Koski L B, Morton R A, Golding G B
Department of Biology, McMaster University, Hamilton, Ontario, Canada.
Mol Biol Evol. 2001 Mar;18(3):404-12. doi: 10.1093/oxfordjournals.molbev.a003816.
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.
水平基因转移现在被认为是一种重要的进化机制。已经提出了几种检测水平转移基因的方法。这些方法要么基于核苷酸组成，要么基于在密切相关物种中未能找到相似基因。在密切相关物种之间垂直进化的基因可分为保留同源染色体位置的基因（位置直系同源基因）和不保留的基因。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，我们确定了自这两个物种在1亿年前分化以来的2728个位置直系同源基因。一组1144个新的大肠杆菌基因与其伤寒沙门氏菌对应基因异常分化。这些新基因包括那些水平转移到大肠杆菌中的基因，以及那些重排或缺失的基因对成员。位置直系同源基因被用于研究识别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伤寒沙门氏菌中没有明显的直系同源基因，而许多组成非典型的基因实际上有位置直系同源基因。采用系统发育方法来确认新基因群体中水平转移的选定例子。我们对80个大肠杆菌基因的分析确定，一些以前基于碱基组成和密码子偏好被归类为水平转移的基因是天然的，而以前被归类为天然的基因似乎是水平转移的。因此，仅非典型核苷酸组成并不是水平转移的可靠指标。
