Distinct Patterns of SSR Distribution in the Arabidopsis thaliana and Rice Genomes


by Mark J. Lawson and Liqing Zhang

Published in Genome Biology on Feb. 21, 2006
Link to article

Abstract

Background:
SSRs (simple sequence repeats) in DNA have been traditionally thought of as
functionally unimportant and have been studied mainly as genetic markers. However, a
recent handful of studies have shown that SSRs in different positions of a gene can play
important roles in determining protein function, genetic development, and regulation of
gene expression. Here we performed a detailed comparative study on the distribution of
SSRs in the sequenced genomes of Arabidopsis thaliana and rice.
Results:
SSRs in different genic regions (5'-UTR, 3'-UTR, exon, and intron) show distinct
patterns of distribution both within and between the two genomes. Especially notable is
the much higher density of SSRs in 5'-UTRs compared to the other regions and a strong
affinity towards trinucleotide repeats in these regions for both rice and Arabidopsis. On a
genomic level, mononucleotide repeats are the most prevalent type of SSRs in
Arabidopsis and trinucleotide repeats are the most prevalent type in rice. Both plants
share the same most common mononucleotide (A/T) and dinucleotide (AT and AG)
repeats, but share little in common for the other types of repeats.
Conclusion:
Our work provides insight into the evolution and distribution of SSRs in the two
sequenced model plant genomes of monocots and dicots. Our analyses reveal that the
distributions of SSRs appear highly non-random and vary a great deal in different regions
of the genes in the genomes.

Paper: .pdf

Resources:

/public/users/malawso4/research_ssr.html Login | Web Editor | Full Editor
Last modified 2/21/06 11:15 AM by malawso4 (history)
Site contents