In silico analysis of repeat sequences of pig and cattle genome

Yasuhiko Wada1,2 and Takuto Shigemori1

1Faculty of Agriculture, Saga University, Saga city, 840-8502, Japan
2BIRD, Japan Science and Technology Corporation, Tokyo, 102-8666, Japan


Summary

   Human and mouse genome research project reported that the proportion of 
the length of interspersed repeats for the whole genome is higher than 35% 
in mouse genome and higher than 45% in human genome. The evolution and 
function of the interspersed repeats has not yet been clarified. In this 
study, the interspersed repeats were searched from the sampling genome 
sequences. The proportion in the sequences for classes of repeats was 
calculated and the age distribution was analyzed by the nucleotide 
substitution ratio from each consensus sequence.

   The LINE(long interspersed repeat element) was the largest part 
in the mammalian genome, however in the pig genome was slightly less than 
that in the other mammalian genomes. The ratio of SINE(short interspersed 
repeat element) repeats in the human and pig genome was about 14%. The results 
suggest that some mammalian species have the genome in which SINE repeats 
are copied and interspersed at the higher frequency. The peak of 
the distribution of SINE, LINE, LTR element and DNA element in pig genome 
was 10-20%, 30-40%, 20-30% and 20-30%, respectively. BovB/Art2 family was 
only located in the cattle genome and L3/CR1, LINE1 and LINE2 family were 
located in the pig and cattle genome. 

   The recombination of the genome region can be investigated using the SINEs, 
LINEs and other repeats which have the different age distribution. Therefore, 
our results of the age distribution of SINE, LINE and other repeats are 
useful for the research of genome evolution.


Bull. Fac. Agr., Saga Univ. No.91  p.37-43 (2006)