Abstract
Human mitochondrial DNA (mtDNA) is routinely analysed for pathogenic mutations, evolutionary studies, estimation of time of divergence within or between species, phylogenetic studies and identification of degraded remains. The data on various regions of human mtDNA has added enormously to the knowledge pool of population genetics as well as forensic genetics. The displacement-loop (D-loop) in the control region of mtDNA is rated as the most rapidly evolving part, due to the presence of variations in this region. The control region consists of three hypervariable regions. These hypervariable regions (HVI, HVII and HVIII) tend to mutate 5–10 times faster than nuclear DNA. The high mutation rate of these hypervariable regions is used in population genetic studies and human identity testing. In the present data, potentially informative hypervariable regions of mitochondrial DNA (mtDNA) i.e. HVI (np 16024–16365), HVII (np 73–340) and HVIII (np 438–576) were estimated to understand the genetic diversity amongst Brahmin population of Haryana. Blood samples had been collected from maternally unrelated individuals from the different districts of Haryana. An array of parameters comprising of polymorphic sites, transitions, transversions, deletions, gene diversity, nucleotide diversity, pairwise differences, Tajima's D test, Fu's Fs test, mismatch observed variance and expected heterozygosity were estimated. The observed polymorphisms with their respective haplogroups in comparison to rCRS were assigned.
Highlights
Data accessibilityTables and Figures DNA from blood samples were extracted by using PCI method [1]. PCR amplification was carried out using SureCycler 8800 (Agilent Technologies, USA)
Data on haplotype diversity in the hypervariable region I, II and III of mitochondrial DNA (mtDNA) amongst the Brahmin population of Haryana
The three hypervariable regions, i.e. the HVI lying between np16024 and 16365, HVII lying between np 73–340 and HVIII lying between np 438–576 were amplified using both forward and reverse primers
Summary
Tables and Figures DNA from blood samples were extracted by using PCI method [1]. PCR amplification was carried out using SureCycler 8800 (Agilent Technologies, USA). Sample size No of polymorphic sites No of observed transitions No of observed transversions No of observed substitutions No of observed indels Nucleotide composition (%) C T A G Mean number of pairwise differences Heterozygosity/sample No of Haplotypes Gene Diversity Nucleotide Diversity Ss2 of haplotype frequencies (RMP) Alleles Frequency (Mean 7 S.D) Sum of square deviation Harpending's raggedness index Mismatch distribution observed mean Mismatch observed variance Tajima's D test Fu's FS test. Sample size No of polymorphic sites No of observed transitions No of observed transversions No of observed substitutions No of observed indels Nucleotide composition (%) C T A G Mean number of pairwise differences Heterozygosity No of Haplotypes Gene Diversity Nucleotide Diversity Ss2 of haplotype frequencies (RMP) Alleles Frequency (Mean 7 S.D) Sum of square deviation Harpending's raggedness index Mismatch distribution observed mean Mismatch observed variance Tajima's D test Fu's FS test
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