Sequence analysis of four caprine mitochondria DNA lineages

The complete mitochondrial DNA (mtDNA) (16640bp in length) was sequenced from four Chinese goat lineages representing the four major mtDNA haplogroups in goats. A total of 124 single nucleotide polymorphisms (SNPs) were found in encoding regions, and the overall ratio of transitions:transversions was 40:1 revealing a heavy transition/transversion rate in domestic goats. Eighteen non-synonymous sites were found for the total number of SNPs; the sites did not affect the predicted functions of protein for these four goat mtDNA lineages. In the region for coding tRNA and rRNA, SNPs occurred in loops, unstructured single strand and stems that were conformed with the principle of G-U pairing. We came to the conclusion that these substitutions could not change secondary structure of RNAs, and there was no positive selection on goat mitochondrial coding region according to the result of dN/dS (0.0399–0.1529) by comparing the goat with other reported mitochondrial genomes.