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Jang JE, Jeong HJ, Kim AL, Choi YR, Lazkov GA, Jang CG, Choi HJ, Gil HY. The complete chloroplast genome of Eremurus zoae Vved. (Asphodelaceae), an endemic species of Kyrgyz Republic. Mitochondrial DNA B Resour 2024; 9:437-441. [PMID: 38586509 PMCID: PMC10993749 DOI: 10.1080/23802359.2024.2336003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/23/2024] [Indexed: 04/09/2024] Open
Abstract
Eremurus zoae Vved. 1971 is a perennial herbaceous plant in the family Asphodelaceae and an endemic species of the Kyrgyz Republic; however, its complete chloroplast genome sequence has not been reported. Here, we investigated the complete chloroplast (cp) genome of E. zoae using next-generation sequencing. The cp genome was 153,744 bp long, with a large single copy (84,020 bp), a small single copy (16,766 bp), and a pair of inverted repeats (26,479 bp). The genome encodes 132 genes, including 86 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis revealed that the genus Eremurus forms a monophyletic group and E. zoae is closely related to E. chinensis. This study provides a molecular foundation for future phylogenetic studies of Eremurus.
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Affiliation(s)
- Ju Eun Jang
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, South Korea
| | - Hyeon Jin Jeong
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, South Korea
| | - Aleksey L. Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, South Korea
| | - Ye-Rim Choi
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, South Korea
| | - Georgii A. Lazkov
- Institute for Biology, National Academy of Sciences, Bishkek, Kyrgyzstan
| | - Chang-Gee Jang
- Department of Biology Education, Kongju University, Gongju, South Korea
| | - Hyeok Jae Choi
- Department of Biology & Chemistry, Changwon National University, Changwon, South Korea
| | - Hee-Young Gil
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, South Korea
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Nyamgerel N, Baasanmunkh S, Oyuntsetseg B, Tsegmed Z, Bayarmaa GA, Lazkov G, Pyak E, Gil HY, Park I, Choi HJ. Comparative plastome analysis and taxonomic classification of snow lotus species (Saussurea, Asteraceae) in Central Asia and Southern Siberia. Funct Integr Genomics 2024; 24:42. [PMID: 38396290 PMCID: PMC10891264 DOI: 10.1007/s10142-024-01309-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 01/17/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024]
Abstract
Four species of Saussurea, namely S. involucrata, S. orgaadayi, S. bogedaensis, and S. dorogostaiskii, are known as the "snow lotus," which are used as traditional medicines in China (Xinjiang), Kyrgyzstan, Mongolia, and Russia (Southern Siberia). These species are threatened globally, because of illegal harvesting and climate change. Furthermore, the taxonomic classification and identification of these threatened species remain unclear owing to limited research. The misidentification of medicinal species can sometimes be harmful to health. Therefore, the phylogenetic and genomic features of these species need to be confirmed. In this study, we sequenced five complete chloroplast genomes and seven nuclear ITS regions of four snow lotus species and other Saussurea species. We further explored their genetic variety, selective pressure at the sequence level, and phylogenetic relationships using the chloroplast genome, nuclear partial DNA sequences, and morphological features. Plastome of the snow lotus species has a conserved structure and gene content similar to most Saussurea species. Two intergenic regions (ndhJ-ndhK and ndhD-psaC) show significantly high diversity among chloroplast regions. Thus, ITS and these markers are suitable for identifying snow lotus species. In addition, we characterized 43 simple sequence repeats that may be useful in future population genetic studies. Analysis of the selection signatures identified three genes (rpoA, ndhB, and ycf2) that underwent positive selection. These genes may play important roles in the adaptation of the snow lotus species to alpine environments. S. dorogostaiskii is close to S. baicalensis and exhibits slightly different adaptation from others. The taxonomic position of the snow lotus species, confirmed by morphological and molecular evidence, is as follows: (i) S. involucrata has been excluded from the Mongolian flora due to misidentification as S. orgaadayi or S. bogedaensis for a long time; (ii) S. dorogostaiskii belongs to section Pycnocephala subgenus Saussurea, whereas other the snow lotus species belong to section Amphilaena subgenus Amphilaena; and (iii) S. krasnoborovii is synonymous of S. dorogostaiskii. This study clarified the speciation and lineage diversification of the snow lotus species in Central Asia and Southern Siberia.
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Affiliation(s)
- Nudkhuu Nyamgerel
- Department of Biology and Chemistry, Changwon National University, Changwon, Korea
| | | | - Batlai Oyuntsetseg
- Department of Biology, School of Arts and Science, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Zagarjav Tsegmed
- Department of Biology and Chemistry, Changwon National University, Changwon, Korea
| | - Gun-Aajav Bayarmaa
- Department of Biology, School of Arts and Science, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Georgy Lazkov
- Institute for Biology, National Academy of Sciences, Bishkek, Kyrgyzstan
| | - Elizaveta Pyak
- Department of Botany, Tomsk State University, Tomsk, Russia
| | - Hee-Young Gil
- Department of Forest Biodiversity and Herbarium, Korea National Arboretum, Pocheon, Korea
| | - Inkyu Park
- Department of Biology and Chemistry, Changwon National University, Changwon, Korea.
| | - Hyeok Jae Choi
- Department of Biology and Chemistry, Changwon National University, Changwon, Korea.
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Ha YH, Chang KS, Gil HY. Characteristics of chloroplast and mitochondrial genomes and intracellular gene transfer in the Korean endemic shrub, Sophora koreensis Nakai (Fabaceae). Gene 2024; 894:147963. [PMID: 37926173 DOI: 10.1016/j.gene.2023.147963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/24/2023] [Accepted: 11/01/2023] [Indexed: 11/07/2023]
Abstract
Sophora koreensis Nakai, an endemic species distributed only in the Korean Peninsula, is of great geographical, economic, and taxonomic importance. Although its complete chloroplast (cp) genome sequence has been reported, its mitochondrial (mt) genome sequence has not yet been studied. Therefore, in this study, we aimed to investigate its mt genome sequence and compare it with those reported for other Fabaceae species. Total genomic DNA was extracted from fresh S. koreensis leaves collected from natural habitats in Gangwon-do Province, South Korea. This was followed by polymerase chain reaction (PCR) amplification of cpDNA insertions in the mt genome and the detection of microsatellites and dispersed repeats in the cp and mt genomes. Finally, the cp and mt genomes of S. koreensis were compared with those reported for other Fabaceae species. The cp sequence of S. koreensis showed identical gene orders and contents as those previously reported. Only six substitutions and one deletion were detected with 99 % homology. Conversely, the complete mt genome sequence, which was 517,845 bp in length and encoded 61 genes, including 43 protein-coding, 15 transfer RNAs, and 3 ribosomal RNA genes, was considerably different from that of S. japonica in terms of gene order and composition. Further, the mt genome of S. koreensis included ca. 7 and 3 kb insertions, representing an intracellular gene transfer (IGT) event, and the regions with these insertions were determined to be originally present in the cp genome. This IGT event was also confirmed via PCR amplification. IGT events can be induced via biological gene expression control or the use of repetitive sequences, and they provide important insights into the evolutionary lineage of S. koreensis. However, further studies are needed to clarify the gene transfer mechanisms between the two organelles.
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Affiliation(s)
- Young-Ho Ha
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon-si, Gyeonggi-do 11186, Republic of Korea
| | - Kae Sun Chang
- DMZ Botanic Garden, Korea National Arboretum, Yanggu-gun, Gangwon-do 24564, Republic of Korea
| | - Hee-Young Gil
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon-si, Gyeonggi-do 11186, Republic of Korea.
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Yang J, Kim SH, Gil HY, Choi HJ, Kim SC. New insights into the phylogenetic relationships among wild onions ( Allium, Amaryllidaceae), with special emphasis on the subgenera Anguinum and Rhizirideum, as revealed by plastomes. Front Plant Sci 2023; 14:1124277. [PMID: 37025138 PMCID: PMC10070991 DOI: 10.3389/fpls.2023.1124277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
The genus Allium, with over 900 species, is one of the largest monocotyledonous genera and is widely accepted with 15 recognized subgenera and 72 sections. The robust subgeneric and sectional relationships within Allium have long been not resolved. Based on 76 species of Allium (a total of 84 accessions), we developed a highly resolved plastome phylogenetic framework by integrating 18 newly sequenced species (20 accessions) in this study and assessed their subgeneric and sectional relationships, with special emphasis on the two subgenera Anguinum and Rhizirideum. We retrieved the three major evolutionary lines within Allium and found that the two subgenera Anguinum and Rhizirideum are monophyletic whereas others are highly polyphyletic (e.g., Allium, Cepa, Polyprason, and Melanocrommyum). Within the subgenus Anguinum, two strongly supported sublineages in East Asian and Eurasian-American were found. Allium tricoccum in North America belonged to the Eurasian clade. The distinct taxonomic status of A. ulleungense and its sister taxon were further determined. In subg. Rhizirideum, the Ulleung Island endemic A. dumebuchum shared its most recent common ancestor with the species from Mongolia and the narrow Korean endemic A. minus. Two Ulleung Island endemics were estimated to originate independently during the Pleistocene. In addition, a separate monotypic sectional treatment of the east Asian A. macrostemon (subg. Allium) and sister relationship between A. condensatum and A. chinense was suggested.
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Affiliation(s)
- JiYoung Yang
- Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, Daegu, Republic of Korea
| | - Seon-Hee Kim
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Hee-Young Gil
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
| | - Hyeok-Jae Choi
- Department of Biology and Chemistry, Changwon National University, Changwon, Republic of Korea
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
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Tojibaev KS, Karimov FI, Hoshimov HR, Gulomov R, Lazkov GA, Jang CG, Gil HY, Jang JE, Batoshov AR, Iskandarov A, Choi HJ. Important plant areas (IPAs) in the Fergana Valley (Central Asia): The Bozbu-Too-Ungortepa massif. NC 2023. [DOI: 10.3897/natureconservation.51.94477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
This paper discusses identifying Important Plant Areas (IPAs) in one of the most densely populated regions of Central Asia—the Fergana valley. The recognition of IPA sites is an attempt to introduce new ways of conserving local plant diversity with a high concentration of endemic species in Central Asia, where conservation methods of the former Soviet Union still prevail. The research revealed the current state and geography of many rare species and enriched the flora of Uzbekistan and Kyrgyzstan with several rare species. The second IPA is the transboundary territory of the Fergana valley, uniting the southern spurs of the Chatkal range and the Ungortepa-BozbuToo massif. We documented the distribution of 62 species in the IPAs under the sub-criteria of Plantlife International. Our study aimed at continuing studies on the IPAs in this region, addressing specific conservation challenges, such as conserving national endemics and endangered species that grow outside protected areas and GIS mapping of endemic species.
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Ha YH, Gil HY, Kim SC, Choi K, Kim JH. Genetic structure and geneflow of Malus across the Korean Peninsula using genotyping-by-sequencing. Sci Rep 2022; 12:16262. [PMID: 36171257 PMCID: PMC9519971 DOI: 10.1038/s41598-022-20513-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/14/2022] [Indexed: 11/09/2022] Open
Abstract
This study was to understand the genetic structure and diversity of the Korean Malus species. We used genotyping-by-sequencing (GBS) technology to analyze samples of 112 individuals belonging to 18 populations of wild Malus spp. Using GBS, we identified thousands of single nucleotide polymorphisms in the species analyzed. M. baccata and M. toringo, two dominant mainland species of the Korean Peninsula, were distinguishable based on their genetic structure. However, M. toringo collected from Jeju Island exhibited a different genetic profile than that from the mainland. We identified M. cf. micromalus as a hybrid resulting from the Jeju Island M. toringo (pollen donor) and the mainland M. baccata, (pollen recipient). Putative M. mandshurica distributed on the Korean Peninsula showed a high structural and genetic similarity with M. baccata, indicating that it might be an ecotype. Overall, this study contributes to the understanding of the population history and genetic structure of Malus in the Korean Peninsula.
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Affiliation(s)
- Young-Ho Ha
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, 11186, Republic of Korea.,Department of Life Science, Gachon University, Seongnam, Gyeonggi-do, 13120, Republic of Korea
| | - Hee-Young Gil
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, 11186, Republic of Korea
| | - Sang-Chul Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, 11186, Republic of Korea
| | - Kyung Choi
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, 11186, Republic of Korea
| | - Joo-Hwan Kim
- Department of Life Science, Gachon University, Seongnam, Gyeonggi-do, 13120, Republic of Korea.
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Tojibaev KS, Karimov FI, Hoshimov HR, Jang CG, Na NR, Park MS, Chang KS, Gil HY, Baasanmunkh S, Choi HJ. Important plant areas (IPAs) in the Fergana Valley (Central Asia): The badlands of the northern foothills. NC 2022. [DOI: 10.3897/natureconservation.49.84834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Here, we aimed to identify important plant areas (IPAs) in the Fergana Valley, one of the most densely human-populated regions in Central Asia with a diverse array of endemic and endangered species. The IPA programme in FV aims to identify and protect a global network of plant conservation sites. We conducted a field survey from 2018 to 2021 to re-identify specimens collected from Fergana Valley and stored at the National Herbarium of Uzbekistan (TASH). An analysis of the floristic, geobotanical and collected data allowed for the identification of the badlands in the northern foothills (Chap tract and surrounding areas) as an IPA site. We modified the interpretation of criterion A for IPAs to suit the circumstances of Mountainous Central Asia and documented the distribution of 29 species in the IPAs under these sub-criteria. To our knowledge, this is the first study to identify an IPA in Uzbekistan and provide geographic coordinates with locations for the herbarium specimens used to create the IPA set for Central Asia. Our study provides a foundation for applying future IPAs in this region, addressing specific conservation challenges, such as conserving rare and endangered species that grow outside protected areas and GIS mapping of endemic species.
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Yang J, Park S, Gil HY, Pak JH, Kim SC. Characterization and Dynamics of Intracellular Gene Transfer in Plastid Genomes of Viola (Violaceae) and Order Malpighiales. Front Plant Sci 2021; 12:678580. [PMID: 34512682 PMCID: PMC8429499 DOI: 10.3389/fpls.2021.678580] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/28/2021] [Indexed: 06/13/2023]
Abstract
Functional gene transfer from organelles to the nucleus, known as intracellular gene transfer (IGT), is an ongoing process in flowering plants. The complete plastid genomes (plastomes) of two Ulleung island endemic violets, Viola ulleungdoensis and V. woosanensis, were characterized, revealing a lack of the plastid-encoded infA, rpl32, and rps16 genes. In addition, functional replacement of the three plastid-encoded genes in the nucleus was confirmed within the genus Viola and the order Malpighiales. Three strategies for the acquisition of a novel transit peptide for successful IGT were identified in the genus Viola. Nuclear INFA acquired a novel transit peptide with very low identity between these proteins, whereas the nuclear RPL32 gene acquired an existing transit peptide via fusion with the nuclear-encoded plastid-targeted SOD gene (Cu-Zn superoxide dismutase superfamily) as one exon, and translated both proteins in the cytosol using alternative mRNA splicing. Nuclear RPS16 contains an internal transit peptide without an N-terminal extension. Gene loss or pseudogenization of the plastid-borne rpl32 and rps16 loci was inferred to occur in the common ancestor of the genus Viola based on an infrageneric phylogenetic framework in Korea. Although infA was lost in the common ancestor of the order Malpighiales, the rpl32 and rps16 genes were lost multiple times independently within the order. Our current study sheds additional light on plastid genome composition and IGT mechanisms in the violet genus and in the order Malpighiales.
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Affiliation(s)
- JiYoung Yang
- Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, Daegu, South Korea
| | - Seongjun Park
- Institute of Natural Science, Yeungnam University, Gyeongsan, South Korea
| | - Hee-Young Gil
- DMZ Botanic Garden, Korea National Arboretum, Yanggu, South Korea
| | - Jae-Hong Pak
- Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, Daegu, South Korea
- Department of Biology, School of Life Science, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu, South Korea
- Department of Integrative Natural Sciences for the East Sea Rim, Kyungpook National University, Daegu, South Korea
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
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Choi KS, Ha YH, Gil HY, Choi K, Kim DK, Oh SH. Two Korean Endemic Clematis Chloroplast Genomes: Inversion, Reposition, Expansion of the Inverted Repeat Region, Phylogenetic Analysis, and Nucleotide Substitution Rates. Plants (Basel) 2021; 10:397. [PMID: 33669616 PMCID: PMC7922562 DOI: 10.3390/plants10020397] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 12/12/2022]
Abstract
Previous studies on the chloroplast genome in Clematis focused on the chloroplast structure within Anemoneae. The chloroplast genomes of Cleamtis were sequenced to provide information for studies on phylogeny and evolution. Two Korean endemic Clematis chloroplast genomes (Clematis brachyura and C. trichotoma) range from 159,170 to 159,532 bp, containing 134 identical genes. Comparing the coding and non-coding regions among 12 Clematis species revealed divergent sites, with carination occurring in the petD-rpoA region. Comparing other Clematis chloroplast genomes suggested that Clematis has two inversions (trnH-rps16 and rps4), reposition (trnL-ndhC), and inverted repeat (IR) region expansion. For phylogenetic analysis, 71 protein-coding genes were aligned from 36 Ranunculaceae chloroplast genomes. Anemoneae (Anemoclema, Pulsatilla, Anemone, and Clematis) clades were monophyletic and well-supported by the bootstrap value (100%). Based on 70 chloroplast protein-coding genes, we compared nonsynonymous (dN) and synonymous (dS) substitution rates among Clematis, Anemoneae (excluding Clematis), and other Ranunculaceae species. The average synonymoussubstitution rates (dS)of large single copy (LSC), small single copy (SSC), and IR genes in Anemoneae and Clematis were significantly higher than those of other Ranunculaceae species, but not the nonsynonymous substitution rates (dN). This study provides fundamental information on plastid genome evolution in the Ranunculaceae.
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Affiliation(s)
- Kyoung Su Choi
- Institute of Natural Science, Yeungnam University, Gyeongsan-si, Gyeongbuk-do 38541, Korea;
- Department of Life Sciences, Yeungnam University, Gyeongsan-si, Gyeongbuk-do 38541, Korea
| | - Young-Ho Ha
- Forest Biodiversity Division, Korea National Arboretum, 415 Gwangneungsumogwon-ro, Soheul-eup, Pocheon-si, Gyeonggi-do 11186, Korea; (Y.-H.H.); (D.-K.K.)
- Department of Life Science, Gachon University, Seongnam-si, Gyeonggi-do 13120, Korea
| | - Hee-Young Gil
- DMZ Botanic Garden, Korea National Arboretum, 916-70, Punchbowl-ro, Haean-myeon, Yanggu, Gangwon-do 24564, Korea;
| | - Kyung Choi
- Research Planning and Coordination Division, Korea National Arboretum, 415 Gwangneungsumogwon-ro, Soheul-eup, Pocheon-si, Gyeonggi-do 11186, Korea;
| | - Dong-Kap Kim
- Forest Biodiversity Division, Korea National Arboretum, 415 Gwangneungsumogwon-ro, Soheul-eup, Pocheon-si, Gyeonggi-do 11186, Korea; (Y.-H.H.); (D.-K.K.)
| | - Seung-Hwan Oh
- Forest Biodiversity Division, Korea National Arboretum, 415 Gwangneungsumogwon-ro, Soheul-eup, Pocheon-si, Gyeonggi-do 11186, Korea; (Y.-H.H.); (D.-K.K.)
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Gil HY, Maki M, Pimenova EA, Taran A, Kim SC. Origin of the critically endangered endemic species Scrophularia takesimensis (Scrophulariaceae) on Ulleung Island, Korea: implications for conservation. J Plant Res 2020; 133:765-782. [PMID: 32815044 DOI: 10.1007/s10265-020-01221-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/12/2020] [Indexed: 06/11/2023]
Abstract
Scrophularia takesimensis is a critically endangered endemic species of Ulleung Island, Korea. A previous molecular phylogenetic study based on nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) sequences with very limited sampling suggested that it is most closely related to the clade comprising S. alata and S. grayanoides. To determine the origin of S. takesimensis, we sampled a total of 171 accessions including S. takesimensis (9 populations and 63 individuals) and two closely related species, S. alata (11 populations and 68 individuals) and S. grayanoides (5 populations and 40 individuals) from eastern Asia and sequenced ITS and two chloroplast DNA (cpDNA) non-coding regions. Previously sequenced representative species of Scrophularia (109 taxa for ITS and 80 taxa for cpDNA) were combined with our data set and analyzed. While the global scale ITS phylogenetic tree suggests monophyly for each of the three eastern Asian species, S. takesimensis appears to be more closely related (albeit weakly) to a clade containing eastern North American/Caribbean species than to either S. alata or S. grayanoides. By contrast, the global scale cpDNA phylogenetic tree demonstrates that the eastern North America/Caribbean clade is sister to a clade comprising the three eastern Asian species. In addition, the monophyletic S. takesimensis is deeply embedded within paraphyletic S. alata, sharing its most recent common ancestor with populations from Japan/Sakhalin. Two divergent, geographically structured cp haplotype groups within S. takesimensis suggest at least two independent introductions from different source areas. A new and accurate chromosome number of S. takesimensis (2n = 94) is reported and some conservation strategies are discussed.
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Affiliation(s)
- Hee-Young Gil
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, South Korea
- DMZ Botanic Garden, Korea National Arboretum, 916-70, Punchbowl-ro, Haean-myeon, 24564, Yanggu, South Korea
| | - Masayuki Maki
- Division of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Aoba, Sendai, 980-8578, Japan
| | | | - Aleksandr Taran
- Sakhalin Branch of Botanical Garden-Institute FEB RAS, Yuzhno-Sakhalinsk, Russia
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, South Korea.
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Ha YH, Gil HY, Kim DK. First report of complete chloroplast genome sequence of monotypic genus Astilboides (Saxifragaceae) in North East Asia. Mitochondrial DNA B Resour 2020; 5:3616-3617. [PMID: 33367032 PMCID: PMC7594876 DOI: 10.1080/23802359.2020.1824595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The complete chloroplast genome sequence of Astilboides tabularis, one of endemic species of Eastern Asia, was determined. The chloroplast genome was 157,147 bp in length with large single-copy (87,703 bp), small single-copy (18,268 bp) and a pair of inverted repeats (25,588 bp). In total, 131 genes were encoded, including 86 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The phylogenetic analysis using concatenated 77 protein-coding genes of 15 species chloroplast genome revealed that A. tabularis was sister to the clade containing Bergenia, Oresitrophe, and Mukdenia.
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Affiliation(s)
- Young-Ho Ha
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea.,Department of Life Sciences, Gachon University, Seongnam, Republic of Korea
| | - Hee-Young Gil
- DMZ Botanic Garden, Korea National Arboretum, Yanggu, Republic of Korea
| | - Dong-Kap Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
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Ha YH, Gil HY, Kim DK. Characterization of the complete plastome sequence of Asplenium × bimixtum (Aspleniaceae). Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1750993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Young-Ho Ha
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, Republic of Korea
- Department of Life Sciences, Gachon University, Seongnam, Republic of Korea
| | - Hee-Young Gil
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, Republic of Korea
| | - Dong-Kap Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, Republic of Korea
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Ha YH, Gil HY, Lee J, Kim DK, Choi K, Chang KS, Oh SH. The complete chloroplast genome sequence of Liparis yongnoana, an endemic orchid of Korea. Mitochondrial DNA B Resour 2019; 4:2666-2667. [PMID: 33365674 PMCID: PMC7706914 DOI: 10.1080/23802359.2019.1644220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The complete chloroplast genome sequence of Liparis yongnoana was determined and analyzed in this study. The chloroplast genome size is 153,165 bp in length with 36.9% GC content. It comprises a large single-copy region (LSC) of 83,690 bp, a small single copy region (SSC) of 17,661 bp, and a pair of inverted repeat regions (IRa and IRb) of 25,907 bp separated by the SSC. The genome contains 132 genes, including 86 protein-coding, eight ribosomal RNA, and 38 transfer RNA genes. Phylogenetic analysis inferred from 16 Orchidaceae chloroplast genomes suggested that L. yongnoana was closely related to L. loeselii.
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Affiliation(s)
- Young-Ho Ha
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon-si, Republic of Korea
- Department of Life Science, Gachon University, Seongnam-si, Republic of Korea
| | - Hee-Young Gil
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon-si, Republic of Korea
| | - Jungsim Lee
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon-si, Republic of Korea
| | - Dong Kap Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon-si, Republic of Korea
| | - Kyung Choi
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon-si, Republic of Korea
| | - Kae Sun Chang
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon-si, Republic of Korea
| | - Seung-Hwan Oh
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon-si, Republic of Korea
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Gil HY, Kim Y, Kim SH, Jeon JH, Kwon Y, Kim SC, Park J. The complete chloroplast genome of Pyrus ussuriensis Maxim. (Rosaceae). Mitochondrial DNA Part B 2019. [DOI: 10.1080/23802359.2019.1581585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Hee-Young Gil
- Korea National Arboretum, Gyeonggi-do, Republic of Korea
| | - Yongsung Kim
- InfoBoss Co., Ltd., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Seon-Hee Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
| | - Ji-Hyeon Jeon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
| | - Youl Kwon
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
| | - Jongsun Park
- InfoBoss Co., Ltd., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
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Gil HY, Ha YH, Choi KS, Lee JS, Chang KS, Choi K. The chloroplast genome sequence of an aquatic plant, Sparganium eurycarpum subsp. coreanum (Typhaceae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1572471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Hee-Young Gil
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, Korea
| | - Young-Ho Ha
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, Korea
| | - Kyoung Su Choi
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, Korea
| | - Jung Sim Lee
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, Korea
| | - Kae Sun Chang
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, Korea
| | - Kyung Choi
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, Korea
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Gil HY, Kim SC. The plastome sequence of Ulleung Rowan, Sorbus ulleungensis (Rosaceae), a new endemic species on Ulleung Island, Korea. Mitochondrial DNA B Resour 2018; 3:284-285. [PMID: 33474144 PMCID: PMC7800943 DOI: 10.1080/23802359.2018.1443042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The complete chloroplast genome sequence of Sorbus ulleungensis, a recently described endemic species to Ulleung Island of Korea, was determined. The genome size was 159,632 bp in length with 36.5% GC content. It included a pair of inverted repeats (IRa and IRb) of 26,402 bp, which were separated by small single copy (SSC: 18,824 bp) and large single copy (LSC: 88,003 bp) regions. The cp genome contained 111 genes, including 78 protein coding genes, 29 tRNA genes, and four rRNA genes. Phylogenetic analysis of the combined 78 protein coding genes and four rRNA genes showed that S. ulleungensis was most closely related to Pyrus pyrifolia.
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Affiliation(s)
- Hee-Young Gil
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
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Yun SA, Gil HY, Kim SC. The complete chloroplast genome sequence of Saussurea polylepis (Asteraceae), a vulnerable endemic species of Korea. Mitochondrial DNA B Resour 2017; 2:650-651. [PMID: 33473934 PMCID: PMC7799718 DOI: 10.1080/23802359.2017.1375881] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The complete chloroplast genome sequence of Saussurea polylepis, one of vulnerable and endemic species of Korea, was determined. The genome size was 152,488 bp in length with 37.7% GC content. It included a pair of inverted repeats (IRa and IRb) of 25,191 bp, which were separated by small single copy (SSC: 18,689 bp) and large single copy (LSC: 83,417 bp) regions. The cp genome contained 113 genes, including 80 protein-coding genes, 29 tRNA genes, and four rRNA genes. Phylogenetic analysis of the combined 80 protein coding genes and four rRNA genes showed that S. polylepis was closely related to S. chabyoungsanica.
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Affiliation(s)
- Seon A Yun
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Gyeonggi-do, Korea
| | - Hee-Young Gil
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Gyeonggi-do, Korea
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Gyeonggi-do, Korea
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Gil HY, Kim SC. Viola woosanensis, a recurrent spontaneous hybrid between V. ulleungdoensis and V. chaerophylloides (Violaceae) endemic to Ulleung Island, Korea. J Plant Res 2016; 129:807-822. [PMID: 27206724 DOI: 10.1007/s10265-016-0830-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/23/2016] [Indexed: 06/05/2023]
Abstract
Ulleung Island is an oceanic volcanic island in Korea, which has never been connected to the adjacent continent. Previous studies highlighted Ulleung Island as an excellent system to study the pattern and process of early stages of flowering plant evolutions on oceanic island. The predominant mode of speciation in flowering plants on Ulleung Island appears to be anagenesis. However, the potentially important role of hybrid speciation among incompletely reproductively isolated lineages cannot be ruled out. Viola woosanensis (Violaceae) is of purportedly hybrid origin between V. ulleungdoensis (i.e., formerly recognized as V. selkirkii in Ulleung Island) and V. chaerophylloides, based on morphology. To examine the origin of V. woosanensis, we sampled a total of 80 accessions, including V. woosanensis and its putative parental species and sequenced nrDNA ITS, and four highly variable chloroplast noncoding regions (trnL-trnF, rpl16 intron, atpF-atpH, and psbA-trnH). Representative species of Viola from Korea were also included in the phylogenetic analyses (maximum parsimony, maximum likelihood, and Bayesian inference). Additive polymorphic sites in the nrDNA ITS regions were confirmed by cloning amplicons from representative species. The molecular data strongly supported the hybrid origin of V. woosanensis, and the maternal and paternal parent were determined to be V. ulleungdoensis and V. chaerophylloides, respectively. The presence of two parental ribotypes in V. woosanensis (with the exception in one population) was confirmed by cloning, suggesting V. woosanensis is primarily the F1 generation. No trace of backcrossing and introgression with its parents was detected due to low fertility of hybrid species. We found a multiple and unidirectional hybrid origin of V. woosanensis. Additional studies are required to determine which factors contribute to asymmetric gene flow of Viola species in Ulleung Island.
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Affiliation(s)
- Hee-Young Gil
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-Do, 16419, Korea
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-Do, 16419, Korea.
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Park SK, Gil HY, Kim H, Chang CS. A Reconsideration of the List of National Endemic Plants (appendix 4-1) Under the Creation and Furtherance of Arboretums Act Proposed by Korea Forest Service. ACTA ACUST UNITED AC 2013. [DOI: 10.14578/jkfs.2013.102.1.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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