Ubiquitous Micro-Modular Homologies among Genomes from Viruses to Bacteria to Human Mitochondrial DNA: Platforms for Recombination during Evolution?
2022
Stefanie Weber | Christina M. Ramirez | Walter Doerfler
The emerging <i>Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2)</i> and its variants have raised tantalizing questions about evolutionary mechanisms that continue to shape biology today. We have compared the nucleotide sequence of <i>SARS-CoV-2</i> RNA to that of genomes of many different viruses, of endosymbiotic proteobacterial and bacterial DNAs, and of human mitochondrial DNA. The entire 4,641,652 nt DNA sequence of <i>Escherichia coli K12</i> has been computer-matched to <i>SARS-CoV-2</i> RNA. Numerous, very similar micro-modular clusters of 3 to 13 nucleotides lengths were detected with sequence identities of 40 to >50% in specific genome segments between <i>SARS-CoV-2</i> and the investigated genomes. These clusters were part of patch-type homologies. Control sequence comparisons between 1000 randomly computer-composed sequences of 29.9 kb and with the A, C, G, T base composition of <i>SARS-CoV-2</i> genome versus the reference Wuhan <i>SARS-CoV-2</i> sequence showed similar patterns of sequence homologies. The universal A, C, G, T genetic coding mode might have succeeded in evolution due in part to its built-in capacity to select for a substantial reservoir of micro-modular domains and employ them as platforms for integrative recombination. Their role in <i>SARS-CoV-2</i> interspecies transition and the generation of variants appears likely, but their actual involvement will require detailed investigations.
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