A comparative analysis of complete mitochondrial genomes from two individual specimens of the monogenean flatworm Dactylogyrus baueri has uncovered an extreme 3.7-fold length difference in their non-coding regions, despite highly conserved protein-coding sequences. The discovery marks the first reported case of mitochondrial non-coding region length variation consistent with replication slippage at the intraspecific level within monogenean flatworms.
The genus Dactylogyrus has long served as a classic model for investigating host-parasite coevolutionary dynamics, yet structural variation within its mitochondrial non-coding regions had previously remained largely unexplored. Tandem repeats situated inside mitochondrial non-coding regions represent a primary evolutionary driver of genome size variation across diverse organisms.
To investigate mitogenomic architecture across geographic origins, the researchers sequenced the complete mitochondrial genomes of the two representative Dactylogyrus baueri specimens using stepwise polymerase chain reaction amplification coupled with Sanger sequencing. Tandem repeat arrays across the sequences were identified computationally using Tandem Repeats Finder, while potential nucleic acid secondary structures were predicted through UNAFold.
The comparative sequencing demonstrated that the coding regions of both parasites remained remarkably conserved, establishing high overall genetic similarity. However, their non-coding regions diverged dramatically in total length. The specimen collected from the Lancang River in Nanjian possessed an ancestral-like, single-copy non-coding sequence. In contrast, the specimen obtained from the Irrawaddy River in Ruili displayed extensive expansion driven by tandem duplication, accounting for the overall 3.7-fold dimensional disparity observed between the two mitogenomes.
Detailed structural mapping revealed that the elongated Ruili non-coding region harbors a large-scale 681-base-pair tandem repeat unit arranged in a head-to-tail orientation, present in approximately 5.1 copies. Tandem repeats of such substantial length are rarely documented in flatworm genomes and are considerably larger than previously identified analogous structures in related taxa. The Nanjian specimen retained only a single, highly similar copy of this sequence, highlighting that large-scale duplication events can alter non-coding regions substantially between conspecific individuals.
Sliding window analysis of GC skew further illuminated the mechanistic footprint of this structural divergence. In the Ruili specimen, the GC skew profile revealed five periodic troughs that aligned precisely with the five complete 681-base-pair repeat units. This periodic pattern strongly supports a model of genome expansion driven by replication slippage. Conversely, sliding window analysis of the Nanjian non-coding region detected only a single trough, matching its single-copy configuration.
The analysis also identified a 33-base-pair stem-loop secondary structure that remained structurally conserved across both specimens while maintaining high GC skew values. Due to its sequence conservation and structural stability, the researchers designated this motif as a candidate functional element potentially involved in the regulation of the mitochondrial replication origin. However, the authors explicitly emphasized that direct experimental validation will be required to confirm its precise regulatory role in mitochondrial DNA replication.
The sharp contrast between nearly identical coding sequences and extreme non-coding structural diversity suggests that structural rearrangements in non-coding regions can precede functional divergence in protein-coding genes between geographic lineages.
The authors noted significant limitations regarding the scope of the study, emphasizing that the results are derived from sequencing single representative individuals from each locality. Consequently, the findings represent a comparative observation between two specific organisms rather than a population-level characterization.
Subject of Research: Intraspecific mitochondrial non-coding region structural variation and replication slippage in Dactylogyrus baueri
Article Title: Replication slippage footprint in the mitochondrial non-coding region: extreme structural variation and GC skew gradient analysis in conspecific Dactylogyrus from two geographic origins
Article References: Jia, T., Meng, F.-Y., Xu, J.-D., Xu, W.-J., & Fan, L.-X. (2026). Replication slippage footprint in the mitochondrial non-coding region: extreme structural variation and GC skew gradient analysis in conspecific Dactylogyrus from two geographic origins. BMC Genomics. https://doi.org/10.1186/s12864-026-13561-6
Image Credits: AI Generated
DOI: 10.1186/s12864-026-13561-6
Keywords: Dactylogyrus baueri, mitochondrial genome, non-coding region, tandem repeats, replication slippage, GC skew, structural variation, Monogenea, Carassius auratus, Lancang River, Irrawaddy River, Sanger sequencing, UNAFold, Tandem Repeats Finder, secondary structure, stem-loop motif
News Source: Scienmag.
