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Cho MS, Kim Y, Kim SH, Jeon JH, Yang J, Kim SC. Phylogenetic relationships and genetic diversity of the Korean endemic Phedimus latiovalifolius (Crassulaceae) and its close relatives. Sci Rep 2024; 14:16255. [PMID: 39009598 PMCID: PMC11251145 DOI: 10.1038/s41598-024-63272-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/27/2024] [Indexed: 07/17/2024] Open
Abstract
Phedimus latiovalifolius (Y.N.Lee) D.C.Son & H.J.Kim is exclusively distributed in the high mountains in the Korean Peninsula, mainly along the Baekdudaegan mountain range. Despite its morphological and distributional distinction from other Phedimus Raf. species, its taxonomic identity and phylogenetic relationship with congeneric species remain unclear. This study employs genotyping-by-sequencing-derived genome-wide single nucleotide polymorphisms to establish the monophyly of P. latiovalifolius and its relationship with closely related species. Genetic diversity and population differentiation of P. latiovalifolius are also assessed to provide baseline genetic information for future conservation and management strategies. Our phylogenetic analyses robustly demonstrate the monophyletic nature of P. latiovalifolius, with P. aizoon (L.) 't Hart identified as its closest sister lineage. There is no genetic evidence supporting a hybrid origin of P. latiovalifolius from P. aizoon involving either P. ellacombeanus (Praeger) 't Hart or P. kamtschaticus (Fisch.) 't Hart. Population genetic analyses reveal two major groups within P. latiovalifolius. A higher genetic variation is observed in P. ellacombeanus than in the congeneric species. Notably, most of the genetic variation exists within P. latiovalifolius populations. Given its distribution and the potential role of Baekdudaegan as an East Asian Pleistocene refugia, P. latiovalifolius could be considered rare and endemic, persisting in the refugium across glacial/interglacial cycles.
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Affiliation(s)
- Myong-Suk Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Yongsung Kim
- Honam National Institute of Biological Resources, Mokpo, 58762, Korea
| | - Seon-Hee Kim
- Department of Botany, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Ji-Hyeon Jeon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - JiYoung Yang
- Institute for Dok-Do and Ulleung-Do Island, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
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Yang J, Park CG, Cho MS, Kim SC. Wasabi Gone Wild? Origin and Characterization of the Complete Plastomes of Ulleung Island Wasabi ( Eutrema japonicum; Brassicaceae) and Other Cultivars in Korea. Genes (Basel) 2024; 15:457. [PMID: 38674391 PMCID: PMC11049635 DOI: 10.3390/genes15040457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024] Open
Abstract
Korean wasabi occurs naturally on the young oceanic, volcanic Ulleung Island off the east coast of the Korean Peninsula. Although the Ulleung Island wasabi is reported as Eutrema japonicum and has been suggested to be morphologically identical to cultivars in Korea, very little is known about its taxonomic identity and relationship with other cultivars. In this study, we sequenced the complete chloroplast DNA sequences of three naturally occurring Ulleung Island wasabi plants and six cultivars ('Daewang', 'Daruma', 'Micado', 'Orochi', 'Green Thumb', and 'Shogun') from continental Korea and determined the taxonomic identity of Korean wasabi on Ulleung Island. The size and organization of the complete chloroplast genomes of the nine accessions were nearly identical to those of previously reported wasabi cultivars. In addition, phylogenetic analysis based on the complete plastomes suggested that Ulleung Island wasabi most likely comprises various wasabi cultivars with three chlorotypes ('Shogun', 'Green Thumb', and a unique Chusan type). Based on the complete plastomes, we identified eight chlorotypes for the major wasabi cultivars and the Ulleung Island wasabi. Two major groups (1-'Mazuma' and 'Daruma', and 2-'Fujidaruma'/'Shimane No. 3'/Ulleung Island wasabi/five cultivars in Korea) were also identified based on mother line genealogical history. Furthermore, different types of variations (mutations, insertions/deletions (indels), mononucleotide repeats, and inversions) in plastomes were identified to distinguish different cultivar lines and five highly divergent hotspots. The nine newly obtained complete plastomes are valuable organelle genomic resources for species identification and infraspecific phylogeographic studies on wild and cultivated wasabi.
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Affiliation(s)
- JiYoung Yang
- Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea;
| | - Cheon Gyoo Park
- Gangwondo Agricultural Research and Extension Services, Wild Vegetable Reseaerch Institute, Alpine Agricultural Experiment Station, Taebaek-si 26046, Republic of Korea;
| | - Myong-Suk Cho
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon 16419, Republic of Korea;
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon 16419, Republic of Korea;
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Raman G, Choi KS, Park S. Population Structure and Genetic Diversity Analyses Provide New Insight into the Endemic Species Aster spathulifolius Maxim. and Its Evolutionary History. PLANTS (BASEL, SWITZERLAND) 2023; 13:88. [PMID: 38202396 PMCID: PMC10780962 DOI: 10.3390/plants13010088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/23/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024]
Abstract
Aster spathulifolius, an ecologically significant plant species native to the coastal regions of Korea and Japan, remains understudied in terms of its genetic structure and evolutionary history. In this study, we employed four chloroplast markers and the nuclear ITS region from 15 populations of A. spathulifolius from both Korea and Japan, including their islands, to unravel the spatial genetic structure, differentiation, gene flow, phylogenetic, and biogeographical relationships. Analysis based on multiple methods identified a low level of genetic diversity, genetic differentiation and gene flow among A. spathulifolius populations. Network analysis and principal coordinates analysis showed that 15 populations could be divided into two groups: mainland and island. Furthermore, UPGMA, neighbor-net, maximum-likelihood and Bayesian inference-based phylogenetic tree confirmed that these populations formed two distinct clades. Therefore, the island populations might be treated as A. spathulifolius populations rather than A. oharai populations. Divergence time analysis estimated the divergence of A. spathulifolius lineages approximately 23.09 million years ago, while ancestral area reconstruction analysis suggested Korea as the potential origin, conflicting with alternative scenarios. These findings contribute to a comprehensive understanding of the evolutionary history, genetic structure, and adaptive strategies of A. spathulifolius in coastal environments. Our study challenges previous assumptions and underscores the necessity for further population studies to elucidate the intricate dynamics of this distinctive plant species.
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Affiliation(s)
- Gurusamy Raman
- Department of Life Sciences, Yeungnam University, Gyeongsan 38541, Gyeongsanbuk-do, Republic of Korea;
| | - Kyoung Su Choi
- Plant Research Team, Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea;
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan 38541, Gyeongsanbuk-do, Republic of Korea;
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Lee M, Lee HY, Kang JS, Lee H, Park KJ, Park JY, Yang TJ. Authentication of Allium ulleungense, A. microdictyon and A. ochotense based on super-barcoding of plastid genome and 45S nrDNA. PLoS One 2023; 18:e0294457. [PMID: 37983242 PMCID: PMC10659177 DOI: 10.1371/journal.pone.0294457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/31/2023] [Indexed: 11/22/2023] Open
Abstract
Allium ulleungense (AU) and A. microdictyon (AM) are valuable medicinal and edible vegetables, referred to as mountain garlic in Korea. The identification of AU, AM and a neighboring species A. ochotense (AO) is difficult because of their morphological similarities. We collected samples from three species and 46 cultivated collections to understand the genetic diversity of these valuable Allium species. Among them, we sequenced six collections, including three species and three cultivating collections to obtain data from the plastid genome (plastome) and nuclear 45S ribosomal DNA (nrDNA) for super-barcoding. The AM and AO showed around 60 single nucleotide polymorphisms (SNPs) and 39 Insertion/Deletion (InDels) in the plastome but no variations in the nrDNA sequences. Conversely, the AU and AM showed more than 170 SNPs and 80 InDels in the plastomes, and 20 SNPs and 1 InDel were found in the 45S nrDNA sequences. Among the three cultivating collections, one TB collection was determined to be the AU type in both plastome and nrDNA sequences. However, the other two collections, JB and SA, showed the AM type plastome but were heterozygous in the 45S nrDNA sequences, indicating both AU and AM types (putative AM x AU hybrid). Ten molecular markers were developed based on sequence variations to identify these three species and assess their genetic diversity. A total of 49 collections were genotyped using the ten developed markers and classified into five groups: 14 AU, 22 AM, 1 AO, 3 putative AM x AU hybrids, and 9 putative AU x AM hybrid collections. Super-barcoding with plastomes and nrDNAs revealed the genetic diversity of the three Allium species and putative hybrids between species. The newly developed markers will facilitate species and hybrid identification, thereby benefiting marker-assisted molecular breeding of Allium species.
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Affiliation(s)
- Minyoung Lee
- Department of Agriculture, Plant Genomics & Breeding Institute, Research Institute of Agriculture and Life Science, Forestry and Bioresources, College of Agriculture & Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hyo Young Lee
- Gangwondo State Agricultural Research & Extension Services, Wild Vegetable Research Institute, Pyeongchang-gun, Gangwon State, Republic of Korea
| | - Jong-Soo Kang
- Department of Agriculture, Plant Genomics & Breeding Institute, Research Institute of Agriculture and Life Science, Forestry and Bioresources, College of Agriculture & Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hyeji Lee
- Department of Agriculture, Plant Genomics & Breeding Institute, Research Institute of Agriculture and Life Science, Forestry and Bioresources, College of Agriculture & Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Ki-Jin Park
- Gangwondo State Agricultural Research & Extension Services, Wild Vegetable Research Institute, Pyeongchang-gun, Gangwon State, Republic of Korea
| | - Jee Young Park
- Department of Agriculture, Plant Genomics & Breeding Institute, Research Institute of Agriculture and Life Science, Forestry and Bioresources, College of Agriculture & Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Tae-Jin Yang
- Department of Agriculture, Plant Genomics & Breeding Institute, Research Institute of Agriculture and Life Science, Forestry and Bioresources, College of Agriculture & Life Sciences, Seoul National University, Seoul, Republic of Korea
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Raman G, Choi KS, Lee EM, Morden CW, Shim H, Kang JS, Yang TJ, Park S. Extensive characterization of 28 complete chloroplast genomes of Hydrangea species: A perspective view of their organization and phylogenetic and evolutionary relationships. Comput Struct Biotechnol J 2023; 21:5073-5091. [PMID: 37867966 PMCID: PMC10589384 DOI: 10.1016/j.csbj.2023.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023] Open
Abstract
The tribe Hydrangeeae displays a unique, distinctive disjunct distribution encompassing East Asia, North America and Hawaii. Despite its complex trait variations and polyphyletic nature, comprehensive phylogenomic and biogeographical studies on this tribe have been lacking. To address this gap, we sequenced and characterized 28 plastomes of Hydrangeeae. Our study highlights the highly conserved nature of Hydrangeaceae chloroplast (cp) genomes in terms of gene content and arrangement. Notably, synapomorphic characteristics of tandem repeats in the conserved domain of accD were observed in the Macrophyllae, Chinenses, and Dichroa sections within the Hydrangeeae tribe. Additionally, we found lower expression of accD in these sections using structure prediction and quantitative real-time PCR analysis. Phylogenomic analyses revealed the subdivision of the Hydrangeeae tribe into two clades with robust support values. Consistent with polyphyletic relationships, sect. Broussaisia was identified as the basal group in the tribe Hydrangeeae. Our study also provides insights into the phylogenetic relationships of Hydrangea petiolaris in the Jeju and Ulleung Island populations, suggesting the need for further studies with more samples and molecular data. Divergence time estimation and biogeographical analyses suggested that the common ancestors of the tribe Hydrangeeae likely originated from North America and East Asia during the Paleocene period via the Bering Land Bridge, potentially facilitating migration within the tribe between these regions. In conclusion, this study enhances our understanding of the evolutionary history and biogeography of the tribe Hydrangeeae, shedding light on the dispersal patterns and origins of this intriguing plant group with its unique disjunct distribution.
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Affiliation(s)
- Gurusamy Raman
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
| | - Kyoung-Su Choi
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
- Plant Research Team, Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea
| | - Eun Mi Lee
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
| | - Clifford W. Morden
- School of Life Sciences, University of Hawai]i at Mānoa, Honolulu, HI, USA
| | - Hyeonah Shim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jong-Soo Kang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
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Koji T, Iwata H, Ishimori M, Takanashi H, Yamasaki Y, Tsujimoto H. Multispectral Phenotyping and Genetic Analyses of Spring Appearance in Greening Plant, Phedimus spp. PLANT PHENOMICS (WASHINGTON, D.C.) 2023; 5:0063. [PMID: 37383728 PMCID: PMC10292581 DOI: 10.34133/plantphenomics.0063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 06/09/2023] [Indexed: 06/30/2023]
Abstract
The change in appearance during the seasonal transitions in ornamental greening plants is an important characteristic. In particular, the early onset of green leaf color is a desirable trait for a cultivar. In this study, we established a method for phenotyping leaf color change by multispectral imaging and performed genetic analysis based on the phenotypes to clarify the potential of the approach in breeding greening plants. We performed multispectral phenotyping and quantitative trait locus (QTL) analysis of an F1 population derived from 2 parental lines of Phedimus takesimensis, known to be a drought and heat-tolerant rooftop plant species. The imaging was conducted in April of 2019 and 2020 when dormancy breakage occurs and growth extension begins. Principal component analysis of 9 different wavelength values showed a high contribution from the first principal component (PC1), which captured variation in the visible light range. The high interannual correlation in PC1 and in the intensity of visible light indicated that the multispectral phenotyping captured genetic variation in the color of leaves. We also performed restriction site-associated DNA sequencing and obtained the first genetic linkage map of Phedimus spp. QTL analysis revealed 2 QTLs related to early dormancy breakage. Based on the genotypes of the markers underlying these 2 QTLs, the F1 phenotypes with early (late) dormancy break, green (red or brown) leaves, and a high (low) degree of vegetative growth were classified. The results suggest the potential of multispectral phenotyping in the genetic dissection of seasonal leaf color changes in greening plants.
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Affiliation(s)
- Taeko Koji
- The United Graduate School of Agricultural Sciences,
Tottori University, 4-101 Koyamacho minami, Tottori-shi, Tottori 680-8553, Japan
| | - Hiroyoshi Iwata
- Graduate School of Agricultural and Life Sciences,
The University of Tokyo, 1-1-1 Yayoi-chou, Bunkyo, Tokyo 113-8657, Japan
| | - Motoyuki Ishimori
- Graduate School of Agricultural and Life Sciences,
The University of Tokyo, 1-1-1 Yayoi-chou, Bunkyo, Tokyo 113-8657, Japan
| | - Hideki Takanashi
- Graduate School of Agricultural and Life Sciences,
The University of Tokyo, 1-1-1 Yayoi-chou, Bunkyo, Tokyo 113-8657, Japan
| | - Yuji Yamasaki
- Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori-shi, Tottori 680-0001, Japan
| | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori-shi, Tottori 680-0001, Japan
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Deng Z, Huang K, Xie P, Xie S, Zhang N, Yin H, Ping M, Wang Y. The complete chloroplast genome sequence of Sedum bulbiferum (Crassulaceae). Mitochondrial DNA B Resour 2023; 8:598-602. [PMID: 37250209 PMCID: PMC10210845 DOI: 10.1080/23802359.2022.2160220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 12/15/2022] [Indexed: 05/31/2023] Open
Abstract
Sedum bulbiferum is a traditional medicinal plant in China, with few reports on its chloroplast genome. In this study, the chloroplast genome of Sedum bulbiferum was characterized, and its phylogenetic position among other closely related species was studied. The results showed that the full length of the chloroplast genome was 150,074 bp, containing a large single-copy (LSC) region and a small single-copy (SSC) region of 81,730 and 16,726 bp, respectively, as well as two inverted repeat regions (IRs) of 25,809 bp like other plants. A total of 128 genes were found, including 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis showed that Sedum bulbiferum is closely related to Sedum emarginatum, Sedum alfredii, Sedum tricarpum, Sedum plumbizincicola, and Sedum sarmentosum.
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Affiliation(s)
- Zijie Deng
- Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, China
| | - Kerui Huang
- Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, China
| | - Peng Xie
- Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, China
| | - Suisui Xie
- The First High School of Changsha, China
| | - Ningyun Zhang
- Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, China
| | - Hanbin Yin
- Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, China
| | - Mo Ping
- Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, China
| | - Yun Wang
- Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, China
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Kim Y, Kim SH, Yang J, Cho MS, Koldaeva M, Ito T, Maki M, Kim SC. Plastome-based backbone phylogeny of East Asian Phedimus (Subgenus Aizoon: Crassulaceae), with special emphasis on Korean endemics. FRONTIERS IN PLANT SCIENCE 2023; 14:1089165. [PMID: 36998693 PMCID: PMC10043388 DOI: 10.3389/fpls.2023.1089165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/23/2023] [Indexed: 06/19/2023]
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.
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Affiliation(s)
- Yongsung Kim
- Department of Islands and Coast Biodiversity, Division of Botany, Honam National Institute of Biological Resources, Mokpo, Republic of Korea
| | - Seon-Hee Kim
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - JiYoung Yang
- Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, Daegu, Republic of Korea
| | - Myong-Suk Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
| | - Marina Koldaeva
- Botanical Garden-Institute, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Takuro Ito
- Botanical Gardens, Tohoku University, Sendai, Japan
| | | | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
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Choi TY, Son DC, Shiga T, Lee SR. Phedimusdaeamensis (Crassulaceae), a new species from Mt. Daeam in Korea. PHYTOKEYS 2022; 212:57-71. [PMID: 36761305 PMCID: PMC9836587 DOI: 10.3897/phytokeys.212.82604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 09/28/2022] [Indexed: 06/18/2023]
Abstract
Phedimus individuals from Mt. Daeam, once referred to as Phedimussikokianus, exhibit certain morphological characters that are unique within the genus. Phedimus is one of the most notorious groups for taxonomic problems due to the high morphological variation found in leaf shape, stem numbers, phyllotaxis and seed structure. Taxa in Phedimus also easily hybridize, further leading to taxonomic confusion. To carefully confirm the identity of the putative new species from Mt. Daeam, we examined morphological characters from ~100 herbarium sheets of six closely related Phedimus species. A molecular phylogenetic approach was also employed to delimit the species boundary and infer the phylogenetic relationships among the seven Phedimus species, including the species from Mt. Daeam. Both morphological and molecular phylogenetic results indicated that the species found on Mt. Daeam is a new species that is more closely related to P.middendorffianus and P.takesimensis than to the remaining four Phedimus species. Here, we provided a full description of the new species P.daeamensis as well as an updated key for the seven Phedimus species examined.
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Affiliation(s)
- Tae-Young Choi
- Department of Biology Education, College of Education, Chosun University, Gwangju 61452, Republic of KoreaChosun UniversityGwangjuRepublic of Korea
| | - Dong Chan Son
- Division of Forest Biodiversity and Herbarium, Korea National Arboretum, Pocheon 11186, Republic of KoreaDivision of Forest Biodiversity and Herbarium, Korea National ArboretumPocheonRepublic of Korea
| | - Takashi Shiga
- Faculty of Education, Niigata University, Niigata, JapanNiigata UniversityNiigataJapan
| | - Soo-Rang Lee
- Department of Biology Education, College of Education, Chosun University, Gwangju 61452, Republic of KoreaChosun UniversityGwangjuRepublic of Korea
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Cho MS, Takayama K, Yang J, Maki M, Kim SC. Genome-Wide Single Nucleotide Polymorphism Analysis Elucidates the Evolution of Prunus takesimensis in Ulleung Island: The Genetic Consequences of Anagenetic Speciation. FRONTIERS IN PLANT SCIENCE 2021; 12:706195. [PMID: 34539700 PMCID: PMC8445234 DOI: 10.3389/fpls.2021.706195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
Of the two major speciation modes of endemic plants on oceanic islands, cladogenesis and anagenesis, the latter has been recently emphasized as an effective mechanism for increasing plant diversity in isolated, ecologically homogeneous insular settings. As the only flowering cherry occurring on Ulleung Island in the East Sea (concurrently known as Sea of Japan), Prunus takesimensis Nakai has been presumed to be derived through anagenetic speciation on the island. Based on morphological similarities, P. sargentii Rehder distributed in adjacent continental areas and islands has been suggested as a purported continental progenitor. However, the overall genetic complexity and resultant non-monophyly of closely related flowering cherries have hindered the determination of their phylogenetic relationships as well as the establishment of concrete continental progenitors and insular derivative relationships. Based on extensive sampling of wild flowering cherries, including P. takesimensis and P. sargentii from Ulleung Island and its adjacent areas, the current study revealed the origin and evolution of P. takesimensis using multiple molecular markers. The results of phylogenetic reconstruction and population genetic structure analyses based on single nucleotide polymorphisms detected by multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq) and complementary cpDNA haplotypes provided evidence for (1) the monophyly of P. takesimensis; (2) clear genetic differentiation between P. takesimensis (insular derivative) and P. sargentii (continental progenitor); (3) uncertain geographic origin of P. takesimensis, but highly likely via single colonization from the source population of P. sargentii in the Korean Peninsula; (4) no significant reduction in genetic diversity in anagenetically derived insular species, i.e., P. takesimensis, compared to its continental progenitor P. sargentii; (5) no strong population genetic structuring or geographical patterns in the insular derivative species; and (6) MIG-seq method as an effective tool to elucidate the complex evolutionary history of plant groups.
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Affiliation(s)
- Myong-Suk Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Koji Takayama
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - JiYoung Yang
- Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, Daegu, South Korea
| | | | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
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