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

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 b...

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Autores principales: Kim, Yongsung, Kim, Seon-Hee, Yang, JiYoung, Cho, Myong-Suk, Koldaeva, Marina, Ito, Takuro, Maki, Masayuki, Kim, Seung-Chul
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10043388/
https://www.ncbi.nlm.nih.gov/pubmed/36998693
http://dx.doi.org/10.3389/fpls.2023.1089165
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author Kim, Yongsung
Kim, Seon-Hee
Yang, JiYoung
Cho, Myong-Suk
Koldaeva, Marina
Ito, Takuro
Maki, Masayuki
Kim, Seung-Chul
author_facet Kim, Yongsung
Kim, Seon-Hee
Yang, JiYoung
Cho, Myong-Suk
Koldaeva, Marina
Ito, Takuro
Maki, Masayuki
Kim, Seung-Chul
author_sort Kim, Yongsung
collection PubMed
description 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.
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spelling pubmed-100433882023-03-29 Plastome-based backbone phylogeny of East Asian Phedimus (Subgenus Aizoon: Crassulaceae), with special emphasis on Korean endemics Kim, Yongsung Kim, Seon-Hee Yang, JiYoung Cho, Myong-Suk Koldaeva, Marina Ito, Takuro Maki, Masayuki Kim, Seung-Chul Front Plant Sci Plant Science 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. Frontiers Media S.A. 2023-03-14 /pmc/articles/PMC10043388/ /pubmed/36998693 http://dx.doi.org/10.3389/fpls.2023.1089165 Text en Copyright © 2023 Kim, Kim, Yang, Cho, Koldaeva, Ito, Maki and Kim https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Kim, Yongsung
Kim, Seon-Hee
Yang, JiYoung
Cho, Myong-Suk
Koldaeva, Marina
Ito, Takuro
Maki, Masayuki
Kim, Seung-Chul
Plastome-based backbone phylogeny of East Asian Phedimus (Subgenus Aizoon: Crassulaceae), with special emphasis on Korean endemics
title Plastome-based backbone phylogeny of East Asian Phedimus (Subgenus Aizoon: Crassulaceae), with special emphasis on Korean endemics
title_full Plastome-based backbone phylogeny of East Asian Phedimus (Subgenus Aizoon: Crassulaceae), with special emphasis on Korean endemics
title_fullStr Plastome-based backbone phylogeny of East Asian Phedimus (Subgenus Aizoon: Crassulaceae), with special emphasis on Korean endemics
title_full_unstemmed Plastome-based backbone phylogeny of East Asian Phedimus (Subgenus Aizoon: Crassulaceae), with special emphasis on Korean endemics
title_short Plastome-based backbone phylogeny of East Asian Phedimus (Subgenus Aizoon: Crassulaceae), with special emphasis on Korean endemics
title_sort plastome-based backbone phylogeny of east asian phedimus (subgenus aizoon: crassulaceae), with special emphasis on korean endemics
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10043388/
https://www.ncbi.nlm.nih.gov/pubmed/36998693
http://dx.doi.org/10.3389/fpls.2023.1089165
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