Rarity of tagSNPs across transferred mtDNA inserts in human genome

The study deals with the single nucleotide polymorphism (SNPs, HapMap data) around the mtDNA insertions in human genome. The results obtained from this study suggest that application of tagSNP approach for large scale genotyping targeting NUMT integration sites may be difficult due to lack of informative mutations around these loci. This warrants development of new approaches to tag mtDNA inserts in genome-wide association studies.     

黄瓜生殖细胞分离及其线粒体DNA的观察与拷贝数定量分析

该研究以6～8月上午10点左右摘取的新鲜黄瓜花朵为材料,采用渗透压冲击的方法分离黄瓜生殖细胞,并应用竞争型定量PCR技术测定其线粒体DNA数量,分析生殖细胞在发育过程中线粒体DNA的变化,以明确高丰度线粒体DNA的来源,为进一步研究被子植物调控线粒体DNA扩增的分子机制奠定基础。结果显示:(1)DAPI染色观察发现,黄瓜生殖细胞的细胞核周围存在大量的细胞器DNA荧光点,表明黄瓜生殖细胞的细胞质中存在大量的线粒体DNA。(2)成熟黄瓜生殖细胞平均包含(1 037±126)个线粒体DNA拷贝。(3)成熟生殖细胞内线粒体DNA含量为早期生殖细胞的14.5倍,表明成熟生殖细胞中的线粒体DNA主要来自于生殖细胞形成后其内活跃的线粒体DNA扩增。研究认为,黄瓜生殖细胞内活跃的线粒体DNA是黄瓜线粒体父系遗传的基础。     

The complete mitochondrial genome of Temminck's ground pangolin (Smutsia temminckii; Smuts, 1832) and phylogenetic position of the Pholidota (Weber, 1904)

Temmincki's ground pangolin is primarily a nocturnal mammal belonging to the order Pholidota. The body is covered in hard overlapping scales and these animals find refuge in burrows, feeding only on termites and ants. In this study, the whole mtDNA of Temmincki's ground pangolin was sequenced and the phylogenetic position of Pholidota determined within Eutheria, using whole mtDNA sequences from various representative species. The results indicate that the whole mtDNA of Temmincki's ground pangolin is 16,559 bp long and shared some similarities with the whole mtDNA of the back-bellied tree pangolin and the Chinese pangolin. Phylogenetic analysis indicate that the order Pholidota is closely related and share a recent common ancestor with the order Carnivora rather than with the ant/insect eating order Xenarthra and the group Afrotheria. A time measured phylogeny of Pholidota estimated a split from Carnivora at around 87 mya, followed by a split of the African pangolins from their Asian counterparts such as the Chinese pangolin at around 47 mya. This suggests a Laurasian origin and convergent evolution of the Pholidota with respect to Xenarthra and Afrotheria.     

MitoMorphy: an alignment and annotation tool for human mitochondrial DNA polymorphisms

MitoMorphy uses a number of publicly available human mitochondrial DNA (mtDNA) sequences from different ethnic groups to compare and annotate the associated polymorphic data. It provides an integrated display of mtDNA sequence comparison, sequence variation, and annotation for 695 different mtDNA sequences from many different ethnic groups around the world.     

Phylogeographic sympatry and isolation of the Eurasian badgers (Meles, Mustelidae, Carnivora): Implications for an alternative analysis using maternally as well as paternally inherited genes

In the present study, to further understand the phylogenetic relationships among the Eurasian badgers (Meles, Mustelidae, Carnivora), which are distributed widely in the Palearctic, partial sequences of the mitochondrial DNA (mtDNA) control region (539-545 base-pairs) as a maternal genetic marker, and the sex-determining region on the Y-chromosome gene (SRY: 1052-1058 base-pairs), as a paternal genetic marker, were examined. The present study revealed ten SRY haplotypes from 47 males of 112 individuals of the Eurasian Continent and Japan. In addition, 39 mtDNA haplotypes were identified from those animals. From the phylogeography of both the uniparentally inherited genes, four lineages were recognized as Japanese, eastern Eurasian, Caucasian, and western Eurasian. The distribution patterns of the mtDNA lineages showed the existence of a sympatric zone between the eastern and western Eurasian lineages around the Volga River in western Russia. Furthermore, the present study suggested that in the Japanese badgers, the larger genetic differentiation of the Shikoku population was attributable to geographic history in the Japanese islands.     

Relative information content of polymorphic microsatellites and mitochondrial DNA for inferring dispersal and population genetic structure in the olive sea snake, Aipysurus laevis

Polymorphic microsatellites are widely considered more powerful for resolving population structure than mitochondrial DNA (mtDNA) markers, particularly for recently diverged lineages or geographically proximate populations. Weaker population subdivision for biparentally inherited nuclear markers than maternally inherited mtDNA may signal male-biased dispersal but can also be attributed to marker-specific evolutionary characteristics and sampling properties. We discriminated between these competing explanations with a population genetic study on olive sea snakes, Aipysurus laevis. A previous mtDNA study revealed strong regional population structure for A. laevis around northern Australia, where Pleistocene sea-level fluctuations have influenced the genetic signatures of shallow-water marine species. Divergences among phylogroups dated to the Late Pleistocene, suggesting recent range expansions by previously isolated matrilines. Fine-scale population structure within regions was, however, poorly resolved for mtDNA. In order to improve estimates of fine-scale genetic divergence and to compare population structure between nuclear and mtDNA, 354 olive sea snakes (previously sequenced for mtDNA) were genotyped for five microsatellite loci. F statistics and Bayesian multilocus genotype clustering analyses found similar regional population structure as mtDNA and, after standardizing microsatellite F statistics for high heterozygosities, regional divergence estimates were quantitatively congruent between marker classes. Over small spatial scales, however, microsatellites recovered almost no genetic structure and standardized F statistics were orders of magnitude smaller than for mtDNA. Three tests for male-biased dispersal were not significant, suggesting that recent demographic expansions to the typically large population sizes of A. laevis have prevented microsatellites from reaching mutation-drift equilibrium and local populations may still be diverging.     

The mitochondrial theory of aging: dead or alive?

The mitochondrial theory of aging is based around the idea of a vicious cycle, in which somatic mutation of mtDNA engenders respiratory chain dysfunction, enhancing the production of DNA-damaging oxygen radicals. In turn, this is proposed to result in the accumulation of further mtDNA mutations. Finally, a bioenergetic crisis leads to overt tissue dysfunction and degeneration. A substantial body of circumstantial evidence seems to support this idea. However, the extent of detectable mtDNA mutation is far less than can easily be reconciled to this hypothesis, unless it is assumed that a subset of cells with much higher than average mtDNA mutation load is systematically lost by apoptosis. A rigorous test of the hypothesis remains to be undertaken, but would require a direct manipulation of the rate of mtDNA mutagenesis, to test whether this could alter the kinetics of aging.     

Abundant sequence variation around the mitochondrial origin of replication in the human opportunistic yeast pathogen Candida albicans from a tropical island in China

Due to its haploid nature and its predominantly uniparental mode of inheritance, the mitochondrial genome has been analyzed extensively in population and evolutionary genetic studies of eukaryotes. Among the mitochondrial DNA (mtDNA) fragments, the region surrounding the origin of replication is the most commonly studied. However, most of the studies have focused on animals and little is known about the extent and patterns of sequence variation around the mtDNA origin of replication (mtOri) in fungi. In this study, we found abundant variation in a 597bp fragment surrounding the mtOri for 53 isolates of the pathogenic yeast Candida albicans obtained from a diverse group of hosts in Hainan, a tropical island of China. Within this DNA fragment, a total of 17 haplotypes were found for the 53 isolates. The extent of sequence variation for this group of strains was similar to that for 24 strains that represented the global nuclear genotype diversity. In contrast to those in animals where there were significant biases in favor of transitional mutations (e.g. the transition to transversion ratio is about 20 in human mtDNA), our data showed a transition to transversion ratio of approximately 0.5 around mtOri in C. albicans. Our analysis revealed no apparent geographic pattern of sequence variation based on the birthplaces of the analyzed hosts. However, the sample from patients had a lower genotypic diversity than those from healthy hosts borne either in Hainan or elsewhere in China. Our results suggest that C. albicans mtDNA has a base substitution pattern different from its nuclear genome and that sequences from the mtOri region could enhance our understanding of C. albicans genome evolution and population structuring.     

Genetic Analysis of Systematic Mitochondrial Heteroplasmy in Rabbits

One unusual property of rabbit mitochondrial DNA (mtDNA) is the existence of repeated 153-bp motifs in the vicinity of the replication origin of its H strand. Furthermore, every individual is heteroplasmic: it carries mtDNA molecules with a variable number of repeats. A systematic study of 8 females and their progeny has been devised to analyze mtDNA transmission through generations. The results suggest that three mechanisms are acting simultaneously. (1) Genetic drift in the germ line is revealed by the evolution of heteroplasmy when two major molecular forms are present in a female. (2) A high mutation rate (around 10(-2) per animal generation) generating molecular diversity, by deletion and addition of repeated units, is required to explain the observation of heteroplasmy in every individual. Moreover, the rates of mutation from the most frequent type to the other types are unequal. The deletion of one unit is more frequent than a deletion of two units, which is in turn more frequent than a deletion of three. (3) Selection for shorter molecules in somatic cells is probable. The frequency distribution of mtDNA types depends on the organ analyzed (kidney-spleen and liver vs. gonads).     

Segregation of mitochondria in the cytoplasm of Xenopus vitellogenic oocytes

In actively growing vitellogenic oocytes of Xenopus laevis mitochondria segregate into 2 populations. One stays around the nucleus, actively replicates mitochondrial DNA (mtDNA), and builds up most of the stock of the mitochondria in the full-grown oocyte. The other moves toward the vegetal pole and stops replicating mtDNA early in vitellogenesis. Organelles of this population are components of the germ plasm of the cell.     

mtDNA variation among Greenland Eskimos: the edge of the Beringian expansion

The Eskimo-Aleut language phylum is distributed from coastal Siberia across Alaska and Canada to Greenland and is well distinguished from the neighboring Na Dene languages. Genetically, however, the distinction between Na Dene and Eskimo-Aleut speakers is less clear. In order to improve the genetic characterization of Eskimos in general and Greenlanders in particular, we have sequenced hypervariable segment I (HVS-I) of the mitochondrial DNA (mtDNA) control region and typed relevant RFLP sites in the mtDNA of 82 Eskimos from Greenland. A comparison of our data with published sequences demonstrates major mtDNA types shared between Na Dene and Eskimo, indicating a common Beringian history within the Holocene. We further confirm the presence of an Eskimo-specific mtDNA subgroup characterized by nucleotide position 16265G within mtDNA group A2. This subgroup is found in all Eskimo groups analyzed so far and is estimated to have originated <3,000 years ago. A founder analysis of all Eskimo and Chukchi A2 types indicates that the Siberian and Greenland ancestral mtDNA pools separated around the time when the Neo-Eskimo culture emerged. The Greenland mtDNA types are a subset of the Alaskan mtDNA variation: they lack the groups D2 and D3 found in Siberia and Alaska and are exclusively A2 but at the same time lack the A2 root type. The data are in agreement with the view that the present Greenland Eskimos essentially descend from Alaskan Neo-Eskimos. European mtDNA types are absent in our Eskimo sample.     

Segregation patterns of a novel mutation in the mitochondrial tRNA glutamic acid gene associated with myopathy and diabetes mellitus.

We have identified a novel mtDNA mutation in a 29-year-old man with myopathy and diabetes mellitus. This T-->C transition at mtDNA position 14709 alters an evolutionarily conserved nucleotide in the region specifying for the anticodon loop of the mitochondrial tRNA(Glu). The nt-14709 mutation was heteroplasmic but present at very high levels in the patient's muscle, white blood cells (WBCs), and hair follicles; lower proportions of mutated mtDNA were observed in WBCs and hair follicles of all examined maternal relatives. In the patient's muscle, abnormal fibers showed mitochondrial proliferation, severe focal defects in cytochrome c oxidase activity, and absence of cross-reacting material for mitochondrially synthesized polypeptides. These fibers had higher levels of mutated mtDNA than did surrounding "normal" fibers. Although the percentage of mutated mtDNA in WBCs from family members were distributed around the percentage observed in the mothers, the pattern was different in hair follicles, where the mutated population tended to increase in subsequent generations. PCR/RFLP analysis of single hairs showed that the intercellular variations in the percentage of mutated mtDNA differed among family members, with younger generations having a more homogeneous distribution of mutated mtDNA in different hair follicles. These results suggest that the intercellular distribution of the mutated and wild-type mtDNA populations may drift toward homogeneity in subsequent generations.     

Respiratory-competent yeast mitochondrial DNAs generated by deleting intergenic regions

Two respiratory-competent yeast strains having mitochondrial (mt) DNA characterized by single non-overlapping deletions, encompassing intergenic sequences, have been crossed. Diploid daughter clones have been screened by electrophoresis of mtDNA fragments, and a respiratory-competent clone (ER8.75), having a recombinant small mtDNA with both parental deletions, has been detected. ER8.75 mtDNA lacks around 20% of wild-type intergenic sequences, encompassing three ori/rep sequences. This mutant could be helpful in analyzing the organelle genome and, particularly, the function of intergenic sequences.     

Twinkle and POLG defects enhance age-dependent accumulation of mutations in the control region of mtDNA

Autosomal dominant and/or recessive progressive external ophthalmoplegia (ad/arPEO) is associated with mtDNA mutagenesis. It can be caused by mutations in three nuclear genes, encoding the adenine nucleotide translocator 1, the mitochondrial helicase Twinkle or DNA polymerase γ (POLG). How mutations in these genes result in progressive accumulation of multiple mtDNA deletions in post- mitotic tissues is still unclear. A recent hypothesis suggested that mtDNA replication infidelity could promote slipped mispairing, thereby stimulating deletion formation. This hypothesis predicts that mtDNA of ad/arPEO patients will contain frequent mutations throughout; in fact, our analysis of muscle from ad/arPEO patients revealed an age-dependent, enhanced accumulation of point mutations in addition to deletions, but specifically in the mtDNA control region. Both deleted and non-deleted mtDNA molecules showed increased point mutation levels, as did mtDNAs of patients with a single mtDNA deletion, suggesting that point mutations do not cause multiple deletions. Deletion breakpoint analysis showed frequent breakpoints around homopolymeric runs, which could be a signature of replication stalling. Therefore, we propose replication stalling as the principal cause of deletion formation.     

Mitochondrial DNA and human evolution

For the past seven years or so, much discussion and controversy in the field of human evolution has revolved around the application and interpretation of studies of human mitochondrial DNA variation, particularly the hypothesis that all mtDNA types in contemporary populations can be traced back to a single African ancestor who lived about 200,000 years ago. In this review I describe the evidence that led to this hypothesis, subsequent work, and where things stand now, particularly with respect to recent criticisms concerning the adequacy of phylogenetic analyses of the mtDNA data. I also describe a new method of analyzing mtDNA data that suggests that all human populations underwent a dramatic expansion some 40,000 years ago, possibly in association with revolutionary advances in human behavior, as well as an important implication of population expansions for mtDNA disease studies.     

Multiple nuclear pseudogenes of mitochondrial DNA exist in the canine genome

Many copies of nuclear counterparts of mitochondrial DNA (mtDNA) were found in nuclear DNA from sperm heads of the domestic dog, Canis familiaris, by DNA-DNA hybridization and DNA sequencing. Nuclear counterparts homologous to the mtDNA D-loop region were cloned into lambda phage vectors (EMBL4 and lambda gt11), and nucleotide sequences of seven different mtDNA pseudogenes were then determined. The seven pseudogenes were E3 (474 bp; 82% homology with canine mtDNA), E13 (1867 bp; 67%), 8B (2375 bp; 78%), 12A (2650 bp; 79%), 33 (4131 bp; 86%), 47 (4251 bp; 86%), and E17 (5721 bp; 71%). These seven mtDNA pseudogenes corresponded to portions of cytoplasmic mtDNA containing the genes ile, ND1, leu, 16S rRNA, val, 12S rRNA, phe, D-loop, pro, thr, cytb, and glu. A neighbor-joining phylogenetic tree constructed from 12S rRNA sequences in mtDNA pseudogenes 8B, 33, 47, and E17 and in 10 mtDNA fragments from other species showed that these four pseudogenes form a monophyletic clade with canine mtDNA. A neighbor-joining phylogenetic tree based on the 318-bp cytb region showed that the canine pseudogenes existed before the divergence of 17 related canids, and their divergence dates were calculated at around 4.4 to 8.6 million years ago.     

Molecular characterization of relatedness among colour variants of Asian Arowana (Scleropages formosus)

Morphological identification of fish taxa can sometimes prove difficult because phenotypic variation is either being affected by environmental factors, phenotypic characters are highly conserved or marker selection has been inappropriate. DNA based markers especially neutral mitochondrial DNA (mtDNA) have been used widely in recent times to provide better resolution of systematic relationships among vertebrate taxa. The Asian Arowana (Scleropages formosus) is a high value ornamental fish belonging to the family Osteoglossidae with a number of different colour variants distributed geographically across different locations around Southeast Asia. Systematic relationships among colour variants still remain unresolved. Partial sequences of the Cytochrome B (Cyt B) and DNA barcoding gene, Cytochrome C Oxidase I (COI) were used here to assess genetic relationships among colour variants and as a tool for molecular identification for differentiating among colour variants in this species. Results of the study show that in general, colour pattern shows no relationship with extent of COI or Cyt B mtDNA differentiation and so cannot be used to identify taxa. Partial sequences of the mtDNA genes were sufficient however, to identify S. formosus from a closely related species within the order Osteoglossidae.     

Concordant divergence in proteins and mitochondrial DNA between two vole species in the genusClethrionomys

The bank vole (Clethrionomys glareolus) and the northern red-backed vole (C. rutilus) are two closely related species where interspecific crosses result in fertile female but sterile male offspring. Mitochondrial DNA (mtDNA) fromC. rutilus has passed the species barrier and is found inC. glareolus from northern Fennoscandia. The present report shows that the genetic distance between the two species, calculated from enzyme data (Nei'sD), is 0.64. Isoelectric focusing of muscle proteins resolved around 55 bands, of which each species had 6 or 7 bands not present in the other species. Sequence divergence of mtDNA from the two species is 13.9%. A comparison between protein and mtDNA distances in other species pairs reveals a high correlation between the two measures, indicating that differences in mtDNA between taxa are not random when compared to divergence in protein-coding nuclear genes. The relationship between genetic divergence in proteins and that in mtDNA betweenClethrionomys glareolus andC. rutilus is similar to that found in other species pairs. It is also shown that despite large differences on the protein level it is still, in some cases, possible for species pairs to produce fertile hybrid females.This study was sponsored by the Swedish Natural Science Research Council, the Erik Philip-Sörensen Foundation, and the Nilsson-Ehle Foundation.     

Mitochondrial genome recombination in the zone of contact between two hybridizing conifers

Variation in mitochondrial DNA was surveyed at four gene loci in and around the zone of contact between two naturally hybridizing conifers, black spruce (Picea mariana) and red spruce (P. rubens) in northeastern North America. Most of the mtDNA diversity of these species was found in populations next to or into the zone of contact, where some individuals bore rare mitotypes intermediate between the common mitotypes observed in the allopatric areas of each species. Sequence analysis and tests for mtDNA recombination point to this phenomenon, rather than to recurrent mutation, as the most tenable hypothesis for the origin of these rare mitotypes. From the 10 mitotypes observed, at least 4 would be the product of recombination between 4 of the 5 putative ancestral mitotypes. Tests for cytonuclear disequilibrium and geographical structure of the putative recombinant mitotypes suggest that mtDNA recombination is not frequent and relatively recent on the geological time scale. mtDNA recombination would have been promoted by transient heteroplasmy due to leakage of paternal mtDNA since the Holocene secondary contact between the two species.