Mitochondrial Dna最新文献

A 307 bp segment of Cytochrome b gene of mtDNA was sequenced and analyzed for 90 individuals of Cirrhinus mrigala collected across the three rivers, namely Ganges, Narmada and Brahmaputra. Analyses revealed the presence of 14 haplotypes with haplotype diversity (h) ranging from 0.304 to 0.692, and nucleotide diversity (π) 0.002-0.043. The majority of variation was found within the population (96.21%), and the FST value (0.035) as well as the value of exact test of population differentiation (0.893) were found to be insignificant (p<0.05). Analysis of molecular variance (AMOVA) also indicated insignificant differentiation among sub-populations. Generally, low genetic differences were observed even though those populations were from different geographic locations. The present study suggests a single panmictic population of C. mrigala across the three rivers of India.

The population genetic structure of the small yellow croaker (Larimichthys polyactis) between China and Korea was further estimated by broad-scale sampling locations (Gulf of Bohai, Yellow Sea including Korea). One hundred and seventeen individuals from eight localities from coastal waters of China and Korea were analyzed based on mtDNA control region sequences (5' mtDNA CR). A total of 97 polymorphic sites were checked, which defined 136 haplotypes. A pattern with high levels of haplotype diversity (h=0.994 ± 0.002) and nucleotide diversity (л=0.020 ± 0.010) was detected in the examined range, and the genetic diversity of Korea populations was higher than that of China populations. Population genetic structure analyses (MDS, AMOVA, Fst, Barrier) showed that significant genetic differentiation existed between China and Korea populations. The migration analysis indicated asymmetry migration also existed among populations, which was consistent with the result of population genetic structure. Using a variety of phylogenetic methods, coalescent reasoning, and molecular dating interpreted in conjunction with paleoclimateic and physiographic evidence, we inferred that the genetic make-up of extant populations of L. polyactis was shaped by Pleistocene environmental impacts on the historical demography of this species. Coalescent analyses (Neutrality tests, Mismatch distribution analysis, Bayesian skyline analyses) showed that the species along coastline of China and Korea has experienced population expansions originated in its most recent history at about 32-196 kya and 166-662 kya before present, respectively.

The Stripe-Backed Shrew, Sorex cylindricauda belongs to the family Soricidae, and distributes in northwestern Yunnan, central Sichuan, southern Gansu and Shaanxi. In this study, the complete mitochondrial genome sequence of S. cylindricauda was determined. The mitogenome is 17,191 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 control region, with a base composition of 33.2% A, 30.2% T, 23.8% C and 12.8% G. The study contributes to illuminating taxonomic status of Stripe-Backed Shrew Sorex cylindricauda.

The species boundaries and evolutionary relationships of two closely related genera, Megalobrama and Parabramis, were inferred from the partial mitochondrial cytochrome oxidase subunit I (COI) gene, NADH dehydrogenase subunit 2 (ND2) gene and their concatenated segment. Phylogenetic reconstructions showed that among the three breams, Megalobrama amblycephala and Megalobrama skolkovii are more closely related to each other than either is to Megalobrama terminalis. The taxonomy of M. pellegrini should be reconsidered. The divergence time estimation based on the assumption of a global molecular clock indicated that speciation and dispersal of the two genera might have occurred at approximately Pliocene to Late Pleistocene, due to major paleo-environmental events associated with monsoon evolution and the formation of the Three Gorges of the Yangtze River.

Next generation sequencing methods allow rapid, economical accumulation of data that have many applications, even at relatively low levels of genome coverage. However, the utility of shotgun sequencing data sets for specific goals may vary depending on the biological nature of the samples sequenced. We show that the ability to assemble mitogenomes from three avian samples of two different tissue types varies widely. In particular, data with coverage typical of microsatellite development efforts (∼1×) from DNA extracted from avian blood failed to cover even 50% of the mitogenome, relative to at least 500-fold coverage from muscle-derived data. Researchers should consider possible applications of their data and select the tissue source for their work accordingly. Practitioners analyzing low-coverage shotgun sequencing data (including for microsatellite locus development) should consider the potential benefits of mitogenome assembly, including internal barcode verification of species identity, mitochondrial primer development, and phylogenetics.

The complete sequence mitochondrial genome of Takydromus sexlineatus was determined using long PCR and conserved primers walking approaches. The genome was 18,943 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region (CR). The gene composition and order of T. sexlineatus were similar to most other squamate reptiles. All protein-coding genes begin with ATG as initiation codon except COI using GTG. Seven genes (ATP8. ND4L. ND5. Cytb. ND1. COI and ND6) ended with TAA, TAG, AGGA and AGA stop codon, the remaining 6 genes had incomplete stop codons T/TA. The overall base composition of the genome in descending order was 31.48% A, 24.67% C, 30.79% T and 13.05% G, with a slight A + T bias of 62.27%. CR is located between the tRNA-Pro and tRNA-Phe genes and is 3562 bp in length, some tandem repeat sequences, conserved elements (CSB1-3) and termination associated sequences (TAS1-3) were found in the control region.

Genetic variation and population structure of northern snakehead (Channa argus) from eight locations in China were investigated using mitochondrial DNA control region and adjacent regions sequences. Sequence analysis showed that there were 105 haplotypes in 260 individuals, 48 unique haplotypes and 57 shared haplotypes, but no common haplotype shared by all populations. As a whole, the haplotype diversity was high (h=0.989), while the nucleotide diversity was low (π=0.00482). AMOVA analysis detected significant genetic differentiation among all eight populations (FST=0.328, p<0.01) and 66.17% of the total variance was resulted from intra-population differentiation. UPGMA analysis indicated that the eight populations could be divided into four major clusters, which was consistent with that the eight sampled locations were belonged to four isolated river systems. The neutrality and mismatch distribution tests suggested that the eight populations of C. argus in the sampling locations underwent recent population expansion. Among the eight populations, the Erhai Lake population may represent a unique genetic resource and therefore needs to be conserved.

Mitochondrial DNA (mtDNA) defects have been postulated to play an important role in the modulation and/or progression of cancer. In the past decade, a wide spectrum of mtDNA variations have been suggested as potentially sensitive and specific biomarkers for several human cancer types. In this context, single nucleotide polymorphisms (SNPs) described as protective or risk variants have been published, in particular in breast cancer, though not without controversy. Moreover, many mtDNA haplogroups have been associated with different phenotypes and diseases. We genotyped 18 SNPs, 15 of them defining European mtDNA haplogroups, including SNPs described as protective or risk variants, 7 SNPs that determine BRCA1 haplotypes and a BRCA1 intron 7 polymorphism. We included in this study 90 Caucasian unrelated women with breast cancer with familial criteria and 96 controls. Our aim was to clarify the importance of any of these SNPs, mitochondrial haplogroups and BRCA1 haplotypes in the modulation of breast cancer. We detected no significant differences in the distribution of BRCA1 haplotypes between patients and controls. Haplogroup U and the 12308G variant of mtDNA were overrepresented within the control group (p = 0.005 and p = 0.036, respectively) compared to breast cancer. Finally, we identified a significant association between the BRCA1 intron 7 polymorphism and BRCA1 haplotypes. Specifically, (TTC)6/6 and (TTC)6/7 genotypes with the seven polymorphic site cassette of "H2-like" haplotypes, and the (TTC)7/7 genotype associated with the "H1-like" haplotypes (p < 0.001).

Freshwater mussels are among animals having two different, gender-specific mitochondrial genomes. We sequenced complete female mitochondrial genomes from five individuals of Anodonta anatina, a bivalve species common in palearctic ecozone. The length of the genome was variable: 15,637-15,653 bp. This variation was almost entirely confined to the non-coding parts, which constituted approximately 5% of the genome. Nucleotide diversity was moderate, at 0.3%. Nucleotide composition was typically biased towards AT (66.0%). All genes normally seen in animal mtDNA were identified, as well as the ORF characteristic for unionid mitochondrial genomes, bringing the total number of genes present to 38. If this additional ORF does encode a protein, it must evolve under a very relaxed selection since all substitutions within this gene were non-synonymous. The gene order and structure of the genome were identical to those of all female mitochondrial genomes described in unionid bivalves except the Gonideini.

Phylogenetic placement of Pseudorasbora elongate remains unresolved. We determined the first complete mitochondrial genome of P. elongate that its mitogenome data should contribute to clarify the systematics of Pseudorasbora fishes. The mitogenome was 16,607 bp in length, including 13 typical protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region. The overall base composition of the heavy strain was 31.1% for A, 24.8% for C, 28.2% for T and 15.9% for G, with the A + T bias of 59.3%.