Nucleotide Sequence Of Mitochondrial DNA Research Articles

Genetic variation, population structure and cryptic species within the black mudfish, Neochanna diversus, an endemic galaxiid from New Zealand.

To investigate the phylogenetic relationships and geographical structure among landlocked populations of the black mudfish, Neochanna diversus, mitochondrial DNA nucleotide sequence data were sampled from seven populations from the Waikato and Northland regions of New Zealand. The complete D-loop region was sequenced from 70 individuals, with 913 bp from the tRNA-pro end used in population and phylogenetic analysis. A tandem repeat array, which ranged in size up to 200 bp, was found in most populations at the 3' end of the D-loop that was not able to be aligned for analysis. Of the seven sites sampled, two from Northland exhibited significant sequence divergence from all other sites. There was also a clear distinction among remaining Northland sites and those from the Waikato. An additional 518 bp segment of the 16S region was sequenced from all sites and compared with the other New Zealand mudfish species, N. apoda, N. burrowsius and the Tasmanian mudfish Galaxias (Neochanna) cleaveri using Galaxias maculatus as an outgroup. Both D-loop and 16S sequence data provided strong evidence for a cryptic species of mudfish present in Northland. The significant genetic structure apparent in the black mudfish appears most probably to be attributed to geological conditions during the Pliocene, where peat wetlands became apparent in the Waikato while Northland consisted of disjunct 'islands'. Conservation and management of these populations must take into account the historical processes that have shaped these patterns of genetic diversity.

Taxonomic Status and Phylogenetic Relationships of Some Species of the GenusGammarus(Crustacea, Amphipoda) Deduced from Mitochondrial DNA Sequences

Mitochondrial DNA nucleotide sequence analysis was used to determine the extent of genetic differentiation among six species of the genusGammarus(Crustacea, Amphipoda) common in France (G. fossarum, G. pulex, G. lacustris, G. wautieri, G. roeseli, G. marinus). From 23 different populations, 104 specimens were compared to examine their taxonomic status and their phylogenetic relationships. Nucleotide sequences for a 376-base segment of the cytochromecoxidase subunit I (COI) gene were obtained through direct sequencing of amplified DNA. The strong sequence variability found at the interspecific level, generally masked by morphological or ecological similarities, is consistent with that observed for other crustaceans and supports existing species classifications. A high level of genetic variation was observed at the intraspecific level, suggesting that the COI gene will be a powerful marker for amphipod population biology. Based on the mitochondrial DNA results, we propose a phylogenetic hypothesis of the relationships among the six studied species, which is discussed in biogeographic and evolutionary terms.

Molecular phylogeny of vestimentiferans collected around Japan, revealed by the nucleotide sequences of mitochondrial DNA

The phylogenetic relationships among local populations of undescribed vestimentiferan species that belong to the genera Lamellibrachia and Escarpia and had been collected at six sites around Japan were analyzed on the basis of the partial (1023 bp) nucleotide sequences of the mitochondrial gene for cytochrome oxidase I (COI), using a pogonophoran and a polychaete as outgroups. The identical amino acid sequence was deduced from the nucleotide sequence obtained from each of the vestimentiferans analyzed. The strong similarity among deduced amino acid sequences of COI suggested a close relationship between vestimentiferans and pogonophorans. On the basis of the phylogenetic relationships, the analyzed vestimentiferan populations were classified tentatively as five species. The genetic differentiation of vestimentiferans was suggested to occur bathymetrically as well as being a consequence of horizontal segregation. Two of these tentatively identified species inhabit both a hydrothermal area and a cold seep area, as is the case for some species of bivalves that belong to the genera Bathymodiolus and Calyptogena.

Point mutations of mitochondrial genome in Parkinson's disease.

Oxidative stress and subsequent energy crisis have been proposed as the cause of nigral neuronal cell death in Parkinson's disease. We have reported defects in the mitochondrial respiratory chain and increased amount of deleted mitochondrial genome in the nigrostriatal system of patients with Parkinson's disease. Deletion in mitochondrial DNA could be ascribed to somatically acquired premature aging leading to cell death. To elucidate the contribution of maternally transmitted point mutations in mitochondrial DNA to the premature DNA damages, we employed a direct sequencing system and analyzed the total nucleotide sequences of mitochondrial DNA in the brains of five patients with idiopathic Parkinson's disease. There were no predominant point mutations among the patients in contrast to some neuromuscular diseases. However, each patient had several point mutations that would result in a significant change in the gene products. Some of these mutations may be involved either in the increased production of oxygen radicals from the mitochondrial respiratory chain or in the increased susceptibility of the respiratory chain components to oxidative damage. We propose that some of these mutations can be regarded as one of the risk factors accelerating degeneration of nigrostriatal pathway in Parkinson's disease.

Allozyme variation and systematics of African mole-rats (Rodentia: Bathyergidae)

Patterns of allozyme variation were examined within and among eight taxa representing the five genera of endemic African mole-rats of the family Bathergidae. Populations of Georychus capensis and Cryptomys hottentotus exhibited greater degrees of intraspecific allozyme divergence than did populations of Cryptomys damarensis, Bathyergus suillus, or Heliophobius argenteocinereus. Past climatic cycles may have affected bathyergid genera differentially, resulting in the current differences among taxa in patterns of allozyme variation. Analyses of allozyme variation among genera consistently placed Heterocephalus glaber at the base of the bathyergid radiation. However, allozyme data did not resolve phylogenetic relationships among the remaining four mole-rat genera, suggesting that bathyergid genera may represent lineages of ancient origin. Phylogenetic relationships among genera may be difficult to determine due to the levels of genetic change that have accumulated within each lineage. Allozyme variation among genera, in conjunction with mitochondrial DNA nucleotide sequence data, lead to the conclusion that a revision in the taxonomy of the family Bathyergidae is warranted. We suggest that the naked mole-rat, Heterocephalus glaber, be placed in the subfamily Heterocephalinae, whereas the remaining four bathyergid genera be placed in the subfamily Bathyerginae.

PHYLOGENY OF PRIMATES AND OTHER EUTHERIAN ORDERS: A CLADISTIC ANALYSIS USING AMINO ACID AND NUCLEOTIDE SEQUENCE DATA.

Abstract- Genealogical reconstructions carried out by the parsimony method on protein amino acid and DNA nucleotide sequence data are providing fresh evidence on cladistic branching patterns at taxonomic levels from the classes of Vertebrata and orders of Eutheria to the genera of Hominoidea. Minimum length trees constructed from amino acid sequence data group Mammalia with Archosauria (i.e., Aves plus Crocodilia), Amniota with Amphibia, and Tetrapoda with Teleostei. Within Mammalia, Edentata and Paenungulata (e.g., Proboscidea) appear as the most anciently separated from other eutherians. Another superordinal eutherian clade consists of Artiodactyla, Cetacea, and Perissodactyla. A third consistently contains Primates, Lagomorpha, and Tupaia. The cladistic positions of such orders as Carnivora, Chiroptera, Insectivora, and Rodentia are not well resolved by the currently still sparse body of sequence data. However, recent dramatic progress in the technology of gene cloning and nucleotide sequencing has opened the way for so enlarging the body of sequence data that it should become possible to solve almost any problem concerning the phylogenetic systematice of extant mammals. An example is provided by hominoid genera. Minimum length trees constructed from mitochondrial DNA nucleotide sequence data very strongly group Pan, Homo, and Gorilla into Homininae and then join Homininae and Ponginae (pongo) into Hominidae as the sister family of Hylobatidae (Hylobates). Resolution of the hominine trichotomy into two dichotomous branchings should be forthcoming as kilobase sequencing of nuclear genes progresses.

Assembly of the mitochondrial membrane system. The DNA sequence of a mitochondrial ATPase gene in Saccharomyces cerevisiae.

The mitochondrial DNA of a cytoplasmic "petite" mutant (DS400/A3) of Saccharomyces cerevisiae has been characterized by restriction endonuclease analysis and by DNA sequencing. The DNA has a repeat length of 1,800 base pairs and contains the oli 1 and pho 2 loci, two known markers of the ATPase proteolipid subunit. The nucleotide sequence has helped to establish the presence in the DS400/A3 DNA of the proteolipid gene flanked by two long stretches of DNA rich in A + T. The sequence of the structural gene is in excellent agreement with the previously reported primary structure of the proteolipid. The DNA sequence also indicates that the mitochondrial codons of yeast are highly nondegenerate. The proteolipid gene has been precisely localized on the restriction map of the wild type genome. In addition, it has been possible to orient the gene with respect to other genetic markers and to determine the direction of its transcription.

Assembly of the mitochondrial membrane system: partial sequence of a mitochondrial ATPase gene in Saccharomyces cerevisiae.

The nucleotide sequence of mitochondrial DNA of a cytoplasmic "petite" mutant of Saccharomyces cerevisiae is reported. The DNA has a repeat length of 1060 base pairs and contains a genetic marker (oli-1) for the ATPase proteolipid. The nucleotide sequence reveals the presence of part of the structural gene of the subunit-9 proteolipid of the ATPase complex and an extended A+T-rich region adjacent to the carboxyl-terminal end of the gene. The structural gene sequence agrees with the primary structure of the protein. These studies point out the feasibility of using the DNA of appropriately marked "petite" mutants to obtain the sequence of mitochondrial genes.

Studies of mouse mitochondrial DNA in escherichia coli: Structure and function of the eucaryotic-procaryotic chimeric plasmids

The mouse mitochondrial DNA genome has been cloned in Escherichia coli by linking it to the pSC101 plasmid replicon at cohesive-ended cleavage sites generated by Eco RI restriction endonuclease. The four possible configurations of chimeric molecules that contain the nucleotide sequences of mitochondrial DNA in their native relationship were distinguished by Hind III restriction endonuclease digestion and electron microscopic heteroduplex analysis. Chimeric molecules utilize the pSC101 replication origin and do not maintain the “D-loop” region or the low frequency of ribonucleotides found in native mitochondrial DNA. Hybridization of the RNA synthesized in E. coli minicells carrying the four types of chimeras indicates that transcription occurs predominantly on the light strand of the mitochondrial DNA in all cases. This result implies that initiation of RNA synthesis occurs within the mitochondrial DNA segment. Although specific polypeptide synthesis is directed by the mitochondrial DNA segment of each of the chimeras in E. coli minicells, the molecular weight distribution of the polypeptides synthesized consists primarily of low molecular weight species and thus differs from that observed in mitochondria in mouse L cells.