Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes.
BACKGROUND
Simple sequence repeats (SSRs) in DNA have been traditionally thought of as functionally unimportant and have been studied mainly as genetic markers. A recent handful of studies have shown, however, that SSRs in different positions of a gene can play important roles in determining protein function, genetic development, and regulation of gene expression. We have performed a detailed comparative study of the distribution of SSRs in the sequenced genomes of Arabidopsis thaliana and rice.


RESULTS
SSRs in different genic regions - 5'untranslated region (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 have the same most common mononucleotide (A/T) and dinucleotide (AT and AG) repeats, but have little in common for the other types of repeats.


CONCLUSIONS
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.
Lawson
Mark J
MJ
Department of Computer Science, Virginia Tech, 655 McBryde, Blacksburg, VA 24060, USA. malawso4@vt.edu
Zhang
Liqing
L
D020121:5' Untranslated Regions / Q000235:genetics; D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics; D020029:Base Pairing; D018745:Genome, Plant; D012275:Oryza / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics; D020449:Repetitive Sequences, Amino Acid; D018911:Trinucleotide Repeats / Q000235:genetics
D020121:5' Untranslated Regions; D029681:Arabidopsis Proteins; D010940:Plant Proteins