Identification of single nucleotide polymorphisms within the mtDNA genome of the domestic dog to discriminate individuals with common HVI haplotypes

Imes, D. L.; Wictum, Elizabeth J.; Allard, Marc W.; Sacks, Benjamin N.

doi:10.1016/j.fsigen.2012.02.004

Cited by 42 publications

(37 citation statements)

References 41 publications

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“…In forensic practice, mtDNA analysis of dog specimens was usually limited to HVS I and HVS II regions. However, it was shown that inclusion of polymorphic positions located within the coding region significantly increases the discrimination power in forensic mtDNA testing [28,32,43,44). Maximum parsimony tree reconstructed in this study allows those specific polymorphic positions located outside the control region to be identified.…”

Section: Origin Of the Major C L Familiaris Haplogroupsmentioning

confidence: 92%

Complete mitochondrial genome database and standardized classification system for Canis lupus familiaris

Duleba

Skonieczna

Bogdanowicz

et al. 2015

Forensic Science International: Genetics

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Section: Origin Of the Major C L Familiaris Haplogroupsmentioning

confidence: 92%

Complete mitochondrial genome database and standardized classification system for Canis lupus familiaris

Duleba

Skonieczna

Bogdanowicz

et al. 2015

Forensic Science International: Genetics

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“…Imes et al . (2012) reported a similar pattern in domestic dogs (Canis lupis familiaris) [30], while greater overall nucleotide diversity has been reported in the HVRII than in the HVRI of Mauritian long-tailed macaques ( Macaca fascicularis , [31]). In some cases, variations outside of the HVRI have proved of equal or greater value in phylogeographic studies: for example, Wilkinson-Herbots et al .…”

Section: Introductionmentioning

confidence: 95%

Effective Characterisation of the Complete Orang-Utan Mitochondrial DNA Control Region, in the Face of Persistent Focus in Many Taxa on Shorter Hypervariable Regions

Banes

Galdikas

2016

PLoS ONE

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The hypervariable region I (HVRI) is persistently used to discern haplotypes, to distinguish geographic subpopulations, and to infer taxonomy in a range of organisms. Numerous studies have highlighted greater heterogeneity elsewhere in the mitochondrial DNA control region, however–particularly, in some species, in other understudied hypervariable regions. To assess the abundance and utility of such potential variations in orang-utans, we characterised 36 complete control-region haplotypes, of which 13 were of Sumatran and 23 of Bornean maternal ancestry, and compared polymorphisms within these and within shorter HVRI segments predominantly analysed in prior phylogenetic studies of Sumatran (~385 bp) and Bornean (~323 bp) orang-utans. We amplified the complete control region in a single PCR that proved successful even with highly degraded, non-invasive samples. By using species-specific primers to produce a single large amplicon (~1600 bp) comprising flanking coding regions, our method also serves to better avoid amplification of nuclear mitochondrial insertions (numts). We found the number, length and position of hypervariable regions is inconsistent between orang-utan species, and that prior definitions of the HVRI were haphazard. Polymorphisms occurring outside the predominantly analysed segments were phylogeographically informative in isolation, and could be used to assign haplotypes to comparable clades concordant with geographic subpopulations. The predominantly analysed segments could discern only up to 76% of all haplotypes, highlighting the forensic utility of complete control-region sequences. In the face of declining sequencing costs and our proven application to poor-quality DNA extracts, we see no reason to ever amplify only specific ‘hypervariable regions’ in any taxa, particularly as their lengths and positions are inconsistent and cannot be reliably defined–yet this strategy predominates widely. Given their greater utility and consistency, we instead advocate analysis of complete control-region sequences in future studies, where any shorter segment might otherwise have proven the region of choice.

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“…According to Kim et al (16), the complete nucleotide sequence of the domestic dog mitochondrial genome consists of 16727 bp, and the non-coding control region (mtCR) or D-loop is located between positions 15458-16727 (1270 bp), where the presence of a heteroplasmic repeat unit divides the mtCR into two subsections, hypervariable region I (HVI) and hypervariable region II (HVII) (15,23).…”

Section: Introductionmentioning

confidence: 99%

Mitochondrial D-loop mutations can be detected in sporadic malignant tumours in dogs

Ślaska

Surdyka

Brodzki³

et al. 2014

Bulletin of the Veterinary Institute in Pulawy

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The aim of this study was to identify mutations in the D-loop region of mtDNA in head, neck, and limb tumours in dogs, and determination of their relationship with the process of neoplastic transformation. Blood and tumour tissue samples from 19 dogs with diagnosed sporadic malignant tumours were analysed. DNA extraction, amplification, and sequencing of the mtDNA D-loop, and bioinformatic analyses were performed. Five mutations and 19 polymorphisms were observed in 68.42% of all tumours. Polymorphic variants were noted in 42.86% of the head and neck tumours and in 58.33% of the limb tumours. Mutations were observed in 21.05% of dogs. The mutations were found in 28.57% of the head and neck tumours and in 16.66% of the limb tumours. The mutations were identified in 50% of the studied epithelial cancers. In the mesenchymal tumours, no mutations in the D-loop region were observed. Mitochondrial haplotype A17 was found in over 40% cases of limb tumours. No association between the age, breed, sex, type of tumour, and detected polymorphic variants were observed. Different mutational changes in the D-loop sequences of mtDNA identified in the blood and tumour tissues may indicate a relationship between the type of tumour and individual changes in the D-loop nucleotide sequences of mtDNA.

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Identification of single nucleotide polymorphisms within the mtDNA genome of the domestic dog to discriminate individuals with common HVI haplotypes

Cited by 42 publications

References 41 publications

Complete mitochondrial genome database and standardized classification system for Canis lupus familiaris

Complete mitochondrial genome database and standardized classification system for Canis lupus familiaris

Effective Characterisation of the Complete Orang-Utan Mitochondrial DNA Control Region, in the Face of Persistent Focus in Many Taxa on Shorter Hypervariable Regions

Mitochondrial D-loop mutations can be detected in sporadic malignant tumours in dogs

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