BRIEF RESEARCH REPORT article
Front. Bioinform.
Sec. Evolutionary Bioinformatics
This article is part of the Research TopicEvolution of Short Genomic Regions: Discoveries, Methods, and ChallengesView all 4 articles
Higher frequency of prokaryotic low complexity regions in core and orthologous genes
Provisionally accepted
- 1Cranbrook Schools, Bloomfield Hills, United States
- 2University of Michigan, Ann Arbor, United States
- 3Oakland University, Rochester, United States
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Prokaryotic genome evolution is shaped by mutation, gene duplication, and horizontal gene transfer, yet the interaction of these mechanisms, particularly in relation to low complexity regions (LCRs), remains poorly understood. LCRs are known to be mutation-prone and have been proposed to promote genetic innovation. However, the interaction between LCR-mediated and paralogy-mediated genetic innovation is still unclear. To clarify the interplay between these two evolutionary forces, we analyzed the distribution of LCRs in protein-coding genes from three closely related enterobacteria (Escherichia coli, Salmonella enterica, and Klebsiella pneumoniae) at both species and population levels. Using pangenomic and orthology-based approaches, we categorized genes by duplication history and conservation status and assessed LCR frequencies across these groups. We found that LCRs were consistently enriched in core and orthologous genes rather than in accessory or paralogous ones. This pattern was stable across evolutionary timescales and particularly pronounced in genes involved in cell cycle control and defense. These results suggest that, contrary to prior assumptions, LCRs may serve conserved functional roles rather than acting primarily as agents of evolutionary plasticity even at population-level timescales.
Keywords: low complexity region (LCR), Comparative genomics, prokaryotes, pangenome, Orthologs and Paralogs
Received: 25 Jul 2025; Accepted: 18 Nov 2025.
Copyright: © 2025 Saravanan, Kravetz and Battistuzzi. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Fabia Ursula Battistuzzi, battistu@oakland.edu
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