Se-Eun Jung1P, Yeeun Lee1, and Sangtae Kim1

1Department of Biology, Sungshin Women’s University, Seoul 01133, Korea

Cyperus (Cyperaceae) comprises approximately 600 species worldwide, including about 18 species native to Korean peninsula, and is characterized by considerable ecological and economic importance in wetland ecosystems. Cyperus microiria Steud., which is widely distributed in Korea, China, and Japan, remains poorly characterized at the genomic level despite its ecological significance. Plant mitochondrial genomes exhibit highly dynamic architectures driven by extensive structural variation and repeat-mediated recombination, resulting in multiple alternative and polymorphic conformations that are difficult to resolve using short-read sequencing alone. To provide a robust genomic foundation for future evolutionary and comparative studies, we generated a high-quality assembly of the mitochondrial genome of C. microiria using a hybrid strategy that combines long-read Oxford Nanopore sequencing with highly accurate short-read Illumina sequencing. The assembled mitochondrial genome exhibited four alternative conformations, reflecting the multipartite and dynamic nature of plant mitochondrial genomes. The complete mitochondrial genome spanned 870,128 bp with a GC content of 41.0% and contained 34 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and three ribosomal RNA (rRNA) genes. Comparative analysis across the Cyperaceae and related Poales lineages demonstrated that while core metabolic genes (e.g., atp, cox, cob, nad, and ccm) are highly conserved, several ribosomal protein genes (specifically rps and rpl families) have undergone lineage-specific losses or copy-number reductions. These findings align with the rapid evolutionary patterns observed in Poales mitogenomes and provide a robust genomic foundation for future studies on the molecular evolution and phylogenetic diversity of the Cyperaceae.