Rhizomal Reclassification of Living Organisms

Abstract

Living organisms interact with each other during their lifetime, leading to genomes rearrangement and sequences transfer. These well-known phenomena give these organisms mosaic genomes, which challenge their classification. Moreover, many findings occurred between the IXXth and XXIst century, especially the discovery of giant viruses and candidate phyla radiation (CPR). Here, we tried to provide an updated classification, which integrates 216 representative genomes of the current described organisms. The reclassification was expressed through a genetic network based on the total genomic content, not on a single gene to represent the tree of life. This rhizomal exploration represents, more accurately, the evolutionary relationships among the studied species. Our analyses show a separated branch named fifth TRUC (Things Resisting Uncompleted Classifications). This taxon groups CPRs together, independently from Bacteria, Archaea (which regrouped also Nanoarchaeota and Asgard members), Eukarya, and the giant viruses (recognized recently as fourth TRUC). Finally, the broadening of analysis methods will lead to the discovery of new organisms, which justify the importance of updating the classification at every opportunity. In this perspective, our pragmatic representation could be adjusted along with the progress of evolutionary studies.

Keywords: Asgard; TRUC; candidate phyla radiation; evolution; giant virus; lifestyle; reclassification; rhizome; sequences transfer; tree of life.

Figure 1

Global timeline of organism discovering and classification depending on the technologies used.

Figure 2

Rhizomes of genomes illustrative of the mosaicism of each life domain including: Schaalia odontolycus (a bacterium), Rickettsia conorii (an intracellular bacteria), Minimicrobia massiliensis (a CPR), Tupanvirus soda lake (a Mimivirus), Nanoarchaeum equitans (a nano-archaea), Methanobrevibacter smithii (an archaea), Prometheoarchaeum syntrophicum (an Asgard), Ostreococcus tauri (a eukaryote) and its mitochondria. Each gene is represented by a curve, coloring according to the origin: bacterial origin in dark red, CPR origin in purple, Eukarya origin in yellow, virus origin in orange, archaea origin in dark blue, nano-archaea origin in light blue, and orfans in grey. The figures were performed using the Gephi online tool.

Figure 3

Rhizome of life: Roots of each gene are represented according to the current reclassification of living organisms: Eukarya (yellow), Archaea (blue), Nano archaea (light blue), Bacteria (red), CPR (dark red) Giant virus (orange). In grey are genes without identified origin (ORFans).

Figure 4

A graphical representation showing the distribution (percentage) of genes in a given genome according to their origin: Archaea (Dark blue), DPANN (Light blue), Eukarya (Yellow), Bacteria (Red), CPR (Purple), Giant virus (Orange) and ORFans (Grey).

Figure 5

Hierarchical clustering by phyletic pattern based on the presence/absence of (A) 737 informational Clusters of Orthologous Groups (COGs) of proteins, (B) 180 translational Clusters of Orthologous Groups (COGs) of proteins, (C) 606 fold proteins superfamily. The Eukarya members are represented in yellow, Archaea, Asgard, and nano-archaea members in blue (dark to light respectively), classical bacteria members in red, intracellular bacteria members in pink, giant virus members in orange, mitochondria members in grey, and CPR members in purple. Each clustering was provided separately in Supplementary Data 1.

Figure 6

Unrooted phylogenetic trees show the analyses of ribosomal genes and the most conserved genes of giant viruses and the other domains. The eukarya members are represented in yellow, archaea members in dark blue, nano archaea members in light-blue, Asgard members in blue, classical bacteria members in red, intracellular bacteria members in pink, giant virus members in yellow mitochondria in black and CPR members in purple. Each tree was provided separately in Supplementary Data 2.