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To address the question of the origin of LUCA, it is necessary to examine models for how the Earth formed, what geochemical environments may have been available on the early Earth, and what types of organics could have been produced in each.
Concerning the organization of these genes in LUCA, it is not still possible to establish if they were (1) scattered throughout its genome, (2) organized in a single more-or-less compact operon, or (3) exhibited a mixed organization (i.e., some scattered genes or organized in more mini-operons).
Since only one lineage from the primordial biosphere gave rise to the three domains of life (i.e. the organismal LUCA), it is likely we have only inherited a subset of the coding diversity that may have existed at this time.
For ancient transfers, especially those that took place before the divergence of the two prokaryotic domains during the time of LUCA, it becomes more challenging to trace the history of transferred genes in part because the donor organism's lineage might have gone extinct since the transfer took place.
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Because the NCBI taxonomy does not have the branching order for the three superkingdoms, according to our method, the origin of this domain is in LUCA and it was lost in the bacterial branch.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com