Localization of swine PRE-1 homologues in 13 loci of Phacochoerus aethiopicus and Tayassu tajacu genomes, and their sequence divergence

S. Sulandari Muladno, T. Harumi, S. Yanai, Y. Wada and H. Yasue

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

Animal Genome Analysis Team
Society for Techno-Innovation of Agriculture, Forestry and Fisheries,
446-1
Ippaizuka, Kamiyokoba, Tsukuba, 
Ibaraki 305, Japan

Summary

   In our previous study, PRE-1 (a swine short interspersed nuclear element, 
SINE) was found to be present in the genomes of animal species related to 
swine (Sus scrofa) i.e. warthog (Phacochoerus aethiopicus) and collared peccary
(Tayassu tajacu) at almost the same frequency as in Sus scrofa. In the present
study, we investigated whether PRE-1 was present in hippopotamus (Hippopotamus
amphibius), which is in the same order but in a different family to Sus scrofa.
Hippopotamus amphibius was found to contain no PRE-1. Then, in order to study
the localization of PRE-1 sequences at locus level and the sequence divergence 
of the PRE-1 of individual loci among Sus scrofa, Phacochoerus aethiopicus and
Tayassu tajacu, primer sets, which can amplify PRE-1 sequences at 13 loci of 
swine genome with the polymerase chain reaction, were prepared to identify any 
corresponding sequences in Phacochoerus aethiopicus and Tayassu tajacu. Twelve
and nine of the 13 primer sets identified fragments in Phacochoerus aethiopicus
and Tayassu tajacu respectively. Ten of the 12 Phacochoerus aethiopicus 
fragments and two of the nine Tayassu tajacu fragments contained PRE-1 sequences.
Based on the divergence between the corresponding PRE-1 sequences at 
individual loci and on the mutation rate of the pseudogenes (r=4.6x10^(-9)),
Phacochoerus aethiopicus and Tayassu tajacu are currently calculated to have
been separated from Sus scrofa later than 1.4 million years before present
(MYBP) and 16.8 MYBP, respectively.

Keywords: hippopotamus, peccary, PRE-1, swine SINE, warthog

Animal Genetics 28: 210-215 (1997)