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

H. Yasue and Y. Wada

Dep. Animal Breeding and Genetics
National Institute of Animal Industry
2 Ikenodai, Kukisaki-machi, Inashiki-gun,
Ibaraki 305, Japan

Summary

   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 pro-
liferated 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=4.6x10^(-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.

Keywords: distribution, PRE-1, swine SINEs

Animal Genetics 27: 95-98 (1996)