Zhang Xiaoyu, Wessler Susan R
Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
Proc Natl Acad Sci U S A. 2004 Apr 13;101(15):5589-94. doi: 10.1073/pnas.0401243101. Epub 2004 Apr 2.
Transposable elements (TEs) are the major component of plant genomes where they contribute significantly to the >1,000-fold genome size variation. To understand the dynamics of TE-mediated genome expansion, we have undertaken a comparative analysis of the TEs in two related organisms: the weed Arabidopsis thaliana (125 megabases) and Brassica oleracea ( approximately 600 megabases), a species with many crop plants. Comparison of the whole genome sequence of A. thaliana with a partial draft of B. oleracea has permitted an estimation of the patterns of TE amplification, diversification, and loss that has occurred in related species since their divergence from a common ancestor. Although we find that nearly all TE lineages are shared, the number of elements in each lineage is almost always greater in B. oleracea. Class 1 (retro) elements are the most abundant TE class in both species with LTR and non-LTR elements comprising the largest fraction of each genome. However, several families of class 2 (DNA) elements have amplified to very high copy number in B. oleracea where they have contributed significantly to genome expansion. Taken together, the results of this analysis indicate that amplification of both class 1 and class 2 TEs is responsible, in part, for B. oleracea genome expansion since divergence from a common ancestor with A. thaliana. In addition, the observation that B. oleracea and A. thaliana share virtually all TE lineages makes it unlikely that wholesale removal of TEs is responsible for the compact genome of A. thaliana.
转座元件（TEs）是植物基因组的主要组成部分，它们对基因组大小超过1000倍的变化有显著贡献。为了了解TE介导的基因组扩张动态，我们对两种相关生物中的TEs进行了比较分析：杂草拟南芥（125兆碱基）和甘蓝（约600兆碱基），后者是许多农作物的祖先物种。将拟南芥的全基因组序列与甘蓝的部分草图进行比较，使得我们能够估计自它们从共同祖先分化以来，相关物种中发生的TE扩增、多样化和丢失模式。尽管我们发现几乎所有的TE谱系都是共享的，但每个谱系中的元件数量在甘蓝中几乎总是更多。第1类（逆转录）元件是这两个物种中最丰富的TE类别，其中LTR和非LTR元件在每个基因组中占最大比例。然而，几类第2类（DNA）元件在甘蓝中扩增到了非常高的拷贝数，它们对基因组扩张有显著贡献。综上所述，该分析结果表明，自与拟南芥从共同祖先分化以来，第1类和第2类TEs的扩增在一定程度上导致了甘蓝基因组的扩张。此外，甘蓝和拟南芥几乎共享所有TE谱系这一观察结果表明，TEs的大规模去除不太可能是拟南芥基因组紧凑的原因。
