Mitochondrial DNA (MITOCHONDR DNA )


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    ABSTRACT: The clariid catfish, Clarias batrachus commonly known as Magur, has declined drastically from natural habitats in India during the last decade. This fish is highly preferred fish by Indian consumers and has high market demand. As a result traders often substitute C. batrachus with a morphologically similar but supposedly banned exotic catfish, C. gariepinus, in India. This study uses rigorous morphological comparisons confirmed by DNA barcode analysis to examine the level of substitution of C. batracus by C. gariepinus in India. Our results indicate that up to 99% (in many cases) of the market samples sold as Magur or C. batrachus were in fact C. gariepinus.
    Mitochondrial DNA 04/2014;
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    ABSTRACT: The swordtail (Xiphophorus helleri) has been used in studies of behavior, phylogenetics, genetics, physiology, cell biology, cancer research, and biomedicine. Mitochondrial DNA (mtDNA) studies are of pressing need in order to assess the population history of the species. In this study, we present the complete mtDNA genome sequence of two specimens: one from a RR-B strain, a 27-generation inbred line; and one non-selective swordtail with red eyes and red body color from the Guangzhou market, measuring 16,638 and 16,635 bp, respectively. The genome comprises 13 protein-coding genes, 22 tRNAs, two rRNAs and a major non-coding region. The comparison of the two specimens' mitogenomes revealed a relatively low number (57) of single nucleotide polymorphisms-29 located in protein-coding genes, 11 in rRNA genes, six in tRNA genes, and six in the non-coding region. We present an important genetic resource for the RR-B strain of swordtails and swordtail species in general.
    Mitochondrial DNA 09/2009; 20(4):72-7.
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    ABSTRACT: To further understand the evolution of snake mitochondrial genomes, the complete mitochondrial DNA (mtDNA) sequences were determined for representative species from two snake families: the Many-banded krait, the Banded krait, the Chinese cobra, the King cobra, the Hundred-pace viper, the Short-tailed mamushi, and the Chain viper. Thirteen protein-coding genes, 22-23 tRNA genes, 2 rRNA genes, and 2 control regions were identified in these mtDNAs. Duplication of the control region and translocation of the tRNAPro gene were two notable features of the snake mtDNAs. These results from the gene rearrangement comparisons confirm the correctness of traditional classification schemes and validate the utility of comparing complete mtDNA sequences for snake phylogeny reconstruction.
    Mitochondrial DNA 06/2009; 20(4):69-71.
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    ABSTRACT: Zaprionus indianus is an Afrotropical drosophilid species that has expanded its geographical range in the Palearctic region and the Americas during the second half of the last century. It has invaded Egypt within the past two decades from East Africa or Asia and became a dominant species in the drosophilid fauna therein, but the exact date of introduction and source of the propagule remain unknown. Here, we investigate the genetic structure of eight geographical populations within and around the Nile Delta using mitochondrial DNA sequences of the cox2 gene and chromosomal inversion polymorphism. A very low level of genetic variability was detected for both markers, mainly attributed to the introduction bottleneck. Nonetheless, both indicate a significant population structure, with a southeastern-northwestern cline. Demographic history analysis suggested northwestern populations to be younger (expanding in ca. 1992) than southeastern ones (expanding in ca. 1985). The In(II)A polymorphism was only observed in the northwestern population, but one-year interval analysis of the Alexandria population revealed the lack of seasonal fluctuation and a trend toward the loss of the polymorphism. Based on these data and faunistic records, we propose a multiple introduction scenario for Z. indianus in Egypt-according to which a first wave in the early 1980s from Sudan through normal northward range expansion or fruit trade, and a second wave in the early 1990s from Asia via fruit trade. We also suggest, from ecological observations, fruit trade data and known adaptive versatility of Z. indianus, date palm, the dominant fruit in Egypt and in the oases where Z. indianus predominates, to play a major role in the spread of the species in the Middle East.
    Mitochondrial DNA 05/2009; 20(2-3):34-40.
  • Mitochondrial DNA 05/2009; 20(2-3):61-3.
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    ABSTRACT: The translation initiation codon of the mitochondrial (mt) cytochrome oxidase I gene, cox1, frequently differs from conventional AUN triplets, and the termination codon is often incomplete. To investigate whether initiation and termination codon usage may depend on the rate of mt genome evolution, a fast evolving locus comprising cox1 and adjacent tRNA-encoding trn genes was sequenced from representatives of the major clades of spider wasps, Pompilidae (Hymenoptera), and then included in insect-wide analyses of codon usage in the context of mtDNA sequence stability. The rapid evolution of Pompilidae trn-cax1 locus was particularly evident in the rearrangement of the trnC and trnY genes, the presence of a trn pseudogene in Psorthaspis, and the relatively high frequency of cox1 nucleotide substitutions. Such extensive genetic diversification, underscored by variability in the arrangement of trn genes even at the subfamily level, contrasted with the conventional form of cox1 initiation and termination codons. Similar preference for codon usage was identified for other fast evolving insect lineages unrelated to Pompilidae. Instead, conventional codons were often absent in slower evolving loci. Analysis of codon usage across a spectrum of evolutionary rates indicates the existence of positive correlation between the incidence of cox1 canonical initiation and termination codons and relative rate of the trn-cox1 locus evolution.
    Mitochondrial DNA 03/2009; 20(1):15-25.
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    ABSTRACT: The ring-tailed mongoose (Galidia elegans) represents one of the most widely distributed mongooses in Madagascar; however, we know little about the ecology of this seemingly ubiquitous species. Currently, G. elegans is divided into three recognized subspecies--G. e. elegans, G. e. dambrensis, and G. e. occidentalis--based on differences in pelage coloration between the distinct geographic locations. We used intraspecific DNA variation to describe the phylogenetic relationships among the described subspecies. Approximately 550 base pairs of the mitochondrial DNA control region were analyzed from 19 G. elegans specimens representing all three subspecies sampled from across the species' geographic range. Sequence data from outgroup taxa were included for comparison. Examination of the recovered sequences revealed a strongly supported distinct genetic signature in the western region of the island, but remained inconclusive with respect to supporting the designation of the northern and eastern 'subspecies' for treatment as divergent intraspecific units for management.
    Mitochondrial DNA 03/2009; 20(1):7-14.
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    ABSTRACT: The mitochondrial genomes of malaria parasites (Plasmodium and related genera) are extremely small and contain just three protein-coding genes. These short linear genomes are tandemly repeated, allowing for amplification of the entire unit using a single pair of outwardly facing primers. Using this approach, I sequenced full mitochondrial genomes for seven new lineages of these parasites belonging to four genera and then, combining these new sequences with other published ones, I examined the phylogenetic utility of each of the three protein-coding genes, alone and when concatenated into a data-set of 3315 nucleotides. Most relationships recovered are consistent with previous studies of the group. Support for an Asian origin of Plasmodium vivax and a sister relationship of Plasmodium falciparum to the rodent malaria parasites was observed in this study. However, if a broad understanding of the evolutionary relationships of this group is to truly be understood, it is clear that loci outside the mitochondrial genome should be explored.
    Mitochondrial DNA 01/2009; 19(6):471-8.
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    ABSTRACT: We determined the complete mitochondrial genomes of Pseudolabrus sieboldi and P. eoethinus, and analyzed the genome organization, codon usage, and transition/transversion mutation ratio of the mitochondrial genome. The mitochondrial genomes of P. sieboldi and P. eoethinus are 16,507 and 16,508 bp in length, respectively, and consisted of 37 genes (13 protein-coding genes, two ribosomal RNAs, and 22 transfer RNAs), which is typical for vertebrate mitochondrial DNA. All protein-coding genes of two species used the initiation codon ATG except the cytochrome c oxidase subunit (CO) 1, which began with GTG as an initiation codon. However, the termination codon for the NADH dehydrogenase subunit (ND) 6 gene encoded with TAA in P. sieboldi, and TAG in P. eoethinus. The 12S and 16S rRNA genes were 949 and 1694 bp, respectively, in P. sieboldi, and were 948 and 1693 bp in P. eoethinus. The A + T content of the two rRNA genes were 52.9% in P. sieboldi and 52.5% in P. eoethinus, which is slightly lower than that of other labrid species. The identity of the 13 protein-coding genes ranged between 67% (ND6) and 94% (CO2 and ATP8). The G + C contents of all of the protein-coding genes of P. sieboldi were slightly higher than those of P. eoethinus. Our data contribute to the identification, and further our understanding, of the comparative genetics of Pseudolabrus species distributed in East Asia.
    Mitochondrial DNA 11/2008; 19(5):453-60.
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    ABSTRACT: Cytochrome c oxidase (COX) plays important roles in oxidative phosphorylation regulation and oxygen sensing transfer. In the present study, single-nucleotide polymorphisms (SNPs) in three mitochondrially coded subunit genes of COX were identified with the technique of single-strand conformation polymorphism in Tibet Chicken and four lowland chicken breeds-Dongxiang Chicken, Silky Chicken, Hubbard ISA White broiler, and Leghorn layer. In total, 14 SNPs were identified in the three genes of COX of the five chicken breeds, and 13 haplotypes were defined for the 14 SNPs. This work will afford reference for the further study on the association of COX with the adaptation to hypoxia.
    Mitochondrial DNA 11/2008; 19(5):461-4.
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    ABSTRACT: Iksookimia choii (Teleostei; Cypriniformes; Cobitidae) is an endangered freshwater fish species because of anthropogenic pressures around its natural habitats. We present the complete mitogenome sequence of L. choii to provide baseline data for use in the development of conservation plans and captive breeding programs. The total size, gene content and arrangement, and cloverleaf secondary structures of transfer RNA genes of I. choii mitogenome were highly homogeneous to previously known vertebrate mitogenomes. Phylogenetic analysis using nucleotide sequences of protein-coding and transfer RNA genes reflected the taxonomic clustering in the familial levels among species of the superfamily Cobitoidea. I. choii, which was recently transferred to the newly erected genus Iksookimia from Cobitis, was phylogenetically affiliated to one of two Cobitis species with strong statistical supports, indicating its taxonomically unstable status.
    Mitochondrial DNA 11/2008; 19(5):438-45.

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