Generation and analysis of end sequence database for T-DNA tagging lines in rice
Generation and analysis of end sequence database for T-DNA tagging lines in rice
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DOI：
10.1104/pp.103.030478
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发表时间：
2003-12-01
期刊：
影响因子：
7.4
通讯作者：
An, GH
中科院分区：
文献类型：
--
作者：
An, SY;Park, S;An, GH
我们分析了由基因捕获载体 pGA2707 标记的 6,749 个品系。这导致 T-DNA 侧翼 3,793 个基因组序列的分离。在插入中，1,846 个 T-DNA 整合到基因区域，1,864 个位于基因间区域。编码区的开头和结尾以及 ATG 起始密码子附近的上游频率也较高。插入位点的总 GC 含量接近于整个水稻 (Oryza sativa) 基因组的测量值。这 1,846 个标记基因的功能分类显示出与水稻染色体中所有基因观察到的分布相似的分布。这表明 T-DNA 插入不偏向特定类别的基因。 1号、4号和10号染色体上分别有764、327和346个T-DNA插入。插入分布不均匀；染色体末端的频率较高，着丝粒附近的频率较低。在某些地点，频率高于周边地区。该序列数据库对于鉴定敲除突变体以阐明水稻基因功能非常有价值。科学界可通过 http://www.postech.ac.kr/life/pfg/risd 获取该资源。
We analyzed 6,749 lines tagged by the gene trap vector pGA2707. This resulted in the isolation of 3,793 genomic sequences flanking the T-DNA. Among the insertions, 1,846 T-DNAs were integrated into genic regions, and 1,864 were located in intergenic regions. Frequencies were also higher at the beginning and end of the coding regions and upstream near the ATG start codon. The overall GC content at the insertion sites was close to that measured from the entire rice (Oryza sativa) genome. Functional classification of these 1,846 tagged genes showed a distribution similar to that observed for all the genes in the rice chromosomes. This indicates that T-DNA insertion is not biased toward a particular class of genes. There were 764, 327, and 346 T-DNA insertions in chromosomes 1, 4 and 10, respectively. Insertions were not evenly distributed; frequencies were higher at the ends of the chromosomes and lower near the centromere. At certain sites, the frequency was higher than in the surrounding regions. This sequence database will be valuable in identifying knockout mutants for elucidating gene function in rice. This resource is available to the scientific community at http://www.postech.ac.kr/life/pfg/risd.