Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice
Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice
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DOI：
10.1101/gr.1466204
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发表时间：
2004-05-01
期刊：
影响因子：
7
通讯作者：
Bennetzen, JL
中科院分区：
文献类型：
--
作者：
Ma, JX;Devos, KM;Bennetzen, JL
我们最初分析了水稻中11个低拷贝数和中等拷贝数的长末端重复序列（LTR）反转录转座子家族，以确定它们的结构如何偏离其预测的祖先形式。根据序列同源性和结构特征鉴定了这些高度片段化的元件。这11个家族共有1000个元素，其拷贝数从1到278不等。这些元素中只有不到四分之一是完整的，而其余的是单独的LTR和各种截短的片段。我们还分析了两个高度重复的LTR反转录转座子家族（Osr 8和Osr 30），并观察到相同的结果。我们的数据表明，不等同源重组和非法重组主要负责LTR-反转录转座子删除。进一步的分析表明，水稻中大多数可检测到的LTR反转录转座子在不到800万年前插入，现在已经丢失了超过三分之二的编码序列。因此，我们预测LTR反转录转座子序列在水稻中的半衰期小于600万年。此外，我们的数据表明，目前水稻基因组中至少有22%（97 Mb）是由LTR-反转录转座子序列组成的，并且在过去的800万年中，超过190 Mb的LTR-反转录转座子序列已从水稻基因组中删除。
We initially analyzed 11 families of low- and middle-copy-number long terminal repeat (LTR) retrotransposons in rice to determine how their structures have diverged from their predicted ancestral forms. These elements, many highly fragmented, were identified oil the basis of sequence homology and structural characteristics. The 11 families, totaling 1000 elements, have copy numbers ranging from 1 to 278. Less than one-quarter of these elements are intact, whereas the remaining are solo LTRs and variously truncated fragments. We also analyzed two highly repetitive families (Osr8 and Osr30) of LTR retrotransposons and observed the same results. Our data indicate that unequal homologous recombination and illegitimate recombination are primarily responsible for LTR-retrotransposon removal. Further analysis suggests that most of the detectable LTR retrotransposons in rice inserted less than 8 million years ago, and have now lost over two-thirds of their encoded sequences. Hence, we predict that the half-life of LTR-retrotransposon sequences in rice is less than 6 million years. Moreover, our data demonstrate that at least 22% (97 Mb) of the Current rice genome is comprised of LTR-retrotransposon sequences, and that more than 190 Mb of LTR-retrotransposon sequences have been deleted from the rice genome in the last 8 million years.