Redefinition of hypervariable region I in mitochondrial DNA control region and comparing its diversity among various ethnic groups

The hypervariable region I (HVR-I) of the mitochondrial DNA control region described in the literature is variable in its 5′and 3′ ends as well as in its length, causing a problem when data from different ethnic groups are to be compared. To redefine HVR-I, which should be highly polymorphic yet relatively short in length, we analyzed 1437 reported sequences distributed among 11 geographic areas in the world. The results showed that the 237-bp (nts 16126–16362) redefined HVR-I (rHVR-I) had a global genetic diversity of 0.9905 and the 154-bp (nts 16209–16362) short HVR-I (sHVR-I) had a global diversity of 0.9735. Being flanked by a stretch of highly conservative sequences, both rHVR-I and sHVR-I can be produced by PCR, even if extracted from badly degraded specimens. Comparing the genetic diversity among 3870 sequences from 25 countries, we found that the genetic diversity of rHVR-I was 0.9869 ± 0.0133 in Asian countries, 0.9685 ± 0.0193 in African countries, 0.9299 ± 0.0664 in European countries, and 0.8477 ± 0.1857 in American countries, whereas that of sHVR-I was 0.9689 ± 0.0284 in Asian countries, 0.9504 ± 0.0334 in African countries, 0.8721 ± 0.0911 in European countries, and 0.8230 ± 0.1693 in American countries. The difference in genetic diversity among these countries is consistent with the notion that genetic diversity roughly reflects the genetic history of a given ethnic group. Our results indicate that a polymorphic, short, and PCR-producible HVR-I can be defined, making the comparison among various ethnic groups possible.