An investigation of the variation in the transition bias among various animal mitochondrial DNA

Belle, Elise M. S.; Piganeau, Gwenaël; Gardner, Michael G.; Eyre‐Walker, Adam

doi:10.1016/j.gene.2005.05.019

Cited by 61 publications

(61 citation statements)

References 37 publications

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“…To confirm the mitochondrial origin of PCR products, we compared Blackthroated Blue Warbler sequence with those from Yellow Warbler (D. petechia; Milot et al 2000) in GenBank and computed transition:transversion (Ti:Tv) ratios to compare with those of other bird species. The Ti:Tv ratio for Black-throated Blue Warbler (9.6 for our data alone, 6.4 for the combined data) is similar to the average ratio for neutral mtDNA sites in birds (Belle et al 2005). We also note the absence of heterozygotes, which would be expected in nuclear copies of mitochondrial genes.…”

Section: Methodssupporting

confidence: 81%

Geographic Variation in the Mitochondrial Control Region of Black-throated Blue Warblers (Dendroica caerulescens)

Grus

Graves

Glenn

2009

The Auk

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Abstract.-We investigated the genetic population structure of the Black-throated Blue Warbler (Dendroica caerulescens), a Nearctic-Neotropic migrant passerine that breeds in cool mixed deciduous-coniferous forests in eastern North America. A cline in plumage color in breeding populations in the central Appalachian Mountains suggests either a contact zone between two formerly allopatric populations or the presence of a strong contemporary selection gradient. Analysis of  base pairs of the mitochondrial control region from  individuals sampled from  populations revealed relatively high haplotype diversity, low nucleotide diversity, and limited but significant phylogeographic structure across the breeding range (analysis of molecular variance [AMOVA], variation among populations .%; P .) and between northern and southern population groups (AMOVA, variation among groups .%; P .). Genetic differentiation among populations did not conform to an isolation-by-distance model. Nucleotide diversity was generally highest in the central Appalachians and lower in geographically peripheral populations. Populations from the northwestern periphery of the breeding range in Michigan had the lowest haplotype diversity and were genetically distinct from populations in the southern Appalachians. The star-shaped haplotype network, extensive sharing of common haplotypes among populations, and the haphazard distribution of rare haplotypes are most likely attributable to the combined effects of postglacial expansion from a single refugium (,-, years ago) and long-distance dispersal events. The existence of a cline in plumage color, in the face of inferred recent gene flow, suggests that a strong selection gradient is operating, perhaps related to the migratory divide postulated from stableisotope data. Received  September , accepted  October .Key words: Appalachian Mountains, Black-throated Blue Warbler, Dendroica caerulescens, genetic structure, glaciation, mitochondrial DNA, plumage color, stable isotopes. Variación Geográfica en la Región Control Mitocondrial de Dendroica caerulescensResumen.-Investigamos la estructura genética poblacional de Dendroica caerulescens, un paseriforme que migra entre el Neártico y el Neotrópico y que se reproduce en áreas frescas de bosques mixtos de coníferas en el este de Norte América. Una clina en la coloración del plumaje en las poblaciones reproductivas de las montañas Apalaches sugiere que existe una zona de contacto entre dos poblaciones que fueron alopátricas, o la presencia de un fuerte gradiente de selección contemporánea. El análisis de  pares de bases de la región control mitocondrial de  individuos muestreados en  poblaciones, reveló una diversidad de haplotipos relativamente alta, una baja diversidad de nucleótidos y una estructura filogeográfica escasa pero significativa en el área de distribución reproductiva (análisis de varianza molecular [AMOVA], variación entre poblaciones .%; P .) y entre los grupos formados por las poblaciones del ...

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Section: Methodssupporting

confidence: 81%

Geographic Variation in the Mitochondrial Control Region of Black-throated Blue Warblers (Dendroica caerulescens)

Grus

Graves

Glenn

2009

The Auk

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“…In contrast, the predominant substitutions in transformed cells are C>T/G>A. It was reported that transitions are more common than transversions in the mtDNA of humans (19, 35) and in 70 species of animals (36). Misincorporation by DNA polymerase γ and the deamination of cytosine to form uracil cause C>T/G>A transitions and have been demonstrated to be the main drivers of mtDNA mutation (37, 38).…”

Section: Discussionmentioning

confidence: 99%

Decreased Mitochondrial Mutagenesis during Transformation of Human Breast Stem Cells into Tumorigenic Cells

et al. 2016

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Rare stochastic mutations may accumulate during dormancy of stem-like cells, but technical limitations in DNA sequencing have limited exploring this possibility. In this study, we employed a recently established deep sequencing method termed Duplex Sequencing to conduct a genome-wide analysis of mitochondrial (mt) DNA mutations in a human breast stem cell model that recapitulates the sequential stages of breast carcinogenesis. Using this method, we found significant differences in mtDNA amongst normal stem cells, immortal/preneoplastic cells, and tumorigenic cells. Putative cancer stem-like cell (CSC) populations and mtDNA copy numbers increased as normal stem cells become tumorigenic cells. Transformed cells exhibited lower rare mutation frequencies of whole mtDNA than did normal stem cells. The predicted mtDNA rare mutation pathogenicity was significantly lower in tumorigenic cells than normal stem cells. Major rare mutation types in normal stem cells are C>T/G>A and T>C/A>G transitions, while only C>T/G>A are major types in transformed cells. We detected a total of 1220 rare point mutations, 678 of which were unreported previously. With only one possible exception (m10342T>C), we did not find specific mutations characterizing mtDNA in human breast CSC; rather, the mitochondrial genome of CSC displayed a decrease in rare mutations overall. Based on our work, we suggest that this decrease (in particular T>C/A>G transitions), rather than the presence of specific mitochondrial mutations, may constitute an early biomarker for breast cancer detection. Our findings support the hypothesis that the mitochondrial genome is altered greatly as a result of the transformation of normal stem cells to CSC, and that mtDNA mutation signatures may aid in delineating normal stem cells from CSC.

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“…The nucleotide compositions revealed a bias against G and transitions were more frequent than transversions. This bias has been reported to be widespread in turtle as compared to animal mitochondrial DNA and follows very different patterns of evolution (Belle et al 2005).…”

Section: Discussionmentioning

confidence: 94%

Variability in DNA COI sequences reveals new haplotypes in freshwater turtles from northern region of India

Bhaskar

Mohindra

2018

Mitochondrial DNA Part B

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The chelonian represents a diverse order of turtles. Little is known about this group from India at molecular level. Cytochrome c oxidase I (COI) sequences of 125 individuals from nine species of freshwater turtles were generated and analyzed. A total of 118 nucleotide positions in COI gene as character-based DNA barcodes for each species were identified. Neighbour-joining (NJ) analyses tree well differentiated freshwater hard shell and softshell turtle. Overall species divergence (K2P) was 13.3%. Analysis of COI sequences from present study, combined with sequences downloaded from NCBI GenBank, revealed new COI haplotypes from Northern region of India.ARTICLE HISTORY

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An investigation of the variation in the transition bias among various animal mitochondrial DNA

Cited by 61 publications

References 37 publications

Geographic Variation in the Mitochondrial Control Region of Black-throated Blue Warblers (Dendroica caerulescens)

Geographic Variation in the Mitochondrial Control Region of Black-throated Blue Warblers (Dendroica caerulescens)

Decreased Mitochondrial Mutagenesis during Transformation of Human Breast Stem Cells into Tumorigenic Cells

Variability in DNA COI sequences reveals new haplotypes in freshwater turtles from northern region of India

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