Sources and predictors of resolvable indel polymorphism assessed using rice as a model
Sources and predictors of resolvable indel polymorphism assessed using rice as a model
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DOI：
10.1007/s00438-004-0979-7
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发表时间：
2004-04-01
影响因子：
3.1
通讯作者：
McCouch, SR
中科院分区：
文献类型：
--
作者：
Edwards, JD;Lee, VM;McCouch, SR
可用限制性内切酶分析的遗传变异的主要来源是碱基替换和插入/缺失(INDELs)。将INDELs检测为限制性片段长度多态(RFLP)的可能性由INDELs的大小和频率决定，而将小INDELs解析为RFLP的能力受限制性片段大小分布的限制。在这项研究中，我们使用了水稻(Oryza sativa L.)量化和比较限制性内切酶检测INDELs的能力。我们特别研究了两个丰富的可转座元件来源的Indel：微型反向重复序列转座元件(METE)和长末端重复序列(LTR)反转录元件。根据这一分析，我们得出结论，在水稻中检测到的多态的主要来源是indels，而不是碱基替换。我们发现，尽管尘螨来源的indels比Ltr逆转录元件来源的indels更丰富，但Ltr逆转录元件由于其较大的尺寸而具有更大的能力产生可见的限制性片段长度多态。我们发现，INDELs在限制性内切酶中可检测性的差异可以用它们在基因组中限制位点的频率和分散程度的差异来解释。描述用限制性内切酶获得的片段大小分布的参数在水稻、拟南芥和人类的测序基因组中高度相关，除了特定识别序列在频率上的一些极端偏差外，这些识别序列对应于这三个不同生物中DNA甲基化水平和方式的变化。因此，我们可以根据限制片段大小的分布来预测限制酶检测来自特定来源的INDELs的相对能力，即使这是针对远亲基因组估计的。
The principal sources of genetic variation that can be assayed with restriction enzymes are base substitutions and insertions/deletions (indels). The likelihood of detecting indels as restriction fragment length polymorphisms (RFLPs) is determined by the size and frequency of the indels, and the ability to resolve small indels as RFLPs is limited by the distribution of restriction fragment sizes. In this study, we use aligned sequences from the indica and japonica subspecies of rice ( Oryza sativa L.) to quantify and compare the ability of restriction enzymes to detect indels. We look specifically at two abundant transposable element-derived indel sources: miniature inverted repeat transposable elements (MITEs) and long terminal repeat (LTR) retroelements. From this analysis we conclude that indels rather than base substitutions are the prevailing source of the polymorphism detected in rice. We show that, although MITE derived indels are more abundant than LTR-retroelement derived indels, LTR-retroelements have a greater capacity to generate visible restriction fragment length polymorphism because of their larger size. We find that the variation in the detectability of indels among restriction enzymes can be explained by differences in the frequency and dispersion of their restriction sites in the genome. The parameters that describe the fragment size distributions obtained with the restriction enzymes are highly correlated across the sequenced genomes of rice, Arabidopsis and human, with the exception of some extreme deviations in frequency for particular recognition sequences corresponding to variations in the levels and modes of DNA methylation in the three disparate organisms. Thus, we can predict the relative ability of a restriction enzyme to detect indels derived from a specific source based on the distribution of restriction fragment sizes, even when this is estimated for a distantly related genome.