Combining Detection and Reconstruction of Periodic Motifs in Genomic Sequences with Transitional Genome Mapping

A method of transitional automorphic mapping of the genome on itself (TAMGI) is aimed at combining detection and reconstruction of periodic motifs in the genomic RNA/DNA sequences. The periodic motifs (whether tandem or sparse) are assumed to be randomly modified by point mutations and indels during molecular evolution and present in the genomes in a hidden form. TAMGI is robust with respect to patched phasing of periodic motifs induced by indels. We developed and tested the relevant theory and statistical criteria for TAMGI applications. The applications of TAMGI are illustrated by the study of hidden periodic motifs in the genomes of the severe acute respiratory syndrome coronaviruses SARS-CoV and SARS-CoV-2 (the latter coronavirus SARS-CoV-2 being responsible for the COVID-19 pandemia) packaged within filament-like helical capsid. Such ribonucleocapsid is transported into spherical membrane envelope with incorporated spike glycoproteins. Two other examples concern the genomes of viruses with icosahedral capsids, satellite tobacco mosaic virus (STMV) and bacteriophage PHIX174. A part of the quasi-periodic motifs in these viral genomes was evolved due to weakly specific cooperative interaction between genomic ssRNA/ssDNA and nucleocapsid proteins. The symmetry of the capsids leads to the natural selection of specific quasi-periodic motifs in the related genomic sequences. Generally, TAMGI provides a convenient tool for the study of numerous molecular mechanisms with participation of both quasi-periodic motifs and complete repeats, the genome organization, contextual analysis of cis/trans regulatory elements, data mining, and correlations in the genomic sequences.