GENOME EVOLUTION AND THE INSERTION/DELETION SPECTRUM

观察到的缺失谱(缺失率和大小分布 在“到货即死”的线条元素副本中，海伦娜展示了 果蝇的DNA损失率大约是果蝇的75倍 比在哺乳动物身上发现的要多。这些数据可能会有重要的影响 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，并且可能用于 基因组大小的差异。然而，还存在一些问题 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，而不是 其他果蝇序列的代表，甚至其他品系的代表 元素。另一种可能性是海伦娜的缺失谱 是有偏见的，因为异染色质中存在许多拷贝，并且 异染色质之间的插入/缺失(INDEL)谱可能不同 和常染色质。第三种可能性是海伦娜和其他人 转座元件具有更高的缺失光谱，这是由于 事实是它们是中间重复的DNA，而那个单拷贝 序列，如伪基因，将具有不同的Indel谱。 解决这些问题的唯一方法是通过获取更多关于 果蝇基因组中的其他类型的序列。因此，我们建议 在物种中测定直线元素赛马的指纹谱 属于黑腹毛虫亚群。这些实验将会进行 以这种方式可以区分常染色质中存在的元素 与异染色质中存在的那些不同。这种方法提供了一种独特的 有机会解决Indel光谱是否不同的问题 在异染色质和常染色质之间；它还允许进行关键测试 查尔斯沃思的“异色墓地”假说 转座元件在 异染色质比常染色质更稳定，因此在 异染色质。(如果为真，异染色质中的线状元件应为， 平均而言，年龄较大的人有更多的核苷酸替换。) 我们还将研究indels相对于核苷酸的光谱。 在黑腹盘藻中存在的两个真实假基因中的替换 和黑腹小蜂亚群中的其他种，即swapsi(a 吞噬假基因)和Lcppsi(一种幼虫卵泡蛋白假基因)。 对目前可用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.