Detection of gene duplications and block duplications in eukaryotic genomes.
Detection of gene duplications and block duplications in eukaryotic genomes.
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DOI：
10.1023/a:1022644628861
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发表时间：
2003-01-01
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影响因子：
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通讯作者：
Nekrutenko, Anton
中科院分区：
文献类型：
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作者：
Li, Wen-Hsiung;Gu, Zhenglong;Nekrutenko, Anton
几个真核基因组已经完全测序，这提供了一个机会，研究的程度和特点（例如，单基因重复、块重复等）基因组中的基因复制。然而，检测基因组中的重复基因并不是一个简单的问题，因为有几个复杂的问题，如结构域改组，存在来自选择性剪接的异构体，以及数据库中的注释错误。我们描述了一种克服这些困难的方法和果蝇，秀丽隐杆线虫，酵母菌的基因组中的基因重复的程度推断，从这种方法。我们还描述了用于检测基因组中的块重复的方法。该方法的应用表明，嵌段复制是酵母和线虫中的普遍现象。然而，这两个物种中的块重复模式明显不同。酵母显示出比线虫更广泛的嵌段复制，其中一些染色体具有超过40%的来自嵌段复制的复制。此外，在酵母中，大多数的块复制发生在染色体之间，而在线虫中，大多数块复制发生在染色体内。
Several eukaryotic genomes have been completely sequenced and this provides an opportunity to investigate the extent and characteristics (e.g., single gene duplication, block duplication, etc.) of gene duplication in a genome. Detecting duplicate genes in a genome, however, is not a simple problem because of several complications such as domain shuffling, the existence of isoforms derived from alternative splicing, and annotational errors in the databases. We describe a method for overcoming these difficulties and the extents of gene duplication in the genomes of Drosophila melanogaster, Caenorhabditis elegans, and yeast inferred from this method. We also describe a method for detecting block duplications in a genome. Application of this method showed that block duplication is a common phenomenon in both yeast and nematode. The patterns of block duplication in the two species are, however, markedly different. Yeast shows much more extensive block duplication than nematode, with some chromosomes having more than 40% of the duplications derived from block duplications. Moreover, in yeast the majority of block duplications occurred between chromosomes, while in nematode most block duplications occurred within chromosomes.