Rogers Matthew B, Watkins Russell F, Harper James T, Durnford Dion G, Gray Michael W, Keeling Patrick J
Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.
BMC Evol Biol. 2007 Jun 11;7:89. doi: 10.1186/1471-2148-7-89.
Lateral gene transfer is increasingly invoked to explain phylogenetic results that conflict with our understanding of organismal relationships. In eukaryotes, the most common observation interpreted in this way is the appearance of a bacterial gene (one that is not clearly derived from the mitochondrion or plastid) in a eukaryotic nuclear genome. Ideally such an observation would involve a single eukaryote or a small group of related eukaryotes encoding a gene from a specific bacterial lineage.
Here we show that several apparently simple cases of lateral transfer are actually more complex than they originally appeared: in these instances we find that two or more distantly related eukaryotic groups share the same bacterial gene, resulting in a punctate distribution. Specifically, we describe phylogenies of three core carbon metabolic enzymes: transketolase, glyceraldehyde-3-phosphate dehydrogenase and ribulose-5-phosphate-3-epimerase. Phylogenetic trees of each of these enzymes includes a strongly-supported clade consisting of several eukaryotes that are distantly related at the organismal level, but whose enzymes are apparently all derived from the same lateral transfer. With less sampling any one of these examples would appear to be a simple case of bacterium-to-eukaryote lateral transfer; taken together, their evolutionary histories cannot be so simple. The distributions of these genes may represent ancient paralogy events or genes that have been transferred from bacteria to an ancient ancestor of the eukaryotes that retain them. They may alternatively have been transferred laterally from a bacterium to a single eukaryotic lineage and subsequently transferred between distantly related eukaryotes.
Determining how complex the distribution of a transferred gene is depends on the sampling available. These results show that seemingly simple cases may be revealed to be more complex with greater sampling, suggesting many bacterial genes found in eukaryotic genomes may have a punctate distribution.
横向基因转移越来越多地被用来解释与我们对生物关系理解相冲突的系统发育结果。在真核生物中，以这种方式解释的最常见观察结果是真核细胞核基因组中出现细菌基因（一个并非明显源自线粒体或质体的基因）。理想情况下，这样的观察结果将涉及单个真核生物或一小群相关真核生物编码来自特定细菌谱系的基因。
在这里我们表明，几个看似简单的横向转移案例实际上比它们最初看起来更复杂：在这些案例中，我们发现两个或更多远缘相关的真核生物群体共享相同的细菌基因，从而导致点状分布。具体来说，我们描述了三种核心碳代谢酶的系统发育：转酮醇酶、甘油醛-3-磷酸脱氢酶和核糖-5-磷酸-3-表异构酶。这些酶各自的系统发育树都包括一个得到有力支持的分支，该分支由几个在生物水平上远缘相关的真核生物组成，但它们的酶显然都源自相同的横向转移。如果采样较少，这些例子中的任何一个看起来都像是细菌到真核生物横向转移的简单案例；综合起来，它们的进化历史不可能如此简单。这些基因的分布可能代表古老的旁系同源事件，或者是从细菌转移到保留它们的真核生物古老祖先的基因。它们也可能是从细菌横向转移到单个真核生物谱系，随后在远缘相关的真核生物之间转移。
确定一个转移基因的分布有多复杂取决于可用的采样。这些结果表明，随着采样增加，看似简单的案例可能会被揭示得更加复杂，这表明在真核生物基因组中发现的许多细菌基因可能具有点状分布。
