Characterization of a SINE species from vicuna and its distribution in animal species including the family Camelidae

Z. Lin, O. Nomura, T.Hayashi, Y.Wada, H. Yasue

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

Summary

Twenty-six sequences of a short interspersed repetitive element (SINE)
with a size of approximately 150 base pairs (bp) were isolated from 
the genomic DNA of Vicugna vicugna (vicuna). RNA polymerase III split
promoter sequence was observed in most of them, and many had direct 
repeats flanking to SINEs as well as a poly(A)-like structure.
The SINE sequences were designated as "vic-1" sequences. Comparison of 
the vic-1 consensus sequence with sequences registered in the DNA 
database (DDBJ/EMBL/GENBANK) revealed that the vic-1 sequence had 
a 79% homology with mouse ala-tRNA gene. In addition, the tRNA-related 
region of the consensus sequence was folded into a cloverleaf structure 
as with mouse ala-tRNA. These findings strongly indicated that vic-1 was
a retroposon derived from ala-tRNA gene. The vic-1 sequences were used 
as a probe for dot-blot hybridization to examine the distribution of 
their homologous sequences in the genomes of various animal species 
spanning 14 orders, of which, homologous sequences were found only 
in the Camelidae family. In order to examine the phylogenetical 
relationship among vicuna, llama, and camel, vic-1 insertion analysis 
and homology analysis of vic-1 sequences were performed at each locus. 
The analyses indicated that vic-1 sequences were generated in a common
ancestor of the animal species, and that camels first branched off from
the clade Camelidae, followed by vicunas and llamas.

Mammalian Genome 12, 305-308 (2001)