Extending the Conserved Phylogenetic Core of Archaea Disentangles the Evolution of the Third Domain of Life

Abstract

Initial studies of the archaeal phylogeny relied mainly on the analysis of the RNA component of the small subunit of the ribosome (SSU rRNA). The resulting phylogenies have provided interesting but partial information on the evolutionary history of the third domain of life because SSU rRNA sequences do not contain enough phylogenetic signal to resolve all nodes of the archaeal tree. Thus, many relationships, and especially the most ancient ones, remained elusive. Moreover, SSU rRNA phylogenies can be heavily biased by tree reconstruction artifacts. The sequencing of complete genomes allows using a variety of protein markers as an alternative to SSU rRNA. Taking advantage of the recent burst of archaeal complete genome sequences, we have carried out an in-depth phylogenomic analysis of this domain. We have identified 200 new protein families that, in addition to the ribosomal proteins and the subunits of the RNA polymerase, form a conserved phylogenetic core of archaeal genes. The accurate analysis of these markers combined with desaturation approaches shed new light on the evolutionary history of Archaea and reveals that several relationships recovered in recent analyses are likely the consequence of tree reconstruction artifacts. Among others, we resolve a number of important relationships, such as those among methanogens Class I, and we propose the definition of two new superclasses within the Euryarchaeota: Methanomada and Diaforarchaea.

A Complex Endomembrane System in the Archaeon Ignicoccus hospitalis Tapped by Nanoarchaeum equitans

“…In our study we could show that a complex endomembrane system does exist within Archaea—i.e., at least in I. hospitalis —supporting hypotheses that suggest an archaeal origin of the eukaryotic endomembrane system. This is in agreement with phylogenetic analyses that place Ignicoccus as a member of the TACK superphylym (Guy and Ettema, 2011), hypothesized to be a sister group of the recently described Asgard archaea and Eukaryotes (Lake et al, 1984; Cox et al, 2008; Foster et al, 2009; Kelly et al, 2011; Williams et al, 2012, 2013; Wolf et al, 2012; Yutin et al, 2012; Lasek-Nesselquist and Gogarten, 2013; Martijn and Ettema, 2013; Koonin and Yutin, 2014; Williams and Embley, 2014; Petitjean et al, 2015; Zaremba-Niedzwiedzka et al, 2017). In TACK archaea, several “eukaryotic signature proteins” (ESPs) are present including homologs to proteins that are involved in membrane remodeling processes in Eukaryotes (Guy and Ettema, 2011).…”

Arguments Reinforcing the Three-Domain View of Diversified Cellular Life

“…This is showcased by the basal positions of M. kandleri and Thermotoga maritima within the archaeal and bacterial subtrees in Spang et al's (2015) trees (Figure  2 in [1]). M. kandleri is a fast-evolving archaeon and its basal position in most phylogenetic trees is now considered a technical artifact [33, 82]. Similarly, the examination of slow-evolving sites in rRNA sequences has revised the phylogenetic placement of T. maritima [83] (see also [84]).…”

Evolution, Metabolism and Molecular Mechanisms Underlying Extreme Adaptation of Euryarchaeota and Its Biotechnological Potential

“…Petitjean et al [6] identified 200 protein families, along with 57 ribosomal proteins and 14 RNA polymerase subunits, which represent 273 phylogenetic markers in 129 archaeal genomes. With this conserved core of archaeal genes, they inferred the phylogeny of the nodes of different orders with high robustness (statistical significance >95%).…”

“…Subsequently, the orders Methanopyrales, Methanobacteriales, and Methanococcales diverged around 3468 Ma ago, and methanogens class I or Methanomada appeared [6]. Later on, the order Thermoplasmatales diverged (3160 Ma ago), followed by the order Archaeoglobales (2799 Ma ago).…”

“…Later on, the order Thermoplasmatales diverged (3160 Ma ago), followed by the order Archaeoglobales (2799 Ma ago). Finally, methanogens class II diverged (Methanocellales, Methanosarcinales, and Methanomicrobiales), and from this group, the order Halobacteriales emerged [6]. However, this hypothesis is debatable as in some topologies, Halobacteriales appear prior to the divergence of methanogens class II [7].…”