Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes.docVIP

Open Access Research 2006LawsonVolume and7, IssZhangue 2, Article R14 Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes Mark J Lawson and Liqing Zhang Address: Department of Computer Science, Virginia Tech, 655 McBryde, Blacksburg, VA 24060, USA. Correspondence: Liqing Zhang. Email: lqzhang@ Published: 21 February 2006 Received: 26 August 2005 Revised: 26 October 2005 Accepted: 30 January 2006 Genome Biology 2006, 7:R14 (doi:10.1186/gb-2006-7-2-r14) The electronic version of this article is the complete one and can be found online at /2006/7/2/R14 ? 2006 Lawson and Zhang; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. RepeatvapryAacloopatternstminpadriaffteiinvreenplantstugdeyngenomesoofmtheic rdistributiongions./pof single sequence repeats in rice and itArabidopsis /itreveals that the repeat patterns Abstract 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 - 5untranslated region (UTR), 3UTR, 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 5UTRs compared to the other regions and a strong affinity towards trinucleotide repeats in these regions for both rice an