Characterization of the repetitive sequences in a 200-kb region around the rice waxy locus:: diversity of transposable elements and presence of veiled repetitive sequences
Characterization of the repetitive sequences in a 200-kb region around the rice waxy locus:: diversity of transposable elements and presence of veiled repetitive sequences
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DOI：
10.1266/ggs.77.69
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发表时间：
2002-04-01
影响因子：
1.1
通讯作者：
Sano, Y
中科院分区：
文献类型：
--
作者：
Nagano, H;Kunii, M;Sano, Y
重复的基因组序列可能具有不同于已知转座元件(TE)的各种结构特征和性质。在这里，利用现有的水稻基因组数据库分析了水稻蜡质基因座周围200kb区域中存在的重复序列的含量和性质。在我们之前的Southern blotting分析中，该区域70%的片段显示出涂抹图案，但根据目前的数据库分析，该区域重复序列的比例仅为15%。在这个200kb区域的重复片段包括75个重复序列，我们将其分为46个亚家族：21个亚家族是已知的TES或重复序列，25个亚家族由新发现的TES或新类型的重复序列组成。该区域不包含长末端重复序列(LTR)反转录转座元件，但微型反向重复序列转座元件(MITE)构成了已鉴定的主要元件类别。这些螨类在结构上表现出明显的分化：有12种成分是已知的螨超家族的新成员，而有5种成分具有新的末端结构，不属于任何已知的TE家族。有趣的是，大约10%的重复序列，包括类似病毒的序列，不具有TES的任何常见特征，这表明一定比例的重复序列可能不具有已知元件的转座机制，分散在紧凑的水稻基因组中。
Repetitive genomic sequences might have various structural features and properties distinct from those of the known transposable elements (TE). Here, the content and properties of the repetitive sequences present in a 200-kb region around the rice waxy locus were analyzed using the available rice genomic database. In our previous Southern blotting analysis, 70% of the segments in this region showed smeared patterns, but according to the present database analysis, the proportion of repetitive sequences in this region was only 15%. The repetitive segments in this 200-kb region comprised 75 repetitive sequences that we classified into 46 subfamilies: 21 subfamilies were known TEs or repetitive sequences and 25 subfamilies consisted of newly identified TEs or novel types of repetitive sequences. The region contains no long terminal repeat (LTR) retrotransposable elements, but miniature inverted repeat transposable elements (MITEs) constituted a major class among the elements identified. These MITEs showed remarkable structural divergence: 12 elements were found to be new members of known MITE superfamilies, while five elements had novel terminal structures, and did not belong to any known TE families. Interestingly, about 10% of the repetitive sequences, including virus-like sequences did not have any of the usual characteristics of TEs, suggesting that a certain proportion of repetitive sequences that might not share the transpositional mechanisms of known elements are dispersed in the compact rice genome.