Little data is available on microsatellite dynamics in the duplicated regions of the rice genome, even though efforts have been made in the past to align genome sequences of its two sub-species. Based on the coordinates of duplicated sequences in the indica genome as available in the public domain, we identified microsatellites in these regions. CCG and GAAAA repeats occurred most frequently. In all, 259 microsatellites could be identified in the duplicated sequences using the criteria of minimum 90% alignability spread over a minimum of 1？Kb sequence. More than 25% of the repeats in duplicated regions occurred in the genic sequences. Only 45 (17%) of these 259 microsatellites were found conserved in the duplicated paralogues. Among these repeats, 40% maintained both sequence and length conservation. The effect of mutability of nearby regions could also be clearly seen in microsatellite regions. The overall purpose of this study was to investigate, whether microsatellites follow an independent course of evolutionary dynamics subsequent to events like genome reshuffling that simply drives these elements to different locations in the genome. To the best of our knowledge, this is the first comprehensive analysis of microsatellite conservation in the duplicated regions of any genome. 1. Introduction Microsatellites represent a class of tandem DNA repeats with 1 to 6？bp long repeat units. These sequences occur in almost all the organisms and frequently constitute the hypervariable regions of the genome. No specific functions have been assigned to most of the microsatellites till date. However, in some cases at least, microsatellite alleles provide protective or adaptive advantage to the host [1]. In many cases, occurrence of different alleles has been found associated with different phenotypes [2]. Microsatellites are not expected to be conserved for long evolutionary periods either, as argued by Buschiazzo and Gemmell [3]. Nevertheless, models of microsatellite mutational dynamics have been developed based on comparison of orthologous microsatellite loci in related taxa [4–7]. However, whether these models also describe microsatellites at paralogous loci created by segmental changes within a genome remains to be investigated. Availability of whole-genome sequences for rice (Oryza sativa L.) allows analysis of noncoding DNA also within the segmentally duplicated regions in addition to the gene order, tandemly arranged genes (TAGs) and gene functions. A collective look emerging from different reports on mapping of duplicated regions in rice genome [8–10]
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