Codon Usage Methods for Horizontal Gene Transfer Detection Generate an Abundance of False Positive and False Negative Results
Codon Usage Methods for Horizontal Gene Transfer Detection Generate an Abundance of False Positive and False Negative Results
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DOI：
10.1007/s00284-012-0205-5
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发表时间：
2012-11-01
影响因子：
2.6
通讯作者：
Ely, Bert
中科院分区：
文献类型：
--
作者：
Friedman, Robert;Ely, Bert
细菌在一个被称为水平基因转移（HGT）的过程中获得新的DNA。为了研究这种DNA转移的进化影响，已经开发了各种方法来检测过去的HGT事件。例如，基于密码子使用的方法通过鉴定密码子使用的非典型模式来检测转移基因的存在。然而，一些遗传基因表现出非典型的密码子使用，一些转移基因具有与遗传基因相似的密码子使用模式。在这项研究中，我们使用甲基杆菌属和柄杆菌属物种的比较系统发育方法来证明即使是精心设计的密码子使用方法也不能检测许多HGT事件，并产生高比例的假阳性（60- 75%）和假阴性（23- 61%）。因此，我们建议谨慎使用密码子使用方法来识别转移的基因，并建议迅速增加的细菌基因组序列的可用性，使系统发育的方法的选择。
Bacteria acquire new DNA in a process known as horizontal gene transfer (HGT). To investigate the evolutionary impact of this transfer of DNA, various methods have been developed to detect past HGT events. For example, codon usage-based methods detect the presence of transferred genes by identifying atypical patterns of codon usage. However, some inherited genes exhibit atypical codon usage and some transferred genes have codon usage patterns similar to those of the inherited genes. In this study, we used a comparative phylogenetic approach with Methylobacterium and Caulobacter species to demonstrate that even well-designed codon usage methods fail to detect many HGT events and generate a high rate of false positives (60-75 %) and false negatives (23-61 %). Therefore, we recommend caution when employing codon usage methods to identify transferred genes and suggest that the rapidly increasing availability of bacterial genome sequences makes the phylogenetic approach the method of choice.