Transition-transversion bias is not universal: a counter example from grasshopper pseudogenes.
Transition-transversion bias is not universal: a counter example from grasshopper pseudogenes.
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过渡 - 转换偏差不是普遍的：蚱hopper假基因的反词。
DOI：
10.1371/journal.pgen.0030022
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发表时间：
2007-02-02
期刊：
影响因子：
4.5
通讯作者：
Nichols, Richard A.
中科院分区：
文献类型：
--
作者：
Keller, Irene;Bensasson, Douda;Nichols, Richard A.
后生动物的DNA序列的比较表明，过渡超过transversional取代。这种偏倚的部分原因是甲基化胞嘧啶突变为胸腺嘧啶的比率相对较高。后突变过程也引入了偏好，特别是编码区中密码子使用偏好的选择。然而，一般认为，可能由于突变的潜在化学作用，存在着普遍的偏向，倾向于转换而不是颠换。令人惊讶的是，这种潜在的趋势只在两种后生动物中进行了评估，即果蝇和哺乳动物。在这里，我们调查了第三组，并没有发现这样的偏见。我们的特点是点取代谱Podisma pedestris，一个非常大的基因组蝗虫物种。突变的积累进行了调查，在两个假基因家族，核线粒体和核糖体DNA序列。胞嘧啶-鸟嘌呤（CpG）二核苷酸表现出甲基化位点预期的高转换频率。其他胞嘧啶残基的转换速率明显较低。考虑到这种甲基化效应后，转换率和颠换率之间没有显著差异。这些结果与其他类群的报告，并导致我们拒绝普遍的过渡/颠换偏置的假设。相反，我们建议在点替代过程中的种间差异。有些突变比其他突变发生得更频繁。如果我们要解释物种和个体之间积累的差异，我们就需要理解这些偏见。应用包括估计进化谱系分化的时间和检测DNA序列中自然选择的特征。然而，突变的偏见一直被掩盖，因为自从突变出现以来，自然选择已经消除了一些，而允许其他人坚持到现在。因此，我们研究的突变积累在基因组的区域是免费的选择在一个巨大的基因组蚱蜢。使用这种方法的所有其他动物研究发现，具有相似生化特性的DNA碱基之间存在过量的突变（转换而不是颠换）。这种偏差被广泛解释为突变的基本生化基础的结果。然而，一旦我们排除了与DNA甲基化相关的突变，我们就没有发现转换偏倚的证据，不像少数可比较的动物研究做出了同样的修正。我们认为，这一结果表明，以前没有预料到的物种之间的差异，在选择或突变的DNA。
Comparisons of the DNA sequences of metazoa show an excess of transitional over transversional substitutions. Part of this bias is due to the relatively high rate of mutation of methylated cytosines to thymine. Postmutation processes also introduce a bias, particularly selection for codon-usage bias in coding regions. It is generally assumed, however, that there is a universal bias in favour of transitions over transversions, possibly as a result of the underlying chemistry of mutation. Surprisingly, this underlying trend has been evaluated only in two types of metazoan, namely Drosophila and the Mammalia. Here, we investigate a third group, and find no such bias. We characterize the point substitution spectrum in Podisma pedestris, a grasshopper species with a very large genome. The accumulation of mutations was surveyed in two pseudogene families, nuclear mitochondrial and ribosomal DNA sequences. The cytosine-guanine (CpG) dinucleotides exhibit the high transition frequencies expected of methylated sites. The transition rate at other cytosine residues is significantly lower. After accounting for this methylation effect, there is no significant difference between transition and transversion rates. These results contrast with reports from other taxa and lead us to reject the hypothesis of a universal transition/transversion bias. Instead we suggest fundamental interspecific differences in point substitution processes. Some mutations occur more frequently than others. We need to understand these biases if we are to interpret the differences that have accumulated between species and individuals. Applications include estimating the time since evolutionary lineages diverged and detecting the signature of natural selection in DNA sequences. However, mutational biases have been obscured because, since mutations arose, natural selection has eliminated some whilst allowing others to persist to the present. We therefore study mutations that have accumulated in regions of the genome that are free from selection in a grasshopper with a gigantic genome. All other animal studies using this approach find an excess of mutations between DNA bases having similar biochemical properties (transitions rather than transversions). This bias has been widely interpreted as a consequence of the fundamental biochemical basis of mutation. However, once we exclude mutations associated with DNA methylation, we find no evidence of a transition bias, unlike the few comparable animal studies that make the same correction. We propose that this result indicates previously unanticipated differences between species in the selection on or mutation of their DNA.
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