An in silico Mining for Simple Sequence Repeats from Expressed Sequence Tags of Zebrafish, Medaka, Fundulus, and Xiphophorus
An in silico Mining for Simple Sequence Repeats from Expressed Sequence Tags of Zebrafish, Medaka, Fundulus, and Xiphophorus
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发表时间：
2005
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通讯作者：
Z. Ju;Melissa Wells;Al Martinez;Leona Hazlewood;R. Walter
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作者：
Z. Ju;Melissa Wells;Al Martinez;Leona Hazlewood;R. Walter
涉及模型物种的硬骨鱼基因组项目正在导致公共数据库中基因组和表达 DNA 序列的快速积累。可以挖掘数据库中收集的表达序列标签 (EST) 以进行结构和功能基因组学分析。在这项研究中，我们通过计算机分析了 49,430 个 unigene，代表来自四种模型鱼的总共 692,654 个 EST，以了解它们在开发简单序列重复 (SSR) 或微卫星方面的潜在用途。经过生物信息挖掘，共鉴定出 3,018 个 EST 衍生的 SSR（EST-SSR），其中 2,335 个包含 EST 的 SSR（SSR-EST）。已识别的 SSR-EST 频率范围为剑鱼的 1.5% 到斑马鱼的 7.3%。二核苷酸重复基序是最丰富的SSR，分别占青鳉鱼、眼底鱼、斑马鱼和剑鱼的47%、52%、64%和78%。模拟分析表明，大多数 EST-SSR 具有足够的侧翼序列用于聚合酶链式反应 (PCR) 引物设计。 SSR-EST 的比较 DNA 序列分析确定了几个跨物种 SSR 和序列，可在比较研究中用作交叉参考基因。例如，垂体肿瘤转化基因 (PTTG) 1 相互作用蛋白 (PTTGIP) 内的一个 SSR (CTG)n 的侧翼序列显示出跨越青鳉、眼底、人类和小鼠基因组的保守性。这项研究提供了有关 EST-SSR 的大量信息，可用于多态性标记的开发、基因作图和比较基因组分析。这些 SSR-EST 的功能分析可能揭示它们在这些模型物种的代谢和基因进化中的作用。
Teleost fish genome projects involving model species are resulting in a rapid accumulation of genomic and expressed DNA sequences in public databases. The expressed sequence tags (ESTs) collected in the databases can be mined for the analysis of both structural and functional genomics. In this study, we in silico analyzed 49,430 unigenes representing a total of 692,654 ESTs from four model fish for their potential use in developing simple sequence repeats (SSRs), or microsatellites. After bioinformatical mining, a total of 3,018 EST derived SSRs (EST-SSRs) were identified for 2,335 SSR containing ESTs (SSR-ESTs). The frequency of identified SSR-ESTs ranged from 1.5% for Xiphophorus to 7.3% for zebrafish. The dinucleotide repeat motif is the most abundant SSR, accounting for 47%, 52%, 64%, and 78% for medaka, Fundulus, zebrafish, and Xiphophorus, respectively. Simulation analysis suggests that a majority of these EST-SSRs have sufficient flanking sequences for polymerase chain reaction (PCR) primer design. Comparative DNA sequence analyses of SSR-ESTs identified several cross-species SSRs and sequences that may be used as cross-reference genes in comparative studies. For example, the flanking sequences of one SSR (CTG)n within the pituitary tumor-transforming gene (PTTG) 1 interacting protein (PTTGIP), showed conservation spanning the medaka, Fundulus, human, and mouse genomes. This study provides a large body of information on EST-SSRs that can be useful for the development of polymorphic markers, gene mapping, and comparative genome analysis. Functional analysis of these SSR-ESTs may reveal their role in metabolism and gene evolution of these model species.