Gain and loss of elongation factor genes in green algae.
Gain and loss of elongation factor genes in green algae.
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DOI：
10.1186/1471-2148-9-39
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发表时间：
2009-02-12
影响因子：
3.4
通讯作者：
De Clerck O
中科院分区：
文献类型：
--
作者：
Cocquyt E;Verbruggen H;Leliaert F;Zechman FW;Sabbe K;De Clerck O
翻译装置的两个关键基因，伸长因子-1α(EF-1α)和伸长因子样蛋白(EFL)在真核生物中几乎相互排斥地分布。在绿色植物谱系中，绿藻门除了有Ef-1的α外，其余都编码EFL；链藻门除了有EFL的中胚层外，还含有Ef-1的α。这些结果对EF-1、α和EFL的得失的进化模式提出了疑问。以前的一项研究提出假设，认为EF-1α是原始状态，并且在绿色植物的祖先中获得了一次EFL，随后在病毒科的主要分支中获得了EF-1α或EFL的差异丢失。为了更深入地了解EF-1、α和EFL在绿藻中的分布并验证这一假说，我们筛选了大量绿藻样本中这些基因的存在，并使用连续时间马尔可夫模型在最大似然框架下分析了它们的得失动态。在绿藻门中，EF-1α存在于三个蓝藻目中(即：绿藻目、苔藓目、管藻目)和Ignatius属。描述基因得失动态的模型表明，由于对分支长度的敏感性以及缺乏关于祖先状态或基因得失速率的先验知识，在绿色植物系统发育的主干上是否存在EF-1α和/或Ef1基因是高度不确定的。基于从EF-1α系统发展史获得的见解进行的模型改进减少了不确定性，但仍然暗示了几种同样可能的可能性：原始的EF-1α状态具有多个独立的EFL增益，或者在病原植物或绿藻的祖先中两个基因共存，随后在不同谱系中的一个或另一个基因发生差异丢失。EF-1α在绿藻中比之前认为的更常见。在大量绿色植物样本中证实了EF-1、α和EFL的互斥分布。即使结合了先验知识，由于可能性表面相对平坦，关于伸长因子基因的得失动态的假设也很难进行分析测试。EFL基因的系统发育分析表明，由于根部位置的不确定性，最近的文献中存在误解。
Two key genes of the translational apparatus, elongation factor-1 alpha (EF-1α) and elongation factor-like (EFL) have an almost mutually exclusive distribution in eukaryotes. In the green plant lineage, the Chlorophyta encode EFL except Acetabularia where EF-1α is found, and the Streptophyta possess EF-1α except Mesostigma, which has EFL. These results raise questions about evolutionary patterns of gain and loss of EF-1α and EFL. A previous study launched the hypothesis that EF-1α was the primitive state and that EFL was gained once in the ancestor of the green plants, followed by differential loss of EF-1α or EFL in the principal clades of the Viridiplantae. In order to gain more insight in the distribution of EF-1α and EFL in green plants and test this hypothesis we screened the presence of the genes in a large sample of green algae and analyzed their gain-loss dynamics in a maximum likelihood framework using continuous-time Markov models. Within the Chlorophyta, EF-1α is shown to be present in three ulvophycean orders (i.e., Dasycladales, Bryopsidales, Siphonocladales) and the genus Ignatius. Models describing gene gain-loss dynamics revealed that the presence of EF-1α, EFL or both genes along the backbone of the green plant phylogeny is highly uncertain due to sensitivity to branch lengths and lack of prior knowledge about ancestral states or rates of gene gain and loss. Model refinements based on insights gained from the EF-1α phylogeny reduce uncertainty but still imply several equally likely possibilities: a primitive EF-1α state with multiple independent EFL gains or coexistence of both genes in the ancestor of the Viridiplantae or Chlorophyta followed by differential loss of one or the other gene in the various lineages. EF-1α is much more common among green algae than previously thought. The mutually exclusive distribution of EF-1α and EFL is confirmed in a large sample of green plants. Hypotheses about the gain-loss dynamics of elongation factor genes are hard to test analytically due to a relatively flat likelihood surface, even if prior knowledge is incorporated. Phylogenetic analysis of EFL genes indicates misinterpretations in the recent literature due to uncertainty regarding the root position.
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影响因子：
10.7
作者：
Castresana, J
通讯作者：
Castresana, J
影响因子：
10.7
作者：
Lake, James A.
通讯作者：
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DOI：
10.1073/pnas.94.22.12007
发表时间：
1997-10-28
影响因子：
11.1
作者：
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通讯作者：
Doolittle, WF
影响因子：
3.2
作者：
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Yu, Huilan
DOI：
10.1073/pnas.0711084105
发表时间：
2008-05-13
影响因子：
11.1
作者：
Kamikawa, Ryoma;Inagaki, Yuji;Sako, Yoshihiko
通讯作者：
Sako, Yoshihiko