A SINE species from hippopotamus and its distribution among animal species

O. Nomura, Z.-H. Lin, Muladno, Y.Wada, H.Yasue

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

The Second Research Division
Society for Techno-Innovation of Agriculture, Forestry and Fisheries,
446-1
Ippaizuka, Kamiyokoba, Tsukuba, 
Ibaraki 305, Japan

Summary

   Thirty sequences of a short interspersed repetitive element(SINE) were 
isolated from genomic DNA of Hippopotamus amphibius (hippopotamus). RNA 
polymerase III split promoter sequence was observed in all of the 30 sequences;
 and poly(A)-like structure at 3'-end, as well as direct repeat flanking to 
the repetitive sequence in many of the 30 sequences. A comparison of the
consensus sequence of the 30 sequences with sequences in a DNA database
(DDBJ/GENBANK/EMBL) revealed 93% homology to the consensus sequence of a 
whale SINE, CHR-2, and 73% homology to mouse glutamic acid tRNA. Phylogenetic
analysis of tRNA-related regions of the sequences with all of the mouse
tRNAs revealed that glutamic acid tRNA was genetically closed to the
hippopotamus SINE. In addition, the tRNA-related region of the consensus
sequence was folded into a cloverleaf structure as with mouse glutamic acid
tRNA. These findings led us to conclude that the SINE of hippopotamus was
genetically related to a whale SINE, CHR-2 [the hippopotamus SINE was named
CHR-2(hippo)] and was a retroposon derived from glutamic acid tRNA. Hipo53
and hipo95, which were the genetically most separated CHR-2(hippo) sequences
in the present study, were used as a probe for dot-blot hybridization to
examine the distribution of their homologous sequencesamong animal species.
Although the sidtribution spectra of hipo53 and hipo95 homologous sequences
in animal species differed to some extent, large amounts of both sequences
were found in Hippopotamus amphibius and Globicephala macrorhynchus (whale);
and snall amounts in most of the animal species in Artiodactyla examined.
These findings indicated that the hippopotamus and whale had more recently
branched off from the clade that includes chevrotain and pecorans than the
order animal species in the clade. The 30 CHR-2 (hippo) sequences were aligned,
and the substitution rates among the sequences were calculated with a 
diiferent substitution rate model for transition and for transversion. The
calculation combined with the mutation rate of the pseudogenes (r= 4.6x10^9)
indicated that CHR-2(hippo) sequences diversified at least 132 million years
ago (Myr).

Mammalian Genome 9, 550-555 (1998)