, as their comparison may yield significant insights into the evolution of both the organisms and their genomes. From the more than 24,000 teleost species, only 254 complete mtDNA sequences are available (GenBank status on 06 Sep 2006). In this paper, we report the complete mitochondrial genome sequence of Asian arowana, a basal bonytongue fish species, which belongs to the order of Osteoglossiformes. RESULTS The complete mitochondrial genomic sequence (mtDNA) of Asian arowana (Scleropages formosus) was determined by using shotgun sequencing method. The length of Asian arowana mtDNA is ca. 16,650 bp (its variation is due to polymorphic repeats in the control region), containing 13 protein-coding genes, 22 tRNA and 2 rRNA genes. Twelve of the thirteen protein coding genes were found to be encoded by the heavy strand in the order typically observed for vertebrate mitochondrial genomes, whereas only nad6 was located on the light strand. An interesting feature of Asian arowana mitogenome is that two different repeat arrays were identified in the control region: a 37 bp tandem repeat at the 5' end and an AT-type dinucleotide microsatellite at the 3' end. Both repeats show polymorphism among the six individuals tested; moreover the former one is present in the mitochondrial genomes of several other teleost groups. The TACAT motif described earlier only from mammals and lungfish was found in the tandem repeat of several osteoglossid and eel species. Phylogenetic analysis of fish species representing Actinopterygii and Sarcopterygii taxa has shown that the Asian arowana is located near the baseline of the teleost tree, confirming its status among the ancestral teleost lineages. CONCLUSION The mitogenome of Asian arowana is very similar to the typical vertebrate mitochondrial genome in terms of gene arrangements, codon usage and base composition. However its control region contains two different types of repeat units at both ends, an interesting feature that to our knowledge has never been reported before for other vertebrate mitochondrial control regions. Phylogenetic analysis using the complete mtDNA sequence of Asian arowana confirmed that it belongs to an ancestral teleost lineage.
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Affiliation(s)
- Gen Hua Yue
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, NUS, Singapore 117604, Singapore
| | - Woei Chang Liew
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
| | - Laszlo Orban
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
- Department of Biological Sciences, The National University of Singapore, Singapore
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285
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Zhao JL, Wang WW, Li SF, Cai WQ. Structure of the Mitochondrial DNA Control Region of the Sinipercine Fishes and Their Phylogenetic Relationship. ACTA ACUST UNITED AC 2006; 33:793-9. [PMID: 16980125 DOI: 10.1016/s0379-4172(06)60112-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2005] [Accepted: 01/24/2006] [Indexed: 10/24/2022]
Abstract
The mitochondrial DNA control region of Siniperca chuatsi, S. kneri, S. scherzeri, S. obscura, S. undulata, Coreosiniperca roulei and Coreoperca whiteheadi were amplified by PCR amplification and directly sequenced. The mtDNA control region of the sinipercine fishes could be separated into three domains, namely, the terminal associated sequence domain, the central conserved sequence domain and the conserved sequence block domain. The extended terminal associated sequence (ETAS), three conserved sequence blocks (CSB-F, CSB-E, CSB-D) in the central conserved sequence domain and three conserved sequence blocks (CSB1, CSB2, CSB3) in the conserved sequence block domain were also identified. The phylogenetic relationships among these sinipercine fishes were constructed through neighbor-joining and maximum parsimony methods using Percidae and Serranidae as outgroups. Results showed that sinipercine fishes were a monophyletic group, with Siniperca forming one group, and Coreoperca forming another group. Coreosiniperca roulei did not form an independent group but was merged into the genus Siniperca. Thus it should be renamed as Siniperca roulei.
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Affiliation(s)
- Jin-Liang Zhao
- Key Laboratory of Aquatic Genetic Resources and Aquacultural Ecosystem Certificated by the Ministry of Agriculture, Shanghai Fisheries University, Shanghai 200090, China.
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286
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Kim IC, Jung SO, Lee YM, Lee CJ, Park JK, Lee JS. The complete mitochondrial genome of the rayfish Raja porosa (Chondrichthyes, Rajidae). ACTA ACUST UNITED AC 2006; 16:187-94. [PMID: 16147874 DOI: 10.1080/10425170500087975] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
We isolated mitochondrial DNA from the rayfish Raja porosa by long-polymerase chain reaction (Long-PCR) with conserved primers, and sequenced it by primer walking method using flanking sequences as sequencing primers. R. porosa mitochondrial DNA consists of 16,972 bp and its structural organization is conserved in comparison with other fishes and mammals. Based on the mitochondrial cytochrome b (cyt b) sequence, the phylogenetic position of R. porosa among cartilaginous fishes was inferred using different phylogenetic methods (ML-based quartet puzzling, Neighbor-joining (NJ) and Bayesian approaches). In this paper, we report the characteristics of the R. porosa mitochondrial genome including structural organization, base composition of rRNAs, tRNAs and protein-encoding genes and characteristics of mitochondrial tRNAs. These findings are applicable to comparative mitogenomics of R. porosa with other related taxa.
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Affiliation(s)
- Il-Chan Kim
- Polar BioCenter, Korea Polar Research Institute, Korea Ocean Research & Development Institute, Ansan, South Korea
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287
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Iyengar A, Diniz FM, Gilbert T, Woodfine T, Knowles J, Maclean N. Structure and evolution of the mitochondrial control region in oryx. Mol Phylogenet Evol 2006; 40:305-14. [PMID: 16616521 DOI: 10.1016/j.ympev.2006.02.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2005] [Revised: 02/06/2006] [Accepted: 02/16/2006] [Indexed: 11/22/2022]
Affiliation(s)
- Arati Iyengar
- School of Biological Sciences, University of Southampton, Southampton SO16 7PX, UK.
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288
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Nilsson MA. Phylogenetic relationships of the Banded Hare wallaby (Lagostrophus fasciatus) and a map of the kangaroo mitochondrial control region. ZOOL SCR 2006. [DOI: 10.1111/j.1463-6409.2006.00237.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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289
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Goricki S, Trontelj P. Structure and evolution of the mitochondrial control region and flanking sequences in the European cave salamander Proteus anguinus. Gene 2006; 378:31-41. [PMID: 16764998 DOI: 10.1016/j.gene.2006.04.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2006] [Revised: 04/18/2006] [Accepted: 04/20/2006] [Indexed: 10/24/2022]
Abstract
The European cave salamander Proteus anguinus Laurenti 1768 is one of the best-known subterranean animals, yet its evolutionary history and systematic relationships remain enigmatic. This is the first comprehensive study on molecular evolution within the taxon, using an mtDNA segment containing the control region (CR) and adjacent sequences. Two to seven tandem repeats of 24-32 bp were found in the intergenic spacer region (VNTR1), and three, four or six repeats, 59-77 bp each, in the 3' end of the CR (VNTR2). Different molecular mechanisms account for VNTR2 formation in different lineages of Proteus. The overall CR variation was lower than that of the spacer region, the 3' end of the cytb gene, or the tRNA genes. Individual genes and the concatenated non-repetitive sequences produced similar, well resolved maximum likelihood, Bayesian inference and parsimony trees. The numbers of repeat elements as well as the genealogy of the VNTR2 repeat units were mostly inconsistent with the groupings of the non-repetitive sequences. Different degrees of repeat array homogenization were detected in all major groups. Orthology was established for the first and the second VNTR2 elements of some populations. These two copies may therefore be used for analyses at the population level. The pattern of CR sequence variation points to strong genetic isolation of hydrographically separated populations. Genetic separation of the major groups of populations is incongruent with the current division into subspecies.
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Affiliation(s)
- Spela Goricki
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Vecna pot 111, SI-1000 Ljubljana, Slovenia
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290
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Tang Q, Liu H, Mayden R, Xiong B. Comparison of evolutionary rates in the mitochondrial DNA cytochrome b gene and control region and their implications for phylogeny of the Cobitoidea (Teleostei: Cypriniformes). Mol Phylogenet Evol 2006; 39:347-57. [PMID: 16213167 DOI: 10.1016/j.ympev.2005.08.007] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2005] [Revised: 08/15/2005] [Accepted: 08/18/2005] [Indexed: 10/25/2022]
Abstract
It is widely accepted that mitochondrial DNA (mtDNA) control region evolves faster than protein encoding genes with few exceptions. In the present study, we sequenced the mitochondrial cytochrome b gene (cyt b) and control region (CR) and compared their rates in 93 specimens representing 67 species of loaches and some related taxa in the Cobitoidea (Order Cypriniformes). The results showed that sequence divergences of the CR were broadly higher than those of the cyt b (about 1.83 times). However, in considering only closely related species, CR sequence evolution was slower than that of cyt b gene (ratio of CR/cyt b is 0.78), a pattern that is found to be very common in Cypriniformes. Combined data of the cyt b and CR were used to estimate the phylogenetic relationship of the Cobitoidea by maximum parsimony, neighbor-joining, and Bayesian methods. With Cyprinus carpio and Danio rerio as outgroups, three analyses identified the same four lineages representing four subfamilies of loaches, with Botiinae on the basal-most clade. The phylogenetic relationship of the Cobitoidea was ((Catostomidae+Gyrinocheilidae)+(Botiinae+(Balitorinae+(Cobitinae+Nemacheilinae)))), which indicated that Sawada's Cobitidae (including Cobitinae and Botiinae) was not monophyletic. Our molecular phylogenetic analyses are in very close agreement with the phylogenetic results based on the morphological data proposed by Nalbant and Bianco, wherein these four subfamilies were elevated to the family level as Botiidae, Balitoridae, Cobitidae, and Nemacheilidae.
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Affiliation(s)
- Qiongying Tang
- Institute of Hydrobiology, Chinese Academy of Sciences, Hubei, Wuhan 430072, PR China
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291
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Montoya J, López-Pérez MJ, Ruiz-Pesini E. Mitochondrial DNA transcription and diseases: past, present and future. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:1179-89. [PMID: 16697348 DOI: 10.1016/j.bbabio.2006.03.023] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2006] [Revised: 03/21/2006] [Accepted: 03/31/2006] [Indexed: 11/25/2022]
Abstract
The transcription of mitochondrial DNA has been studied for 30 years. However, many of the earlier observations are still unsolved. In this review we will recall the basis of mitochondrial DNA transcription, established more than twenty years ago, will include some of the recent progress in the understanding of this process and will suggest hypotheses for some of the unexplained topics. Moreover, we will show some examples of mitochondrial pathology due to altered transcription and RNA metabolism.
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Affiliation(s)
- Julio Montoya
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza-Instituto Aragonés de Ciencias de la Salud, Miguel Servet 177, 50013-Zaragoza, Spain.
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292
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Cabria MT, Rubines J, Gómez-Moliner B, Zardoya R. On the phylogenetic position of a rare Iberian endemic mammal, the Pyrenean desman (Galemys pyrenaicus). Gene 2006; 375:1-13. [PMID: 16624502 DOI: 10.1016/j.gene.2006.01.038] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2005] [Revised: 01/25/2006] [Accepted: 01/27/2006] [Indexed: 11/21/2022]
Abstract
The nucleotide sequences of the complete mitochondrial genome and nine partial nuclear genes of the Pyrenean desman (Galemys pyrenaicus) were determined in order to establish the relative phylogenetic position of this species at different taxonomic levels within the placental tree. Phylogenetic relationships of desman within the family Talpidae were inferred based on complete mitochondrial cytochrome b gene nucleotide sequence data. The Pyrenean desman was unambiguously recovered as sister group of the Russian desman (Desmana moschata) confirming the monophyly of the subfamily Desmaninae. However, phylogenetic relationships among major lineages within the Talpidae could not be confidently resolved. Phylogenetic analyses based on mitochondrial (at the amino acid level) and nuclear (at the nucleotide level) sequence data sets confidently placed desman within the Eulipotyphla (that also included moles, shrews, and hedgehogs), and partially recovered placental interordinal relationships. The monophyly of Laurasiatheria (including Eulipotyphla, Chiroptera, Carnivora, Pholidota, Perissodactyla, and Cetartiodactyla) was strongly supported. Mitochondrial amino acid sequences of Pholidota (pangolins) were found to bias phylogenetic inferences due to long-branch attraction effects. A Bayesian inference based on a combined mitochondrial and nuclear data set without Pholidota arrived at an almost fully resolved tree that supported the basal position of Eulipotyphla within Laurasiatheria.
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Affiliation(s)
- María Teresa Cabria
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal, 2, 28006 Madrid, Spain
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293
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Abbott CL, Double MC, Trueman JWH, Robinson A, Cockburn A. An unusual source of apparent mitochondrial heteroplasmy: duplicate mitochondrial control regions in Thalassarche albatrosses. Mol Ecol 2006; 14:3605-13. [PMID: 16156827 DOI: 10.1111/j.1365-294x.2005.02672.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Molecular ecologists, in search of suitable molecular markers, frequently PCR-amplify regions of mitochondrial DNA from total DNA extracts. This approach, although common, is prone to the co-amplification of nuclear copies of transposed DNA sequences (numts), which can then generate apparent mitochondrial sequence heteroplasmy. In this study we describe the discovery of apparent mitochondrial sequence heteroplasmy in Thalassarche albatrosses but eliminate the possibility of true sequence heteroplasmy and numts and instead reveal the source of the apparent heteroplasmy to be a duplicated control region. The two control regions align easily but are not identical in sequence or in length. Comparisons of functionally significant conserved sequence blocks do not provide evidence of degeneration in either duplicate. Phylogenetic analyses of domain I of both control region copies in five Thalassarche species indicate that they are largely evolving in concert; however, a short section within them is clearly evolving independently. To our knowledge this is the first time contrasting evolutionary patterns have been reported for duplicate control regions. Available evidence suggests that this duplication may be taxonomically widespread, so the results presented here should be considered in future evolutionary studies targeting the control region of all Procellariiformes and potentially other closely related avian groups.
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Affiliation(s)
- Cathryn L Abbott
- School of Botany and Zoology, The Australian National University, Canberra ACT 0200, Australia
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294
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Wu HL, Fang SG. Mitochondrial DNA genetic diversity of black muntjac (Muntiacus crinifrons), an endangered species endemic to China. Biochem Genet 2006; 43:407-16. [PMID: 16187164 DOI: 10.1007/s10528-005-6779-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2004] [Accepted: 11/10/2004] [Indexed: 10/25/2022]
Abstract
Genetic diversities based on the mtDNA control region were measured for both a wild population (n = 26) and a captive population (n = 18) of the black muntjac. In total, nine haplotypes were obtained from 44 samples. The wild population exhibited a low nucleotide diversity (pi = 0.00562), which suggests that the black muntjac had a small effective population size historically. In contrast to its low nucleotide diversity, haplotype diversity (h = 0.862) of the wild population was relatively high. Haplotype distribution among local samples shows a distinct difference. As anticipated because of the paucity of available founders, nucleotide diversity (pi = 0.00214) of the captive population was very low. Additionally, a high degree of haplotype identity and an obvious haplotype frequency bias was revealed in the captive population, which implies that the current breeding program should be readjusted to balance distributions of haplotypes, and some new founders should be introduced to the captive population to alleviate potential inbreeding depression.
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Affiliation(s)
- Hai-Long Wu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, P.R. China
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295
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PÉREZ-HARO M, VIÑAS J, MAÑAS F, BATET A, RUIZ-OLMO J, PLA C. Genetic variability in the complete mitochondrial control region of the Eurasian otter (Lutra lutra) in the Iberian Peninsula. Biol J Linn Soc Lond 2005. [DOI: 10.1111/j.1095-8312.2005.00536.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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296
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Mohlke KL, Jackson AU, Scott LJ, Peck EC, Suh YD, Chines PS, Watanabe RM, Buchanan TA, Conneely KN, Erdos MR, Narisu N, Enloe S, Valle TT, Tuomilehto J, Bergman RN, Boehnke M, Collins FS. Mitochondrial polymorphisms and susceptibility to type 2 diabetes-related traits in Finns. Hum Genet 2005; 118:245-54. [PMID: 16142453 DOI: 10.1007/s00439-005-0046-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2004] [Accepted: 07/12/2005] [Indexed: 12/29/2022]
Abstract
Mitochondria play an integral role in ATP production in cells and are involved in glucose metabolism and insulin secretion, suggesting that variants in the mitochondrial genome may contribute to diabetes susceptibility. In a study of Finnish families ascertained for type 2 diabetes mellitus (T2DM), we genotyped single nucleotide polymorphisms (SNPs) based on phylogenetic networks. These SNPs defined eight major haplogroups and subdivided groups H and U, which are common in Finns. We evaluated association with both diabetes disease status and up to 14 diabetes-related traits for 762 cases, 402 non-diabetic controls, and 465 offspring of genotyped females. Haplogroup J showed a trend toward association with T2DM affected status (OR 1.69, P=0.056) that became slightly more significant after excluding cases with affected fathers (OR 1.77, P=0.045). We also genotyped non-haplogroup-tagging SNPs previously reported to show evidence for association with diabetes or related traits. Our data support previous evidence for association of T16189C with reduced ponderal index at birth and also show evidence for association with reduced birthweight but not with diabetes status. Given the multiple tests performed and the significance levels obtained, this study suggests that mitochondrial genome variants may play at most a modest role in glucose metabolism in the Finnish population. Furthermore, our data do not support a reported maternal inheritance pattern of T2DM but instead show a strong effect of recall bias.
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Affiliation(s)
- Karen L Mohlke
- Department of Genetics, University of North Carolina, 4109-F Neurosciences Research Building, 103 Mason Farm Road, CB#7264, 27599-7264, Chapel Hill, NC, USA.
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297
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Bannikova S, Zorov DB, Shoeman RL, Tolstonog GV, Traub P. Stability and Association with the Cytomatrix of Mitochondrial DNA in Spontaneously Immortalized Mouse Embryo Fibroblasts Containing or Lacking the Intermediate Filament Protein Vimentin. DNA Cell Biol 2005; 24:710-35. [PMID: 16274293 DOI: 10.1089/dna.2005.24.710] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To extend previous observations demonstrating differences in number, morphology, and activity of mitochondria in spontaneously immortalized vim(+) and vim(-) fibroblasts derived from wild-type and vimentin knockout mice, some structural and functional aspects of mitochondrial genome performance and integrity in both types of cells were investigated. Primary Vim(+/+) and Vim(-/-) fibroblasts, which escaped terminal differentiation by immortalization were characterized by an almost twofold lower mtDNA content in comparison to that of their primary precursor cells, whereby the average mtDNA copy number in two clones of vim(+) cells was lower by a factor of 0.6 than that in four clones of vim(-) cells. However, during serial subcultivation up to high passage numbers, the vim(+) and vim() fibroblasts increased their mtDNA copy number 1.5- and 2.5-fold, respectively. While early-passage cells of the vim(+) and vim(-) fibroblast clones differed only slightly in the ratio between mtDNA content and mitochondrial mass represented by mtHSP70 protein, after ca. 300 population doublings the average mtDNA/mtmass ratio in the vim(+) and vim() cells was increased by a factor of 2 and 4.5, respectively. During subcultivation, both types of cells acquired the fully transformed phenotype. These findings suggest that cytoskeletal vimentin filaments exert a strong influence on the mechanisms controlling mtDNA copy number during serial subcultivation of immortalized mouse embryo fibroblasts, and that vimentin deficiency causes a disproportionately enhanced mtDNA content in high-passage vim(-) fibroblasts. Such a role of vimentin filaments was supported by the stronger retention potential for mtDNA and mtDNA polymerase (gamma) detected in vim(+) fibroblasts by Triton X-100 extraction of mitochondria and agaroseembedded cells. Moreover, although the vim(+) and vim(-) fibroblasts were equally active in generating free radicals, the vim(-) cells exhibited higher levels of immunologically detectable 8-oxoG and mismatch repair proteins MSH2 and MLH1 in their mitochondria. Because in vim(-) fibroblasts only one point mutation was detected in the mtDNA D-loop control region, these cells are apparently able to efficiently remove oxidatively damaged nucleobases. On the other hand, a number of large-scale mtDNA deletions were found in high-passage vim(-) fibroblasts, but not in low-passage vim(-) cells and vim(+) cells of both low and high passage. Large mtDNA deletions were also induced in young vim(-) fibroblasts by treatment with the DNA intercalator ethidium bromide, whereas no such deletions were found after treatment of vim(+) cells. These results indicate that in immortalized vim(-) fibroblasts the mitochondrial genome is prone to large-scale rearrangements, probably due to insufficient control of mtDNA repair and recombination processes in the absence of vimentin.
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298
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Royo LJ, Alvarez I, Beja-Pereira A, Molina A, Fernández I, Jordana J, Gómez E, Gutiérrez JP, Goyache F. The origins of Iberian horses assessed via mitochondrial DNA. ACTA ACUST UNITED AC 2005; 96:663-9. [PMID: 16251517 DOI: 10.1093/jhered/esi116] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Despite a number of recent studies that have focused on the origin of domestic horses, genetic relationships between major geographical clusters still remain poorly understood. In this study we analyzed a 296 bp mtDNA fragment from the HVI region of 171 horses representing 11 native Iberian, Barb, and Exmoor breeds to assess the maternal phylogeography of Iberian horses. The mtDNA haplogroup with a CCG motif (nucleotide position 15,494 to 15,496) was the most frequent in Iberian and Barb breeds (0.42 and 0.57, respectively), regardless of geographic location or group of breeds. This finding supports the close genetic relationship between the ancestral mare populations of the Iberian Peninsula and Northern Africa. Phenotypic differences among the Northern and Southern Iberian groups of breeds are not explained by population subdivision based on maternal lineages. Our results also suggest that Northern Iberian ponies--which are phenotypically close to British ponies, especially Exmoor--are the result of an introgression rather than population replacement.
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Affiliation(s)
- L J Royo
- Area de Genética y Reproducción Animal, SERIDA, E-33203 Gijón, Asturias, Spain
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299
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Durka W, Babik W, Ducroz JF, Heidecke D, Rosell F, Samjaa R, Saveljev AP, Stubbe A, Ulevicius A, Stubbe M. Mitochondrial phylogeography of the Eurasian beaver Castor fiber L. Mol Ecol 2005; 14:3843-56. [PMID: 16202100 DOI: 10.1111/j.1365-294x.2005.02704.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nucleotide variation in an approximately 490 bp fragment of the mitochondrial DNA control region (mtDNA CR) was used to describe the genetic variation and phylogeographical pattern in the Eurasian beaver (Castor fiber) over its entire range. The sampling effort was focused on the relict populations that survived a drastic population bottleneck, caused by overhunting, at the end of the 19th century. A total of 152 individuals grouped into eight populations representing all currently recognized subspecies were studied. Sixteen haplotypes were detected, none of them shared among populations. Intrapopulation sequence variation was very low, most likely a result of the severe bottleneck. Extreme genetic structure could result from human-mediated extinction of intermediate populations, but it could also be an effect of prior substantial structuring of the beaver populations with watersheds of major Eurasian rivers acting as barriers to gene flow. Phylogenetic analysis revealed the presence of two mtDNA lineages: eastern (Poland, Lithuania, Russia and Mongolia) and western (Germany, Norway and France), the former comprising more divergent haplotypes. The low level of sequence divergence of the entire cytochrome b gene among six individuals representing six subspecies suggests differentiation during the last glacial period and existence of multiple glacial refugia. At least two evolutionary significant units (ESU) can be identified, the western and the eastern haplogroup. The individual relict populations should be regarded as management units, the eastern subspecies possibly also as ESUs. Guidelines for future translocations and reintroductions are proposed.
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Affiliation(s)
- Walter Durka
- UFZ Center for Environmental Research Leipzig-Halle GmbH, Department of Community Ecology (BZF), 06120 Halle (Saale), Germany.
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300
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Cao L, Kenchington E, Zouros E, Rodakis GC. Evidence that the large noncoding sequence is the main control region of maternally and paternally transmitted mitochondrial genomes of the marine mussel (Mytilus spp.). Genetics 2005; 167:835-50. [PMID: 15238532 PMCID: PMC1470915 DOI: 10.1534/genetics.103.026187] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Both the maternal (F-type) and paternal (M-type) mitochondrial genomes of the Mytilus species complex M. edulis/galloprovincialis contain a noncoding sequence between the l-rRNA and the tRNA(Tyr) genes, here called the large unassigned region (LUR). The LUR, which is shorter in M genomes, is capable of forming secondary structures and contains motifs of significant sequence similarity with elements known to have specific functions in the sea urchin and the mammalian control region. Such features are not present in other noncoding regions of the F or M Mytilus mtDNA. The LUR can be divided on the basis of indels and nucleotide variation in three domains, which is reminiscent of the tripartite structure of the mammalian control region. These features suggest that the LUR is the main control region of the Mytilus mitochondrial genome. The middle domain has diverged by only 1.5% between F and M genomes, while the average divergence over the whole molecule is approximately 20%. In contrast, the first domain is among the most divergent parts of the genome. This suggests that different parts of the LUR are under different selection constraints that are also different from those acting on the coding parts of the molecule.
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Affiliation(s)
- Liqin Cao
- Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4J1, Canada
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