从侧面思考基因组。

Mark A Ragan
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引用次数: 0

摘要

也许基因组时代最令人惊讶的发现是原核生物和许多真核生物基因组在很大程度上包含了来自其亲本以外来源的遗传物质。细菌之间的横向遗传转移(LGT)在大约100年前首次被观察到,现在被认为是重要现象的基础,包括抗生素耐药性的传播和降解外源药物的能力。LGT被用来解释一系列令人尴尬的数据,包括基因组的组成异质性,基因序列树之间的分歧,以及生理学和系统学之间的不匹配,这可能太容易了。与此同时,LGT的许多细节仍然未知或有争议,一些关键问题几乎没有被问到。在这里,我批判性地回顾了我们认为我们对LGT的存在、程度、机制和影响的了解;确定重要的开放性问题;并指出了对阐明LGT在基因组进化中的作用特别有希望的研究方向。自然界中存在LGT的证据不仅是推断性的,而且是直接的,潜在的载体无处不在。遗传物质可以在不同的栖息地之间传递,并在病毒体内驻留期间发生显著改变,使供体的推断变得复杂。在原核生物中,被LGT打断的基因大约是完整转移的基因的两倍,大约5个短蛋白结构域可以作为转移的特权单位。未解决的系统发育问题包括正确的零假设,以及作为分析单位的基因。关于LGT对蜂窝网络的影响的主题开始出现,但我说明了为什么泛化还为时过早。LGT与生理和生态位的根本变化有关。目前还需要更好的基因组进化定量模型,而对于包括LGT染色体组装在内的一些观察,还需要建立理论框架。
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Thinking laterally about genomes.

Perhaps the most-surprising discovery of the genome era has been the extent to which prokaryotic and many eukaryotic genomes incorporate genetic material from sources other than their parent(s). Lateral genetic transfer (LGT) among bacteria was first observed about 100 years ago, and is now accepted to underlie important phenomena including the spread of antibiotic resistance and ability to degrade xenobiotics. LGT is invoked, perhaps too readily, to explain a breadth of awkward data including compositional heterogeneity of genomes, disagreement among gene-sequence trees, and mismatch between physiology and systematics. At the same time many details of LGT remain unknown or controversial, and some key questions have scarcely been asked. Here I critically review what we think we know about the existence, extent, mechanism and impact of LGT; identify important open questions; and point to research directions that hold particular promise for elucidating the role of LGT in genome evolution. Evidence for LGT in nature is not only inferential but also direct, and potential vectors are ubiquitous. Genetic material can pass between diverse habitats and be significantly altered during residency in viruses, complicating the inference of donors, In prokaryotes about twice as many genes are interrupted by LGT as are transferred intact, and about 5Short protein domains can be privileged units of transfer. Unresolved phylogenetic issues include the correct null hypothesis, and genes as units of analysis. Themes are beginning to emerge regarding the effect of LGT on cellular networks, but I show why generalization is premature. LGT can associate with radical changes in physiology and ecological niche. Better quantitative models of genome evolution are needed, and theoretical frameworks remain to be developed for some observations including chromosome assembly by LGT.

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