Plastome phylogenomics of the Korean endemic plant Arisaema thunbergii subsp. geomundoense (Araceae).

Studying endemic plants is crucial for enhancing biodiversity in their unique habitats and exploring their evolutionary history. However, classification relying only on morphological traits can be subjective and may lead to inconsistencies in taxonomy. To address this issue, molecular approaches are necessary for precise identification and classification. The Korean endemic plant Arisaema thunbergii Blume subsp. geomundoense S.C.Ko (Araceae Juss.) has been classified based on its distinct spadix appendage color and wrinkled texture. Nevertheless, its taxonomic placement remains uncertain owing to a lack of sufficient molecular research, and it has recently been treated as a synonym of A. thunbergii subsp. urashima (H.Hara) H.Ohashi & J.Murata. To resolve their evolutionary relationships, we sequenced and analyzed the complete plastid genomes of A. thunbergii subsp. geomundoense, A. thunbergii subsp. thunbergii and A. heterophyllum Blume, obtaining genome lengths of 168,650-173,154 bp. Each plastome harbors 78 protein-coding genes (PCGs), 30 tRNA genes, and four rRNA genes, with infA retained as a pseudogene. Phylogenetic reconstruction based on all 78 plastid PCGs robustly supports the monophyly of seven of the 15 recognized sections in Arisaema Mart. and confirm that A. thunbergii subsp. geomundoense is nested within A. thunbergii subsp. thunbergii. Based on these findings, we propose that A. thunbergii subsp. geomundoense should be treated as a synonym of A. thunbergii subsp. thunbergii. Molecular clock estimates indicate that Arisaema first appeared in the Oligocene and subsequently radiated during the Miocene. Utilizing plastome sequences and previously established calibration points, this study refines the evolutionary timeline of Arisaema, highlighting its divergence and adaptation during the Miocene.