# Patch type nucleotide sequence identities between genomes from many different species facilitate illegitimate recombination

## TL;DR

This paper explores how patch-type nucleotide sequence identities across species may facilitate genome remodeling and evolution through illegitimate recombination.

## Contribution

The study proposes that patch-type sequence identities are statistical features of DNA that enable illegitimate recombination and evolutionary innovation.

## Key findings

- Patch-type identities of ~45% are found in diverse genomes and shuffled sequences, suggesting statistical rather than functional origin.
- These patterns may act as signals for illegitimate recombination, aiding DNA integration and rearrangement.
- Simulation data support that base composition can predict these identity patterns and their potential for recombination.

## Abstract

Comparative analyses of nucleotide sequences across diverse taxa, including viruses, bacteria, plants, and mammals, consistently reveal patch-type sequence identities of around 45%. These identities consist of short stretches interspersed by mismatches. Similarly, identity patterns emerge in alignments of randomized shuffled or scrambled sequences. These findings suggest patch-type identities reflect intrinsic statistical properties of the four-letter genetic alphabet. Such patterns likely function as recognition signals for illegitimate recombination, a mechanism that promotes sequence insertions, exchanges, and rearrangements without extensive homology. Patch-type identities have been observed at integration sites of foreign DNA and may play a role in evolutionary innovation and rapid diversification (e. g. SARS-CoV-2). Simulation data support the ideas that the frequency and length distribution of matching segments can be predicted by statistical models based on base composition, yet may also create local environments conducive to recombination. Further, the statistical architecture of the genetic alphabet encodes not only biological information, but also the potential for genome remodeling and adaptation during evolution. By bridging fundamental sequence properties with biological outcomes, this study provides a framework for exploring how randomness at the nucleotide sequence level can give rise to order and complexity across the tree of life.

The online version contains supplementary material available at 10.1038/s41598-026-44124-0.