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Anomalous Phylogenetic Behavior of Ribosomal Proteins in Metagenome-Assembled Asgard Archaea
Genome Biology and Evolution ( IF 3.3 ) Pub Date : 2020-11-18 , DOI: 10.1093/gbe/evaa238
Sriram G Garg 1 , Nils Kapust 1 , Weili Lin 2 , Michael Knopp 1 , Fernando D K Tria 1 , Shijulal Nelson-Sathi 3 , Sven B Gould 1 , Lu Fan 4, 5, 6 , Ruixin Zhu 2 , Chuanlun Zhang 4, 5, 7 , William F Martin 1
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Metagenomic studies permit the exploration of microbial diversity in a defined habitat, and binning procedures enable phylogenomic analyses, taxon description, and even phenotypic characterizations in the absence of morphological evidence. Such lineages include asgard archaea, which were initially reported to represent archaea with eukaryotic cell complexity, although the first images of such an archaeon show simple cells with prokaryotic characteristics. However, these metagenome-assembled genomes (MAGs) might suffer from data quality problems not encountered in sequences from cultured organisms due to two common analytical procedures of bioinformatics: assembly of metagenomic sequences and binning of assembled sequences on the basis of innate sequence properties and abundance across samples. Consequently, genomic sequences of distantly related taxa, or domains, can in principle be assigned to the same MAG and result in chimeric sequences. The impacts of low-quality or chimeric MAGs on phylogenomic and metabolic prediction remain unknown. Debates that asgard archaeal data are contaminated with eukaryotic sequences are overshadowed by the lack of evidence indicating that individual asgard MAGs stem from the same chromosome. Here, we show that universal proteins including ribosomal proteins of asgard archaeal MAGs fail to meet the basic phylogenetic criterion fulfilled by genome sequences of cultured archaea investigated to date: These proteins do not share common evolutionary histories to the same extent as pure culture genomes do, pointing to a chimeric nature of asgard archaeal MAGs. Our analysis suggests that some asgard archaeal MAGs represent unnatural constructs, genome-like patchworks of genes resulting from assembly and/or the binning process.

中文翻译:

宏基因组组装的 Asgard 古细菌中核糖体蛋白的异常系统发育行为

宏基因组研究允许探索特定栖息地中的微生物多样性,分箱程序可以在缺乏形态学证据的情况下进行系统发育分析、分类描述,甚至表型表征。此类谱系包括 asgard 古细菌,最初报道称其代表具有真核细胞复杂性的古细菌,尽管此类古细菌的第一张图像显示具有原核特征的简单细胞。然而,由于两种常见的生物信息学分析程序:宏基因组序列的组装和基于先天序列特性和丰度的组装序列的分箱跨样本。最后,远相关分类群或结构域的基因组序列原则上可以分配给相同的 MAG 并产生嵌合序列。低质量或嵌合 MAG 对系统发育和代谢预测的影响仍然未知。由于缺乏证据表明单个 asgard MAG 来自同一染色体,因此关于 asgard 古细菌数据被真核序列污染的争论被掩盖了。在这里,我们表明,包括 asgard 古菌 MAG 核糖体蛋白在内的通用蛋白质无法满足迄今为止研究的培养古细菌基因组序列所满足的基本系统发育标准:这些蛋白质与纯培养基因组的共同进化历史不同,指向 asgard 古菌 MAG 的嵌合性质。
更新日期:2020-11-18
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