Maternal variation in Huichol and Mixtec populations from Mexico

To determine possible contamination, negative control was added to every experiment.
Primers used for PCR for HVS1, 2, coding region and full sequence are listed in
Supplementary materials (Suppl. Table 1.1, 1.2 and 3 accordingly).
PCR programme for control-region and SNP checking:
* primary denaturation 94ºC 1min30s
* denaturation 94ºC 15s
* primer annealing 56(52) ºC 30s 36-38 cycles
* primer extension 72 ºC 1-2min
* final extension 72 ºC 2-4min
Annealing temperature and number of cycles depend on primer specificity and quality of
template DNA. Primer extension time depends on the sequence length (1000bp~1min).
PCR products were visualized in 1,5 % agarose gel electrophoresis with ethidium bromide
staining.
2.2.3 Product purification
Before sequencing, the amplified products were purified for to remove all the residual primers
and unincorporated nucleotides (dNTP). 1 μl of purifying mixture was added to every
product:
0,9 μl SAP (Shrimp alkaline phosphatase) (1U/μl)
0,1 μl ExoI (Exonuclease I) (1U/μl)
Purification programme:
* dNTP dephosphorylation and degradation of one-strand DNA 37ºC 20min
* inactivation of enzymes 80ºC 15min
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