Simillion Cedric, Vandepoele Klaas, Van Montagu Marc C E, Zabeau Marc, Van de Peer Yves
Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.
Proc Natl Acad Sci U S A. 2002 Oct 15;99(21):13627-32. doi: 10.1073/pnas.212522399. Epub 2002 Oct 8.
Analysis of the genome sequence of Arabidopsis thaliana shows that this genome, like that of many other eukaryotic organisms, has undergone large-scale gene duplications or even duplications of the entire genome. However, the high frequency of gene loss after duplication events reduces colinearity and therefore the chance of finding duplicated regions that, at the extreme, no longer share homologous genes. In this study we show that heavily degenerated block duplications that can no longer be recognized by directly comparing two segments because of differential gene loss, can still be detected through indirect comparison with other segments. When these so-called hidden duplications in Arabidopsis are taken into account, many homologous genomic regions can be found in five to eight copies. This finding strongly implies that Arabidopsis has undergone three, but probably no more, rounds of genome duplications. Therefore, adding such hidden blocks to the duplication landscape of Arabidopsis sheds light on the number of polyploidy events that this model plant genome has undergone in its evolutionary past.
对拟南芥基因组序列的分析表明，与许多其他真核生物的基因组一样，该基因组经历了大规模的基因重复甚至整个基因组的重复。然而，重复事件后基因丢失的高频率降低了共线性，因此找到重复区域的机会减少，在极端情况下，这些区域不再共享同源基因。在本研究中，我们表明，由于基因丢失的差异，无法通过直接比较两个片段来识别的严重退化的区段重复，仍然可以通过与其他片段的间接比较来检测。当考虑到拟南芥中这些所谓的隐藏重复时，可以发现许多同源基因组区域有五到八个拷贝。这一发现强烈暗示拟南芥经历了三轮，但可能不超过三轮的基因组重复。因此，将这些隐藏的区段添加到拟南芥的重复图谱中，有助于了解这种模式植物基因组在其进化历史中经历的多倍体事件的数量。
