The transposable element landscape of the model legume Lotus japonicus
The transposable element landscape of the model legume Lotus japonicus
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DOI：
10.1534/genetics.106.062752
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发表时间：
2006-12-01
期刊：
影响因子：
3.3
通讯作者：
Wessler, Susan R.
中科院分区：
文献类型：
--
作者：
Holligan, Dawn;Zhang, Xiaoyu;Wessler, Susan R.
迄今为止，动植物基因组的最大成分是转座元素（TES）。大量莲花japonicus基因组序列的可用性首次允许对豆类物种中的TE景观进行全面研究。在这里，我们报告了32.4 MB成品TAC克隆中TE的组合计算机辅助和实验分析的结果。尽管计算机辅助分析有助于确定丰度和多样性，但完整的TAC序列的可用性允许鉴定全长TES，这促进了用于全基因组实验分析工具的设计。除了包含先前表征的植物基因组中发现的所有TE类型外，Japonicus的TE成分还包含了几个惊喜。首先，它是第二种（仅次于Oryza sativa）富含包装符号，占据了> 1000个元素，这些元素已捕获和放大基因片段。此外，我们已经确定了似乎是豆类特异性的m子家族，以前仅在真菌物种中被鉴定出来。最后，japonicus基因组包含数百个，也许是成千上万的西里病毒：带有额外ORF的Ty1/类似Copia的元素。值得注意的是，一些japonicus sireviruses最近已经放大，并且可能仍在积极转移。
The largest component of plant and animal genomes characterized to date is transposable elements (TEs). The availability of a significant amount of Lotus japonicus genome sequence has permitted for the first time a comprehensive study of the TE landscape in a legume species. Here we report the results of a combined computer-assisted and experimental analysis of the TEs in the 32.4 Mb of finished TAC clones. While computer-assisted analysis facilitated a determination of TE abundance and diversity, the availability of complete TAC sequences permitted identification of full-length TEs, which facilitated the design of tools for genomewide experimental analysis. In addition to containing all TE types found in previously characterized plant genomes, the TE component of L. japonicus contained several surprises. First, it is the second species (after Oryza sativa) found to be rich in Pack-MULEs, with > 1000 elements that have captured and amplified gene fragments. In addition, we have identified what appears to be a legume-specific MULE family that was previously identified only in fungal species. Finally, the L. japonicus genome contains many hundreds, perhaps thousands of Sireviruses: Ty1/copia-like elements with an extra ORF. Significantly, several of the L. japonicus Sireviruses have recently amplified and may still be actively transposing.