Plastome-based backbone phylogeny of East Asian Phedimus (Subgenus Aizoon: Crassulaceae), with special emphasis on Korean endemics

Yongsung Kim; Seon-Hee Kim; JiYoung Yang; Myong-Suk Cho; Marina Koldaeva; Takuro Ito; Masayuki Maki; Seung-Chul Kim

doi:10.3389/fpls.2023.1089165

Plastome-based backbone phylogeny of East Asian Phedimus (Subgenus Aizoon: Crassulaceae), with special emphasis on Korean endemics

Front Plant Sci. 2023 Mar 14:14:1089165. doi: 10.3389/fpls.2023.1089165. eCollection 2023.

Authors

Yongsung Kim¹, Seon-Hee Kim², JiYoung Yang³, Myong-Suk Cho⁴, Marina Koldaeva⁵, Takuro Ito⁶, Masayuki Maki⁶, Seung-Chul Kim⁴

Affiliations

¹ Department of Islands and Coast Biodiversity, Division of Botany, Honam National Institute of Biological Resources, Mokpo, Republic of Korea.
² Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan.
³ Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, Daegu, Republic of Korea.
⁴ Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea.
⁵ Botanical Garden-Institute, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia.
⁶ Botanical Gardens, Tohoku University, Sendai, Japan.

Abstract

Although the monophyly of Phedimus has been strongly demonstrated, the species relationships among approximately 20 species of Phedimus have been difficult to determine because of the uniformity of their floral characteristics and extreme variation of their vegetative characters, often accompanied by high polyploid and aneuploid series and diverse habitats. In this study, we assembled 15 complete chloroplast genomes of Phedimus species from East Asia and generated a plastome-based backbone phylogeny of the subgenus Aizoon. As a proxy for nuclear phylogeny, we reconstructed the nuclear ribosomal DNA internal transcribed spacer (nrDNA ITS) phylogeny independently. The 15 plastomes of subg. Aizoon were highly conserved in structure and organization; hence, the complete plastome phylogeny fully resolved the species relationships with strong support. We found that P. aizoon and P. kamtschaticus were polyphyletic and morphologically distinct or ambiguous species, and they most likely evolved from the two species complex. The crown age of subg. Aizoon was estimated to be 27 Ma, suggesting its origin to be in the late Oligocene; however, the major lineages were diversified during the Miocene. The two Korean endemics, P. takesimensis and P. zokuriensis, were inferred to have originated recently during the Pleistocene, whereas the other endemic, P. latiovalifolium, originated in the late Miocene. Several mutation hotspots and seven positively selected chloroplast genes were identified in the subg. Aizoon.

Keywords: Aizopsis; Phedimus; aneuploid series; nrDNA ITS; plastome; polyploid; subgenus Aizoon.

Grants and funding

This research was funded in part by the National Institute of Biological Resources (NIBR, grant number 2020NIBR202005201), under the program of “A Study on Plant Resources on DNA Sequences Utilizing Next Generation Sequencing Technique (3rd year).”