# Decoding the first mitogenomes of Polycelis (Platyhelminthes, Tricladida, Planariidae): genomic architecture, evolutionary dynamics, and phylogenomic implication

## TL;DR

This study decodes the mitochondrial genomes of four Polycelis species, revealing their genomic structure and evolutionary relationships within a group of freshwater flatworms.

## Contribution

The first comparative analysis of Polycelis mitogenomes, providing new insights into their evolution and phylogeny.

## Key findings

- Four Polycelis mitogenomes each contain 12 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding region.
- Phylogenomic analysis shows Polycelis forms a monophyletic group within Planariidae with distinct gene rearrangements.
- Evolutionary analysis reveals cox1 has low variability while nad6 shows high sequence diversity.

## Abstract

The genus Polycelis is characterized by the arrangement of multiple eye spots along the anterior dorsal margin of the head. These freshwater planarians are predominantly distributed in high-altitude ecosystems of temperate and subarctic zones across the Northern Hemisphere. Despite their significance as ecological bioindicators and models for regeneration, Polycelis remains controversial in taxonomy and phylogeny due to a critical lack of molecular data. Mitochondrial genomes (mitogenomes) have emerged as powerful tools for resolving deep phylogenetic relationships and species boundaries in morphologically conserved taxa. In this study, we present the first comparative mitogenomic analyses of four Polycelis species and phylogenetic reconstructions within Tricladida.

Through next-generation sequencing, we successfully assembled four complete mitogenomes of Polycelis species. Each circular mitogenome contains 12 protein-coding genes (PCGs), 22 tRNA genes (tRNAs), 2 rRNA genes (rRNAs), and a non-coding region. Comparative genomic analyses revealed conservation in both gene arrangement and nucleotide compositions across the four species. The tandem repeat sequences and stem-loop structures were identified in their non-coding regions. Evolutionary analyses integrating nucleotide diversity (Pi), genetic distance, and Ka/Ks ratios across 12 PCGs demonstrated significant evolutionary heterogeneity: cox1 showed relatively low evolutionary rate, while nad6 displayed the highest sequence variability. Phylogenomic reconstruction using Bayesian inference (BI) and maximum likelihood (ML) methods based on 30 triclad mitogenomes, consistently resolved Polycelis as a monophyletic clade within Planariidae. Four Polycelis species exhibited synapomorphic gene rearrangements.

This study firstly elucidates Polycelis mitogenome architecture, evolutionary dynamics, providing critical insights into the genomic basis of mitochondrial evolution, the utility of mitogenomic data for molecular taxonomy, and the phylogenetic position of Polycelis within Tricladida. Additionally, this research offers valuable references for conservation and utilization of Polycelis genetic resources.

The online version contains supplementary material available at 10.1186/s12864-025-12467-z.