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.
Highlights
Accepted: 23 May 2021Devising a broadly accepted classification system for microorganisms and living things, in general, depends on the tools that are available at a given time to enable the definition of these organisms (Table 1) [1]
At the end of the 19th century and for several decades thereafter, increasing evidence emerged of entities that caused infectious diseases but were not microbes: They were invisible by optical microscopy, ultra-filterable using a Chamberland filter, and did not multiply on inert culture media; these entities were gradually characterized with the advent of cellular cultures and were eventually named viruses (Table 1) [5,6,7,8] (Figure 1)
The phylogenies of the ancestral genes that were constructed in this study, as well as the hierarchical clustering based on the three different sets of proteins and the unique characteristics of CPR [87,99], show a new division in the tree of life: candidate phyla radiation (CPR)
Summary
Devising a broadly accepted classification system for microorganisms and living things, in general, depends on the tools that are available at a given time to enable the definition of these organisms (Table 1) [1]. Eukaryote is a major branch in the tree of life alongside bacteria and archaea This term refers to the presence in a genome of sequences with different evolutionary histories, including some that may be currently unknown. Giant viruses comprise a monophyletic group with an ancient origin that may predate that of eukaryotes, and these viruses have a broad host range These bacteria ( known as obligate intracellular parasites) are unable to multiply independently and require host eukaryotic cells to develop and reproduce, like Rickettsia spp. These microbes are considered facultative intracellular bacteria, if they have the ability to grow inside and outside eukaryotic cells independently like Bartonella henselae and Listeria monocytogenes This term refers to the transfer of genetic information (regardless of whether sequences include full-length ORFs or partial ORFs) between the genomes of a donor species and a recipient species, regardless of their evolutionary relationship.
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