# Unraveling Phylogenetic Relationships Among Six Miscanthus Andersson (Poaceae) Species Through Chloroplast Genome Analysis

## TL;DR

This study uses chloroplast genomes to clarify the evolutionary relationships among six Korean Miscanthus species and related crops.

## Contribution

The study provides complete chloroplast genomes for six Miscanthus species and identifies phylogenetic markers for evolutionary analysis.

## Key findings

- Chloroplast genomes showed conserved structure and non-random distribution of repeats useful for phylogenetic studies.
- Phylogenetic analysis revealed four major clades, including close relationships between African, Himalayan, and Saccharum species.
- Non-coding regions provided key phylogenetic signals, supporting the inclusion of Miscanthus in crop wild relatives inventories.

## Abstract

Background/Objectives: Miscanthus Andersson, a genus of perennial grasses that includes wild relatives of key crop species, remains poorly characterized in terms of genetic diversity and evolutionary relationships. The aim of this study was to elucidate the phylogenetic structure of Miscanthus through comparative genomic analysis of the chloroplast genomes of six Korean species. Methods: Complete chloroplast genomes were assembled and analyzed for six Miscanthus species. Informative nucleotide motifs and their associated gene locations were identified as potential markers, and their phylogenetic relationships with related crops were examined. Results: The chloroplast genomes exhibited a conserved quadripartite structure, with genome sizes and GC contents within typical ranges. Analysis of codon usage showed a preference for A/U-ending codons, consistent with patterns in other angiosperms. Simple sequence repeats and long repeats demonstrated non-random distributions, indicating their value as molecular markers for phylogenetic and population studies. Comparative analyses confirmed structural conservation across Miscanthus species, whereas variation in non-coding regions provided important phylogenetic signals. Phylogenetic reconstruction based on 21 chloroplast genomes revealed four major clades, corroborating previous findings and highlighting complex evolutionary relationships within Miscanthus, including close affinities between African and Himalayan species and the genus Saccharum L. Conclusions: This study provides complete chloroplast genomes of six Miscanthus species, contributing to enhanced understanding of the relationships within the subtribe Saccharinae. The findings support the inclusion of Miscanthus species in the Korea Crop Wild Relatives inventory and highlight their potential as a genetic resource for breeding programs aimed at enhancing crop resilience to environmental stress.