Estimation of the number of authentic orphan genes in bacterial genomes
Estimation of the number of authentic orphan genes in bacterial genomes
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DOI：
10.1093/dnares/11.4.311
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发表时间：
2004-08-31
期刊：
影响因子：
4.1
通讯作者：
Nishikawa, K
中科院分区：
文献类型：
--
作者：
Fukuchi, S;Nishikawa, K
基因组注释产生了相当数量的推定蛋白质缺乏序列相似性的已知蛋白质。他们被称为“孤儿”。孤儿基因的比例在基因组之间变化，并且与基因组大小无关。在本研究中，我们发现，孤儿基因的比例大致与生物体的隔离指数（IIO），在本研究中引入的一个指标，它代表了一个给定的基因组的隔离程度，通过序列相似性来衡量。然而，存在关于线性相关性的离群基因组，其由可能含有过量孤儿基因的那些基因组组成。在密切相关的菌株之间的基因组序列的比较显示，一些注释的基因是不保守的，这表明它们是偶然发生的ORF。在密切相关的基因组中排除这些非保守的ORF改善了孤儿基因的比例与IIO值之间的相关性。假设这种相关性在一般情况下成立，这种关系被用来估计基因组中“真实”孤儿基因的数量。使用这种真实孤儿基因的定义，由过度分配引起的异常，例如，对16个基因组，包括5个古生菌的基因组，校正了结构注释的百分比。
Genome annotation produces a considerable number of putative proteins lacking sequence similarity to known proteins. These are referred to as “orphans.” The proportion of orphan genes varies among genomes, and is independent of genome size. In the present study, we show that the proportion of orphan genes roughly correlates with the isolation index of organisms (IIO), an indicator introduced in the present study, which represents the degree of isolation of a given genome as measured by sequence similarity. However, there are outlier genomes with respect to the linear correlation, consisting of those genomes that may contain excess amounts of orphan genes. Comparisons of genome sequences among closely related strains revealed that some of the annotated genes are not conserved, suggesting that they are ORFs occurring by chance. Exclusion of these non-conserved ORFs within closely related genomes improved the correlation between the proportion of orphan genes and the IIO values. Assuming that the correlation holds in general, this relationship was used to estimate the number of “authentic” orphan genes in a genome. Using this definition of authentic orphan genes, the anomalies arising from over-assignments, e.g., the percentages of structural annotations, were corrected for 16 genomes, including those of five archaea.