Fine scale structural variants distinguish the genomes of Drosophila melanogaster and D. pseudoobscura.
Fine scale structural variants distinguish the genomes of Drosophila melanogaster and D. pseudoobscura.
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DOI：
10.1186/gb-2006-7-7-r67
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发表时间：
2006
期刊：
影响因子：
12.3
通讯作者：
Long, Anthony D.
中科院分区：
文献类型：
--
作者：
Macdonald, Stuart J.;Long, Anthony D.
比较基因组学揭示了精细的结构变异，包括微倒位，区分了两个不同的果蝇物种。比较基因组学的主要目标是确定具有功能意义的基因组元件，这些基因组元件有助于表型多样性。基因组结构的复杂变化(插入、复制、重排、易位)可能广泛存在，并对生物多样性产生重要影响。没有对结构变化的评估，任何对基因组变异的调查都是不完整的。我们重新检查了不同物种黑腹果蝇和拟黑腹果蝇的基因组序列，以确定区分基因组的精细结构特征。我们检测到95个大的插入/缺失事件发生在直源基因对的内含子中，其中大部分代表可转座元件的插入。我们还发现了143个大小在5kb以下的微倒位。这些微倒位位于基因内含子或基因的上游或下游，逆转保守的DNA序列。微倒位内的序列保守性表明它们可能富含功能性遗传元件，它们相对于已知基因的位置意味着它们参与了基因表达的调节。尽管我们发现了跨微倒置的GC含量的明显模式，但这与跨保守的非编码序列块观察到的模式没有区别。长期以来，果蝇一直被认为是一种拥有各种大倒位的属，这些倒位扰乱了染色体的共线性。在这里，我们证明了位于/靠近基因的许多长度在1kb以下的微倒位也可能是果蝇遗传变异的重要来源。对其他果蝇基因组序列的进一步研究可能会发现一系列新的微倒置事件。
Comparative genomics reveals fine-scale structural variants, including microinversions, distinguishing two diverged Drosophila species A primary objective of comparative genomics is to identify genomic elements of functional significance that contribute to phenotypic diversity. Complex changes in genome structure (insertions, duplications, rearrangements, translocations) may be widespread, and have important effects on organismal diversity. Any survey of genomic variation is incomplete without an assessment of structural changes. We re-examine the genome sequences of the diverged species Drosophila melanogaster and D. pseudoobscura to identify fine-scale structural features that distinguish the genomes. We detect 95 large insertion/deletion events that occur within the introns of orthologous gene pairs, the majority of which represent insertion of transposable elements. We also identify 143 microinversions below 5 kb in size. These microinversions reside within introns or just upstream or downstream of genes, and invert conserved DNA sequence. The sequence conservation within microinversions suggests they may be enriched for functional genetic elements, and their position with respect to known genes implicates them in the regulation of gene expression. Although we found a distinct pattern of GC content across microinversions, this was indistinguishable from the pattern observed across blocks of conserved non-coding sequence. Drosophila has long been known as a genus harboring a variety of large inversions that disrupt chromosome colinearity. Here we demonstrate that microinversions, many of which are below 1 kb in length, located in/near genes may also be an important source of genetic variation in Drosophila. Further examination of other Drosophila genome sequences will likely identify an array of novel microinversion events.