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(a) Topology index histograms shown for the V. cholerae CHR. I genome

Topology‐index histograms are shown for the Chlamydia trachomatis genome,

Ab initio gene‐finding can identify the stop codons and, thus, (standard) ORFs. A generalization to codon void regions, with all six frame passes, also leads to recognition of different, overlapping, potential gene regions (and then doubled given the two orientations). A genome‐topology scoring as shown in ssss1 can clearly show differences between bacteria (ssss1) – and is thus a possible “fingerprinting” tool.

The prokaryotic genome analysis is similar to both the prokaryotic and eukaryotic transciptome analysis (where eukaryotic transcriptome analysis is similar since the introns have been removed). The analysis tools for prokaryotic genomes, described thus far, are primarily what are needed for either prokaryotic or eukaryotic transcriptome analysis. Surprisingly, the same overlapping void topologies, with reverse overlap orientation (“duals”), are seen at transcriptome level in eukaryotes as in prokaryotes. For eukaryotic transcripts with overlaps that are “dual”, however, this has special significance. Recall that a transcript that encodes overlapping read direction “duality” (with regulatory regions intact and lengthy ORF size, so highly likely functional), is only from a single genome‐level pre‐messenger ribonucleic acid (mRNA) due to intron splicing in eukaryotes. This is a very odd arrangement (artifact) for eukaryotes unless they evolved from an ancient prokaryote as hypothesized in a number of theories where such an overlap topology would already be in place to “imprint thru.” The specific nature of this transcriptome artifact, however, is best explained via the viral eukaryogenesis hypothesis (see [1, 3]).