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Abstract：
Lateral gene transfer (LGT) has impacted the evolutionary history of eukaryotes, though to a lesser extent than in bacteria and archaea. Detecting LGT and distinguishing it from single gene tree artifacts is difficult, particularly when considering very ancient events (i.e., over hundreds of millions of years). Here, we use two independent lines of evidence--a taxon-rich phylogenetic approach and an assessment of the patterns of gene presence/absence--to evaluate the extent of LGT in the parasitic amoebozoan genus Entamoeba. Previous work has suggested that a number of genes in the genome of Entamoeba spp. were acquired by LGT. Our approach, using an automated phylogenomic pipeline to build taxon-rich gene trees, suggests that LGT is more extensive than previously thought. Our analyses reveal that genes have frequently entered the Entamoeba genome via nonvertical events, including at least 116 genes acquired directly from bacteria or archaea, plus an additional 22 genes in which Entamoeba plus one other eukaryote are nested among bacteria and/or archaea. These genes may make good candidates for novel therapeutics, as drugs targeting these genes are less likely to impact the human host. Although we recognize the challenges of inferring intradomain transfers given systematic errors in gene trees, we find 109 genes supporting LGT from a eukaryote to Entamoeba spp., and 178 genes unique to Entamoeba spp. and one other eukaryotic taxon (i.e., presence/absence data). Inspection of these intradomain LGTs provide evidence of a common sister relationship between genes of Entamoeba (Amoebozoa) and parabasalids (Excavata). We speculate that this indicates a past close relationship (e.g., symbiosis) between ancestors of these extant lineages.
摘要：
横向基因转移(LGT)影响了真核生物的进化史,尽管程度低于细菌和古细菌。检测LGT并将其与单基因树工件区分开来是困难的，特别是在考虑非常古老的事件时(即，超过数亿年)。这里,我们使用两个独立的证据-富含分类单元的系统发育方法和对基因存在/不存在模式的评估-来评估LGT在寄生变形虫属Entamoeba中的程度。先前的工作表明，Entamoebaspp基因组中的许多基因。被LGT收购。我们的方法,使用自动化的系统基因组管道来构建富含分类单元的基因树，表明LGT比以前认为的更广泛。我们的分析表明，基因经常通过非垂直事件进入Entamoeba基因组，包括直接从细菌或古细菌获得的至少116个基因，再加上另外22个基因，其中Entamoeba和一个其他真核生物嵌套在细菌和/或古细菌之间。这些基因可能是新疗法的好候选者，因为针对这些基因的药物不太可能影响人类宿主。尽管我们认识到由于基因树中的系统错误而推断体内转移的挑战，我们发现109个基因支持LGT从真核生物到Entamoebaspp。,和178个Entamoebaspp特有的基因。和另一个真核生物分类单元(即，存在/缺失数据)。对这些体内LGT的检查提供了Entamoeba（Amoebozoa）和副abasalids（Excavata）基因之间共同姐妹关系的证据。我们推测这表明过去的亲密关系(例如，共生）这些现存谱系的祖先之间。
