Computational and experimental characterization of physically clustered simple sequence repeats in plants.
Computational and experimental characterization of physically clustered simple sequence repeats in plants.
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发表时间：
2000-09
期刊：
影响因子：
3.3
通讯作者：
L. Cardle;L. Ramsay;D. Milbourne;M. Macaulay;D. Marshall;R. Waugh
中科院分区：
文献类型：
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作者：
L. Cardle;L. Ramsay;D. Milbourne;M. Macaulay;D. Marshall;R. Waugh
利用公共数据库中不断增加的DNA序列数据，对植物基因组中的简单重复序列（SSR）的类型和频率进行了研究。在拟南芥中，搜索了306个大于10 kb的基因组DNA序列和36，199个EST序列中所有可能的单至五核苷酸重复。SSR在基因组DNA中的平均频率为每6.04kb一个，在EST中则降至每14kb一个。SSR的频率和类型在编码、内含子和基因间DNA之间存在差异。在其他植物物种中也发现了类似的频率。在这些发现的基础上，提出了一种方法，并证明了有针对性的分离的单一或多个，物理聚类SSR链接到任何基因，已被映射使用低拷贝的DNA标记。该方法涉及对所选随机剪切的大插入DNA克隆的少量亚克隆进行样品测序（例如，BAC）。它被证明是可行的和实用的，通过SSR偶然测序的概率。该方法在大麦中得到证实，其中通过与Big1基因杂交选择的单个BAC的34个亚克隆的样品测序揭示了三个SSR。这使得Big1位于大麦连锁群6HS的顶部。
The type and frequency of simple sequence repeats (SSRs) in plant genomes was investigated using the expanding quantity of DNA sequence data deposited in public databases. In Arabidopsis, 306 genomic DNA sequences longer than 10 kb and 36,199 EST sequences were searched for all possible mono- to pentanucleotide repeats. The average frequency of SSRs was one every 6.04 kb in genomic DNA, decreasing to one every 14 kb in ESTs. SSR frequency and type differed between coding, intronic, and intergenic DNA. Similar frequencies were found in other plant species. On the basis of these findings, an approach is proposed and demonstrated for the targeted isolation of single or multiple, physically clustered SSRs linked to any gene that has been mapped using low-copy DNA-based markers. The approach involves sample sequencing a small number of subclones of selected randomly sheared large insert DNA clones (e.g., BACs). It is shown to be both feasible and practicable, given the probability of fortuitously sequencing through an SSR. The approach is demonstrated in barley where sample sequencing 34 subclones of a single BAC selected by hybridization to the Big1 gene revealed three SSRs. These allowed Big1 to be located at the top of barley linkage group 6HS.