Analysis on frequency and density of microsatellites in coding sequences of several eukaryotic genomes.
Analysis on frequency and density of microsatellites in coding sequences of several eukaryotic genomes.
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DOI：
10.1016/s1672-0229(04)02004-2
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发表时间：
2004-02
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过去十年，大多数生物体中都发现了微卫星或简单序列重复（SSR）。由于大规模序列的产生，特别是那些可用于搜索微卫星的序列，这些标记的开发变得越来越方便。考虑到SSR的应用重要性，一些真核物种的可用CDS（编码序列）或EST（表达序列标签）被用来研究各种类型微卫星的频率和密度。根据对蚕中 66.6 Mb、苍蝇 37.2 Mb、蚊子 20.8 Mb、小鼠 60.0 Mb、斑马鱼 34.9 Mb 和秀丽隐杆线虫 33.5 Mb 的 CDS 或 EST 序列的调查，SSR 在蚕中的频率为 1/1.00 Kb，苍蝇中为 1/0.77 Kb，蚊子中为 1/1.03 Kb，小鼠中为 1/1.21 Kb，斑马鱼中为 1/1.25 Kb，线虫中为 1/1.38 Kb。这些物种的总体平均 SSR 频率为 1/1.07 Kb。六核苷酸重复序列（64.5%–76.6%）是所研究物种中最丰富的 SSR 类型，其次是三聚体、二聚体、四聚体、单体和五聚体重复序列。此外，富含A的重复序列在每种类型的SSR中占主导地位，而富含G的重复序列在编码区中很少见。
Microsatellites or simple sequence repeats (SSRs) have been found in most organisms during the last decade. Since large-scale sequences are being generated, especially those that can be used to search for microsatellites, the development of these markers is getting more convenient. Keeping SSRs in viewing the importance of the application, available CDS (coding sequences) or ESTs (expressed sequence tags) of some eukaryotic species were used to study the frequency and density of various types of microsatellites. On the basis of surveying CDS or EST sequences amounting to 66.6 Mb in silkworm, 37.2 Mb in fly, 20.8 Mb in mosquito, 60.0 Mb in mouse, 34.9 Mb in zebrafish and 33.5 Mb in Caenorhabditis elegans, the frequency of SSRs was 1/1.00 Kb in silkworm, 1/0.77 Kb in fly, 1/1.03 Kb in mosquito, 1/1.21 Kb in mouse, 1/1.25 Kb in zebrafish and 1/1.38 Kb in C. elegans. The overall average SSR frequency of these species is 1/1.07 Kb. Hexanucleotide repeats (64.5%–76.6%) are the most abundant class of SSR in the investigated species, followed by trimeric, dimeric, tetrameric, monomeric and pentameric repeats. Furthermore, the A-rich repeats are predominant in each type of SSRs, whereas G-rich repeats are rare in the coding regions.