GENOME EVOLUTION AND THE INSERTION/DELETION SPECTRUM

观察到的缺失谱（缺失率和大小分布） 在LINE元素的“到达时死亡”副本中，Helena显示了一个整体 果蝇的DNA丢失率大约是 比在哺乳动物中发现的要多。 这些数据可能具有重要意义 对于突变压力，DNA序列的进化持久性 其存在不受选择的限制，并且可能 基因组大小的差异。 然而，存在一些问题， 将海伦娜的数据外推到整个基因组 一种可能性是 Helena元素容易被删除，因此 代表其他果蝇序列，甚至其他LINE 元素 另一种可能是海伦娜的缺失谱 是有偏见的，因为许多拷贝存在于异染色质中， 插入/缺失（indel）谱在异染色质之间可能不同 和常染色质。 第三种可能性是海伦娜和其他人 转座因子具有升高的缺失谱， 事实上，它们是中间重复的DNA， 序列如假基因将具有不同的插入缺失谱。 解决这些问题的唯一方法是获得更多的数据， 果蝇基因组中其他类型的序列。 因此我们建议 以确定物种中LINE元素jockey的indel谱 的D.黑腹亚群 这些实验将在 以这种方式，常染色质中存在的元件可以被区分 与异染色质中的不同 这种方法提供了一种独特的 有机会解决插入缺失光谱是否不同的问题 在异染色质和常染色质之间;它也允许一个关键的测试 查尔斯沃思的“异色墓地”假说， 认为转座因子受到较弱的选择， 异染色质比常染色质，因此持续时间更长， 异染色质 (If真的，异染色质中的LINE元件应该是， 平均而言，年龄较大，因此具有更多的核苷酸替换。 我们还将研究插入缺失的光谱，相对于核苷酸 在D. melanogaster 和其它种类的分布。黑腹亚群，即swapsi（a 燕子假基因）和Lcppsi（幼虫citicle蛋白假基因）。 对目前可获得的关于这些假基因的有限数据的分析 产生不确定的、可能不一致的结果。

The deletion spectrum (rate and size distribution of deletions) observed in "dead-on-arrival" copies of the LINE element Helena shows an overall rate of DNA loss in Drosophila that is approximately 75 times greater than that found in mammals. These data may have important implications for mutation pressure, the evolutionary persistence of DNA sequences whose presence is not constrained by selection, and possibly for differences in genome size. However, there are a number of problems in extrapolating the Helena data to the entire genome. One possibility is that the Helena element is prone to deletions, and so is not representative of other Drosophila sequences, or even of other LINE elements. Another possibility is that the deletion spectrum of Helena is biased because many copies are present in heterochromatin, and the insertion/deletion (indel) spectrum may differ between heterochromatin and euchromatin. A third possibility is that Helena and other transposable elements have an elevated deletion spectrum owing to the fact that they are middle repetitive DNA, and that single-copy sequences, such as pseudogenes, would have a different indel spectrum. The only way to resolve these issues is by obtaining additional data on other types of sequences in the Drosophila genome. We therefore propose to determine the indel spectrum in the LINE element jockey in species of the D. melanogaster subgroup. These experiments will be carried out in such a way that elements present in euchromatin can be distinguished from those present in heterochromatin. This approach provides a unique opportunity to address the issue of whether the indel spectrum differs between heterochromatin and euchromatin; it also allows a critical test of the "heterochromatic graveyard" hypothesis of Charlesworth, which states that transposable elements are subject to weaker selection in heterochromatin than in euchromatin, and therefore persist longer in heterochromatin. (If true, LINE elements in heterochromatin should be, on the average, older and therefore have more nucleotide substitutions.) We will also study the spectrum of indels, relative to nucleotide substitutions, in two bona fide pseudogenes present in D. melanogaster and other species in the D. melanogaster subgroup, namely, swapsi (a swallow pseudogene) and Lcppsi (a larval citticle protein pseudogene). Analysis of the limited data presently available for these pseudogenes yields inconclusive, and possibly inconsistent, results.