# Assembly and comparative analysis of four complete mitochondrial genomes of Pulsatilla species

## TL;DR

This study assembles and compares the mitochondrial genomes of four Pulsatilla species to better understand their genetic relationships and medicinal potential.

## Contribution

The study provides the first complete mitochondrial genome assemblies for four Pulsatilla species and reveals insights into their genetic variability.

## Key findings

- The four Pulsatilla species have varying mitochondrial genome sizes and gene compositions.
- Significant differences in repeat sequences and RNA editing sites were observed among the species.
- Phylogenetic analysis grouped the four species into a common subclade, suggesting close genetic relationships.

## Abstract

Pulsatilla species, which belong to the Ranunculaceae family, have garnered significant attention due to their remarkable medicinal attributes and ornamental value. In the present study, four mitochondrial genomes (mitogenomes) of Pulsatilla species were assembled and analyzed. The aim was to lay a research foundation for unraveling the genetic interrelationships among these species and the identification of Traditional Chinese Medicine from Pulsatilla species.

The mitogenomes of P. chinensis, P. chinensis var. kissii, P. cernua, and P. dahurica were assembled into single circular DNA molecules, with lengths of 878,988 bp, 684,203 bp, 747,621 bp, and 824,625 bp, encoding 53, 40, 40, and 49 protein-coding genes, 13, 14, 20, and 33 transfer RNA genes, and 3, 3, 4, and 3 ribosomal RNA genes, respectively. Repeat sequence analysis found a large number of simple sequence repeats (SSRs) and long repeat sequences (LRSs) in four mitogenomes. P. chinensis, P. chinensis var. kissii, P. cernua and P. dahurica had 43, 4, 6, 3 LRSs longer than 1 kb, respectively. Codon bias and RNA editing sites in the protein-coding genes of the four mitogenomes were similar. Furthermore, numerous collinear sequences were identified among the four mitogenomes, and homologous fragments were found by comparing them with their plastome sequences. Based on the phylogenetic trees of mitochondrial PCGs, P. chinensis, P. chinensis var. kissii, P. cernua, and P. dahurica clustered into a common subclade.

The comprehensive analysis of the four Pulsatilla mitogenomes revealed that the genome size, gene composition, and distribution of repeat sequences display variability. This finding offers novel perspectives into the evolution of related species, thereby enriching our understanding of their genetic underpinnings and potential for further exploration in diverse fields.

The online version contains supplementary material available at 10.1186/s12870-025-07527-1.