Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution
Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution
复制标题
DOI：
10.1073/pnas.0605618103
复制
发表时间：
2006-11-21
影响因子：
11.1
通讯作者：
Bennetzen, Jeffrey L.
中科院分区：
文献类型：
--
作者：
Vitte, Clementine;Bennetzen, Jeffrey L.
对五个二倍体被子植物基因组的LTR反转录启动子结构的分析揭示了不同类型基因组多样性的相对水平非常不同。所有物种都表现出最近的LTR反转录转座子迁移率，并通过不相等的同源重组和非法重组去除了高速率的DNA。较大的植物基因组中含有许多LTR反转录转座子家族，每个单倍体基因组有10,000个拷贝，而较小的基因组中只有很少的或没有LTR反转录转座子家族的>；11,000个拷贝，这表明逆转录元件扩增的差异潜力是被子植物基因组大小变异的一个主要因素。对于每个被研究的物种，不同的LTRS中转换突变与颠换突变(ts/tv)的平均比率为>；1.5，这表明这些元件大多是在表观遗传沉默状态下的胞嘧啶5-甲基化。然而，二倍体小麦、单粒小麦和大麦的ts/tv值(分别为1.9和1.6)低于玉米(3.9)、紫花苜蓿(3.6)和莲花(2.5)，这表明这种沉默在这两个小麦族中并不完全。点突变与插入缺失(插入和缺失)的比率，以及与非法重组相比，不相等同源重组去除DNA的相对效率等特征在物种之间存在很大差异。这些后一种变异与基因组大小或系统发育关系无关，表明它们在植物谱系的进化进化过程中经常发生变化。总之，这些结果表明被子植物基因组的大小、含量和结构的不同是同一套机制过程的结果，但在不同的植物谱系中作用的相对效率不同。
Analysis of LTR retrotrainsposon structures in five diploid angiosperm genomes uncovered very different relative levels of different types of genomic diversity. All species exhibited recent LTR retrotransposon mobility and also high rates of DNA removal by unequal homologous recombination and illegitimate recombination. The larger plant genomes contained many LTR retrotransposon families with > 10,000 copies per haploid genome, whereas the smaller genomes contained few or no LTR retrotransposon families with > 11,000 copies, suggesting that this differential potential for retroelement amplification is a primary factor in angiosperm genome size variation. The average ratios of transition to transversion mutations (Ts/Tv) in diverging LTRs were > 1.5 for each species studied, suggesting that these elements are mostly 5-methylated at cytosines in an epigenetically silenced state. However, the diploid wheat Triticum monococcum and barley have unusually low Ts/Tv values (respectively, 1.9 and 1.6) compared with maize (3.9), medicago (3.6), and lotus (2.5), suggesting that this silencing is less complete in the two Triticeae. Such characteristics as the ratios of point mutations to indels (insertions and deletions) and the relative efficiencies of DNA removal by unequal homologous recombination compared with illegitimate recombination were highly variable between species. These latter variations did not correlate with genome size or phylogenetic relatedness, indicating that they frequently change during the evolutionary descent of plant lineages. In sum, the results indicate that the different sizes, contents, and structures of angiosperm genomes are outcomes of the same suite of mechanistic processes, but acting with different relative efficiencies in different plant lineages.