Codon bias and base composition are poor indicators of horizontally transferred genes
Codon bias and base composition are poor indicators of horizontally transferred genes
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DOI：
10.1093/oxfordjournals.molbev.a003816
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发表时间：
2001-03-01
影响因子：
10.7
通讯作者：
Golding, GB
中科院分区：
文献类型：
--
作者：
Koski, LB;Morton, RA;Golding, GB
水平基因转移现在被认为是进化的一个重要机制。已经提出了几种检测水平转移基因的方法。这些方法是基于核苷酸组成或未能在密切相关的物种中找到相似的基因。在密切相关的物种之间垂直进化的基因可以分为保留同源染色体位置的基因（位置直系同源物）和不保留同源染色体位置的基因。通过比较大肠杆菌和伤寒沙门氏菌基因组中的开放阅读框，我们鉴定了2,728个位置直向同源物，因为这些物种分裂了1亿年。1，144例E. coli基因与S.伤寒对应物。这些新基因包括那些已经水平转移到E.大肠杆菌，以及已被重排或删除的基因对的成员。位置直向同源物被用来研究鉴定水平转移基因的组成方法。大量核苷酸组成正常的大肠杆菌基因在沙门氏菌中没有明显的同源物。事实上，伤寒和许多非典型组成的基因确实具有位置直系同源物。系统发育的方法，以确认选定的例子之间的新的基因组的水平传输。我们对80 E.大肠杆菌基因确定了许多先前基于碱基组成和密码子偏好被分类为水平转移的基因是天然的，并且先前被分类为天然的基因似乎是水平转移的。因此，非典型核苷酸组成本身并不是水平传播的可靠指标。
Horizontal gene transfer is now recognized as an important mechanism of evolution. Several methods to detect horizontally transferred genes have been suggested. These methods are based on either nucleotide composition or the failure to find a similar gene in closely related species, Genes that evolve vertically between closely related species can be divided into those that retain homologous chromosomal positions (positional orthologs) and those that do not. By comparing open reading frames in the Escherichia coli and Salmonella typhi genomes, we identified 2,728 positional orthologs since these species split 100 MYA. A group of 1,144 novel E. coli genes were unusually diverged from their S. typhi counterparts. These novel genes included those that had been horizontally transferred into E. coli, as well as members of gene pairs that had been rearranged or deleted. Positional orthologs were used to investigate compositional methods of identifying horizontally transferred genes. A large number of E, coli genes with normal nucleotide composition have no apparent ortholog in S. typhi, and many genes of atypical composition do, in fact, have positional orthologs. A phylogenetic approach was employed to confirm selected examples of horizontal transmission among the novel groups of genes. Our analysis of 80 E. coli genes determined that a number of genes previously classified as horizontally transferred based on base composition and codon bias were native, and genes previously classified as native appeared to be horizontally transferred. Hence, atypical nucleotide composition alone is not a reliable indicator of horizontal transmission.