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

Lawson, Mark J.; Zhang, Liqing

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

dc.contributor.author	Lawson, Mark J.	en
dc.contributor.author	Zhang, Liqing	en
dc.contributor.department	Computer Science	en
dc.date.accessioned	2012-08-24T12:18:45Z	en
dc.date.available	2012-08-24T12:18:45Z	en
dc.date.issued	2006-02-21	en
dc.date.updated	2012-08-24T12:18:45Z	en
dc.description.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 - 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. 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.	en
dc.description.version	Published version	en
dc.format.mimetype	application/pdf	en
dc.identifier.citation	Genome Biology. 2006 Feb 21;7(2):R14	en
dc.identifier.doi	https://doi.org/10.1186/gb-2006-7-2-r14	en
dc.identifier.uri	http://hdl.handle.net/10919/18956	en
dc.language.iso	en	en
dc.rights	Creative Commons Attribution 4.0 International	en
dc.rights.holder	Mark J Lawson et al.; licensee BioMed Central Ltd.	en
dc.rights.uri	http://creativecommons.org/licenses/by/4.0/	en
dc.title	Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes	en
dc.title.serial	Genome Biology	en
dc.type	Article - Refereed	en
dc.type.dcmitype	Text	en