Rapid recent growth and divergence of rice nuclear genomes
Rapid recent growth and divergence of rice nuclear genomes
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DOI：
10.1073/pnas.0403715101
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发表时间：
2004-08-24
影响因子：
11.1
通讯作者：
Bennetzen, JL
中科院分区：
文献类型：
--
作者：
Ma, JX;Bennetzen, JL
以非洲水稻核DNA为参照基因组，研究了水稻亚种间近期序列进化的时间、性质、机制和特异性。这些数据表明，由于它们与共同祖先的分化，它们的基因组大小都大幅增加，分别为2%和6%，这主要是由于LTR-逆转录转座子的扩增。然而，由于不相等的同源重组和非法重组导致的各类DNA序列的丢失，削弱了水稻基因组的生长。在整个基因组中，微小的缺失尤其频繁。在我们分析的>；1Mb的同源区域中，没有发现从水稻或水稻中完全获得或丢失基因的情况，也没有检测到任何精确的转座子切除的例子。观察到基因之间的序列具有非常高的分歧率，这表明转座元件的分子时钟至少比基因内同义碱基替换快2倍。我们发现，容易频繁插入和缺失的区域也显示出更高水平的点突变。这些结果表明，水稻基因组高度动态，在遗传变异的产生和消除方面存在竞争过程。
By employing the nuclear DNA of the African rice Oryza glaberrima as a reference genome, the timing, natures, mechanisms, and specificities of recent sequence evolution in the indica and japonica subspecies of Oryza sativa were identified. The data indicate that the genome sizes of both indica and japonica have increased substantially, >2% and >6%, respectively, since their divergence from a common ancestor, mainly because of the amplification of LTR-retrotransposons. However, losses of all classes of DNA sequence through unequal homologous recombination and illegitimate recombination have attenuated the growth of the rice genome. Small deletions have been particularly frequent throughout the genome. In >1 Mb of orthologous regions that we analyzed, no cases of complete gene acquisition or loss from either indica or japonica were found, nor was any example of precise transposon excision detected. The sequences between genes were observed to have a very high rate of divergence, indicating a molecular clock for transposable elements that is at least 2-fold more rapid than synonymous base substitutions within genes. We found that regions prone to frequent insertions and deletions also exhibit higher levels of point mutation. These results indicate a highly dynamic rice genome with competing processes for the generation and removal of genetic variation.