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首页> 外文期刊>BMC Genomics >Are algal genes in nonphotosynthetic protists evidence of historical plastid endosymbioses?
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Are algal genes in nonphotosynthetic protists evidence of historical plastid endosymbioses?

机译：非光合生物原生生物中的藻类基因是否证明了历史质体内共生酶？

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Background How photosynthetic organelles, or plastids, were acquired by diverse eukaryotes is among the most hotly debated topics in broad scale eukaryotic evolution. The history of plastid endosymbioses commonly is interpreted under the "chromalveolate" hypothesis, which requires numerous plastid losses from certain heterotrophic groups that now are entirely aplastidic. In this context, discoveries of putatively algal genes in plastid-lacking protists have been cited as evidence of gene transfer from a photosynthetic endosymbiont that subsequently was lost completely. Here we examine this evidence, as it pertains to the chromalveolate hypothesis, through genome-level statistical analyses of similarity scores from queries with two diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana, and two aplastidic sister taxa, Phytophthora ramorum and P. sojae. Results Contingency tests of specific predictions of the chromalveolate model find no evidence for an unusual red algal contribution to Phytophthora genomes, nor that putative cyanobacterial sequences that are present entered these genomes through a red algal endosymbiosis. Examination of genes unrelated to plastid function provide extraordinarily significant support for both of these predictions in diatoms, the control group where a red endosymbiosis is known to have occurred, but none of that support is present in genes specifically conserved between diatoms and oomycetes. In addition, we uncovered a strong association between overall sequence similarities among taxa and relative sizes of genomic data sets in numbers of genes. Conclusion Signal from "algal" genes in oomycete genomes is inconsistent with the chromalveolate hypothesis, and better explained by alternative models of sequence and genome evolution. Combined with the numerous sources of intragenomic phylogenetic conflict characterized previously, our results underscore the potential to be mislead by a posteriori interpretations of variable phylogenetic signals contained in complex genome-level data. They argue strongly for explicit testing of the different a priori assumptions inherent in competing evolutionary hypotheses.
机译：背景技术各种真核生物如何获得光合细胞器或质体，是大规模真核生物进化中最受争议的话题之一。质体内共生酶的历史通常在“色藻酸”假说下进行解释，该假说要求某些异养组的许多质体损失，而这些营养组现在已经完全是质体的。在这种情况下，在缺乏质体的原生生物中推定的藻类基因的发现被引用为从光合内共生体转移基因的证据，随后该基因被完全丧失。在这里，我们通过对来自两个硅藻，角藻属Phaeodactylum tricornutum和Thalassiosira pseudonana以及两个具塑性的姊妹类群Phytophthora ramorum和P. sojae的查询的相似性分数进行基因组级统计分析，研究了与色氨酸假说有关的证据。结果对草藻酸酯模型的特定预测进行的应变测试没有证据表明红色藻类对疫霉菌基因组有异常贡献，也没有证据表明存在的推定的蓝细菌序列通过红色藻类内共生进入这些基因组。与质体功能无关的基因的检查为在硅藻中的这两个预测提供了极其重要的支持，硅藻是已知发生红色内共生的对照组，但在硅藻和卵母细胞之间特别保守的基因中没有任何支持。此外，我们发现分类单元之间的总体序列相似性与基因组数据集的相对大小（在基因数量上）之间有很强的联系。结论卵母细胞基因组中“藻类”基因的信号与色氨酸假说不一致，并且可以通过序列和基因组进化的替代模型更好地解释。结合以前表征的众多基因组内系统发生冲突的来源，我们的结果强调了可能被复杂基因组水平数据中所包含的可变系统发生信号的后验解释所误导。他们强烈主张对竞争性进化假设中固有的不同先验假设进行显式检验。

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