Singh Nadia D, Petrov Dmitri A
Department of Biological Sciences, Stanford University, Stanford, California, USA.
Mol Biol Evol. 2004 Apr;21(4):670-80. doi: 10.1093/molbev/msh060. Epub 2004 Jan 22.
Closely related species of Drosophila tend to have similar genome sizes. The strong imbalance in favor of small deletions relative to insertions implies that the unconstrained DNA in Drosophila is unlikely to be passively inherited from even closely related ancestors, and yet most DNA in Drosophila genomes is intergenic and potentially unconstrained. In an attempt to investigate the maintenance of this intergenic DNA, we studied the evolution of an intergenic locus on the fourth chromosome of the Drosophila melanogaster genome. This 1.2-kb locus is marked by two distinct, large insertion events: a nuclear transposition of a mitochondrial sequence and a transposition of a nonautonomous DNA transposon DNAREP1_DM. Because we could trace the evolutionary histories of these sequences, we were able to reconstruct the length evolution of this region in some detail. We sequenced this locus in all four species of the D. melanogaster species complex: D. melanogaster, D. simulans, D. sechellia, and D. mauritiana. Although this locus is similar in size in these four species, less than 10% of the sequence from the most recent common ancestor remains in D. melanogaster and all of its sister species. This region appears to have increased in size through several distinct insertions in the ancestor of the D. melanogaster species complex and has been shrinking since the split of these lineages. In addition, we found no evidence suggesting that the size of this locus has been maintained over evolutionary time; these results are consistent with the model of a dynamic equilibrium between persistent DNA loss through small deletions and more sporadic DNA gain through less frequent but longer insertions. The apparent stability of genome size in Drosophila may belie very rapid sequence turnover at intergenic loci.
果蝇的近缘物种往往具有相似的基因组大小。相对于插入而言，小缺失的强烈失衡表明，果蝇中不受约束的DNA不太可能从亲缘关系很近的祖先那里被动遗传下来，然而果蝇基因组中的大多数DNA是基因间的，并且可能不受约束。为了研究这种基因间DNA的维持情况，我们研究了果蝇黑腹果蝇基因组第四条染色体上一个基因间位点的进化。这个1.2千碱基的位点有两个不同的大插入事件作为标记：一个线粒体序列的核转座和一个非自主DNA转座子DNAREP1_DM的转座。因为我们能够追踪这些序列的进化历史，所以我们能够相当详细地重建该区域的长度进化。我们对果蝇黑腹果蝇物种复合体的所有四个物种：黑腹果蝇（D. melanogaster）、拟果蝇（D. simulans）、塞舌尔果蝇（D. sechellia）和毛里求斯果蝇（D. mauritiana）的这个位点进行了测序。尽管这个位点在这四个物种中的大小相似，但来自最近共同祖先的序列在黑腹果蝇及其所有姐妹物种中保留的不到10%。这个区域似乎通过果蝇黑腹果蝇物种复合体祖先中的几个不同插入而增大了大小，并且自这些谱系分化以来一直在缩小。此外，我们没有发现证据表明这个位点的大小在进化时间上保持不变；这些结果与通过小缺失导致的持续DNA丢失和通过不太频繁但更长的插入导致的更零星的DNA增加之间的动态平衡模型一致。果蝇基因组大小的明显稳定性可能掩盖了基因间位点非常快速的序列更替。
