A swine SINE (PRE-1 sequence) distribution in swine-related animal species and its phylogenetic analysis in swine genome

The distribution of PRE-1 sequence (a swine SINE) among the animal species related to Sus scrofa, i.e. Phacochoerus aethiopicus and Tayassu tajacu, was examined by dot-blot analysis using PRE-1 sequences as a probe. This revealed that Phacochoerus aethiopicus and Tayassu tajacu contained PRE-1 sequences, amounts of which in their genomes are almost the same as that in the swine genome, indicating that these species separated after PRE-1 sequences proliferated to diversify in the genome. In order to estimate the time when the PRE-1 started to diversify in the swine genome, PRE-1 sequences were extracted from GenBank DNA database by homology analysis using the PRE-1 consensus sequence as a probe. The 22 PRE-1 sequences obtained were aligned and their phylogenetic relation was calculated by the neighbour-joining method. The result of the calculation combined with the mutation rate of the pseudogenes (r = 4.6 times 10^-9 indicated that the PRE-1 sequence diversified at least 43.2 million years ago. Taken together, the period of time since the separation of the three species, Sus scrofa, Phacochoerus aethiopicus and Tayassu tajacu, is currently estimated to be less than 43.2 million years.