Bioinformatics Advance Access originally published online on February 5, 2004
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Bioinformatics 20(7) © Oxford University Press 2004; all rights reserved.
Preference of simple sequence repeats in coding and non-coding regions of Arabidopsis thaliana
1 Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China, 2 National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan 430070, People's Republic of China and 3 State Key Laboratory of Genetic Engineering, Fudan–SJTU–Nottingham Plant Biotechnology R&D Center, School of Life Sciences, Morgan-Tan International Center for Life Sciences, Fudan University, Shanghai 200433, People's Republic of China
Received on April 21, 2003; accepted on November 7, 2003
Advance Access Publication February 5, 2004
Motivation: Simple sequence repeats or microsatellites have been found abundantly in many genomes. However, the significance of distribution preference has not been completely understood. Completion of the Arabidopsis genome sequencing allows us to better understand and characterize microsatellites.
Results: Microsatellite distribution was more abundant in 5'-flanking regions of genes compared with that expected in the whole genome, with an over-representation of AG and AAG repeats; there were clear differences from distributions in 3'-flanks and coding fractions, where triplet frequencies evidently corresponded to codon usage. We identified 1140 full-length genes that contained at least one locus of AG or AAG repeats in their upstream sequences, and whose functional characteristics were significantly associated with the repeats. This observation indicates that selective pressure markedly differed in the three transcribed regions, with positive selection of AG and AAG repeats in 5'-flanks close to those genes whose products are preferentially involved in transcription.
Contact: kxtangl{at}yahoo.com
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