Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.
Genetics. 2012 Apr;190(4):1563-74. doi: 10.1534/genetics.111.137349. Epub 2012 Feb 2.
The genome sequence of the paleohexaploid Brassica rapa shows that fractionation is biased among the three subgenomes and that the least fractionated subgenome has approximately twice as many orthologs as its close (and relatively unduplicated) relative Arabidopsis than had either of the other two subgenomes. One evolutionary scenario is that the two subgenomes with heavy gene losses (I and II) were in the same nucleus for a longer period of time than the third subgenome (III) with the fewest gene losses. This "two-step" hypothesis is essentially the same as that proposed previously for the eudicot paleohexaploidy; however, the more recent nature of the B. rapa paleohexaploidy makes this model more testable. We found that subgenome II suffered recent small deletions within exons more frequently than subgenome I, as would be expected if the genes in subgenome I had already been near maximally fractionated before subgenome III was introduced. We observed that some sequences, before these deletions, were flanked by short direct repeats, a unique signature of intrachromosomal illegitimate recombination. We also found, through simulations, that short--single or two-gene--deletions appear to dominate the fractionation patterns in B. rapa. We conclude that the observed patterns of the triplicated regions in the Brassica genome are best explained by a two-step fractionation model. The triplication and subsequent mode of fractionation could influence the potential to generate morphological diversity--a hallmark of the Brassica genus.
古六倍体油菜基因组序列表明，三个亚基因组之间的分裂存在偏向性，且分裂程度最小的亚基因组拥有的直系同源基因数量约为与其亲缘关系最近（相对未重复）的拟南芥的两倍，而另外两个亚基因组的直系同源基因数量则较少。一个进化情景是，两个基因大量丢失的亚基因组（I 和 II）与第三个亚基因组（III）相比，在同一个细胞核中存在的时间更长，后者基因丢失较少。这种“两步”假说与先前提出的真双子叶古六倍体假说基本相同；然而，由于油菜古六倍体较新，因此该模型更具可检验性。我们发现，与亚基因组 I 相比，亚基因组 II 中的外显子内最近发生的小缺失更为频繁，如果在引入亚基因组 III 之前，亚基因组 I 中的基因已经接近最大程度的分裂，那么这是可以预期的。我们观察到，在这些缺失之前，一些序列被短的直接重复序列所包围，这是染色体内非同源重组的独特特征。我们还通过模拟发现，短的（单个或两个基因）缺失似乎主导了油菜中基因的分裂模式。我们得出结论，观察到的 Brassica 基因组中三倍体区域的模式最好用两步分裂模型来解释。三倍体的产生和随后的分裂模式可能会影响产生形态多样性的潜力——这是 Brassica 属的一个标志。
