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Hwang EM, Jeong KS, Yoo SY, Kim J, Choe S, Kim JY. Development of a diagnostic variable number tandem repeat marker and dual TaqMan genotyping assay to distinguish Lophophora species. Int J Legal Med 2024:10.1007/s00414-024-03318-9. [PMID: 39190119 DOI: 10.1007/s00414-024-03318-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 08/20/2024] [Indexed: 08/28/2024]
Abstract
The Lophophora genus of the Cactaceae family includes Lophophora diffusa and Lophophora williamsii, which has traditionally been used as a natural analgesic; however, its use is now under strict regulation worldwide as it contains mescaline, a unique psychotropic agent. Recently, non-medical and illegal distribution and abuse of L. williamsii have increased worldwide; thus, effective species identification methods are urgently needed. Here, we identified a new variable number tandem repeat (VNTR) marker in the trnL intron region to identify and characterize species in forensic analyses. The VNTR marker has a unique structure of tandem repeats, each with 13 nucleotides; one repeat unit was found in L. williamsii and two in L. diffusa. Phylogenetic and length polymorphism analyses confirmed that this novel VNTR marker could distinguish between Lophophora species. Furthermore, our newly developed TaqMan genotyping assay utilizes two probes; the color and position of dots on the discrimination plot differ according to the tandem repeat count within the VNTR marker. The limits of detection of the assay were 0.000063 ng (LW-VNTR probe-1) and 0.000066 ng (LW-VNTR probe-2), indicating high sensitivity. Moreover, when crime scene samples of 16 presumed L. williamsii species were analyzed, the results coincided with those of gas chromatography-mass spectrometry, confirming the applicability of our marker for Lophophora species identification. Thus, the tandem repeats within the trnL intron region can be exploited as a VNTR marker to identify L. williamsii and L. diffusa. Our dual TaqMan genotyping assay based on a novel marker demonstrates potential for forensic applications.
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Affiliation(s)
- Eun-Mi Hwang
- Forensic DNA Division, National Forensic Service, Wonju, 26460, Republic of Korea
| | - Kyu-Sik Jeong
- Forensic DNA Division, National Forensic Service, Wonju, 26460, Republic of Korea
| | - Seong Yeon Yoo
- Forensic DNA Division, National Forensic Service, Wonju, 26460, Republic of Korea
| | - Jihyun Kim
- Forensic Toxicology and Chemistry Division, Seoul Institute, National Forensic Service, Seoul, 08036, Republic of Korea
| | - Sanggil Choe
- Forensic Toxicology Division, National Forensic Service, Wonju, 26460, Republic of Korea
| | - Joo-Young Kim
- Forensic DNA Division, National Forensic Service, Wonju, 26460, Republic of Korea.
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Chang M, Kim JY, Lee H, Lee EJ, Lee WH, Moon S, Choe S, Choung CM. Development of diagnostic SNP markers and a novel SNP genotyping assay for distinguishing opium poppies. Forensic Sci Int 2022; 339:111416. [DOI: 10.1016/j.forsciint.2022.111416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/14/2022] [Accepted: 08/02/2022] [Indexed: 11/04/2022]
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Pereira RFP, Rocha J, Nunes P, Fernandes T, Ravishankar AP, Cruz R, Fernandes M, Anand S, Casal S, de Zea Bermudez V, Crespí AL. Vicariance Between Cercis siliquastrum L. and Ceratonia siliqua L. Unveiled by the Physical-Chemical Properties of the Leaves' Epicuticular Waxes. FRONTIERS IN PLANT SCIENCE 2022; 13:890647. [PMID: 35860538 PMCID: PMC9289549 DOI: 10.3389/fpls.2022.890647] [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: 03/06/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Classically, vicariant phenomena have been essentially identified on the basis of biogeographical and ecological data. Here, we report unequivocal evidences that demonstrate that a physical-chemical characterization of the epicuticular waxes of the surface of plant leaves represents a very powerful strategy to get rich insight into vicariant events. We found vicariant similarity between Cercis siliquastrum L. (family Fabaceae, subfamily Cercidoideae) and Ceratonia siliqua L. (family Fabaceae, subfamily Caesalpinoideae). Both taxa converge in the Mediterranean basin (C. siliquastrum on the north and C. siliqua across the south), in similar habitats (sclerophyll communities of maquis) and climatic profiles. These species are the current representation of their subfamilies in the Mediterranean basin, where they overlap. Because of this biogeographic and ecological similarity, the environmental pattern of both taxa was found to be very significant. The physical-chemical analysis performed on the epicuticular waxes of C. siliquastrum and C. siliqua leaves provided relevant data that confirm the functional proximity between them. A striking resemblance was found in the epicuticular waxes of the abaxial surfaces of C. siliquastrum and C. siliqua leaves in terms of the dominant chemical compounds (1-triacontanol (C30) and 1-octacosanol (C28), respectively), morphology (intricate network of randomly organized nanometer-thick and micrometer-long plates), wettability (superhydrophobic character, with water contact angle values of 167.5 ± 0.5° and 162 ± 3°, respectively), and optical properties (in both species the light reflectance/absorptance of the abaxial surface is significantly higher/lower than that of the adaxial surface, but the overall trend in reflectance is qualitatively similar). These results enable us to include for the first time C. siliqua in the vicariant process exhibited by C. canadensis L., C. griffithii L., and C. siliquastrum.
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Affiliation(s)
- Rui F. P. Pereira
- Chemistry Department and Chemistry Centre, University of Minho, Braga, Portugal
| | - João Rocha
- CQ-VR, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
- Herbarium and Botanical Garden, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
| | - Paulo Nunes
- CQ-VR, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
| | - Tânia Fernandes
- Chemistry Department and Chemistry Centre, University of Minho, Braga, Portugal
| | - Ajith P. Ravishankar
- Department of Applied Physics, School of Engineering Sciences, KTH Royal Institute of Technology, Albanova University Centre, Stockholm, Sweden
| | - Rebeca Cruz
- LAQV-REQUIMTE, Department of Chemical Sciences, Faculty of Pharmacy, Laboratory of Bromatology and Hydrology, University of Porto, Porto, Portugal
| | - Mariana Fernandes
- CQ-VR, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
- Department of Chemistry, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
| | - Srinivasan Anand
- Department of Applied Physics, School of Engineering Sciences, KTH Royal Institute of Technology, Albanova University Centre, Stockholm, Sweden
| | - Susana Casal
- LAQV-REQUIMTE, Department of Chemical Sciences, Faculty of Pharmacy, Laboratory of Bromatology and Hydrology, University of Porto, Porto, Portugal
| | - Verónica de Zea Bermudez
- CQ-VR, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
- Department of Chemistry, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
| | - António L. Crespí
- Herbarium and Botanical Garden, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
- CITAB, Department of Biological and Environmental Engineering, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
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Ony M, Klingeman WE, Zobel J, Trigiano RN, Ginzel M, Nowicki M, Boggess SL, Everhart S, Hadziabdic D. Genetic diversity in North American Cercis Canadensis reveals an ancient population bottleneck that originated after the last glacial maximum. Sci Rep 2021; 11:21803. [PMID: 34750401 PMCID: PMC8576035 DOI: 10.1038/s41598-021-01020-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 10/18/2021] [Indexed: 11/23/2022] Open
Abstract
Understanding of the present-day genetic diversity, population structure, and evolutionary history of tree species can inform resource management and conservation activities, including response to pressures presented by a changing climate. Cercis canadensis (Eastern Redbud) is an economically valuable understory tree species native to the United States (U.S.) that is also important for forest ecosystem and wildlife health. Here, we document and explain the population genetics and evolutionary history of this deciduous tree species across its distributed range. In this study, we used twelve microsatellite markers to investigate 691 wild-type trees sampled at 74 collection sites from 23 Eastern U.S. states. High genetic diversity and limited gene flow were revealed in wild, natural stands of C. canadensis with populations that are explained by two major genetic clusters. These findings indicate that an ancient population bottleneck occurred coinciding with the last glacial maximum (LGM) in North America. The structure in current populations likely originated from an ancient population in the eastern U.S. that survived LGM and then later diverged into two contemporary clusters. Data suggests that populations have expanded since the last glaciation event from one into several post-glacial refugia that now occupy this species’ current geographic range. Our enhanced understanding benchmarks the genetic variation preserved within this species and can direct future efforts in conservation, and resource utilization of adaptively resilient populations that present the greatest genetic and structural diversity.
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Affiliation(s)
- Meher Ony
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | | | - John Zobel
- Department of Forest Resources, University of Minnesota, St. Paul, MN, USA
| | - Robert N Trigiano
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Matthew Ginzel
- Department of Entomology, Purdue University, West Lafayette, IN, USA
| | - Marcin Nowicki
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Sarah L Boggess
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Sydney Everhart
- Department of Plant Pathology, University of Nebraska, Lincoln, NE, USA
| | - Denita Hadziabdic
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA.
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Liu W, Xie J, Zhou H, Kong H, Hao G, Fritsch PW, Gong W. Population dynamics linked to glacial cycles in Cercis chuniana F. P. Metcalf (Fabaceae) endemic to the montane regions of subtropical China. Evol Appl 2021; 14:2647-2663. [PMID: 34815745 PMCID: PMC8591333 DOI: 10.1111/eva.13301] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 08/19/2021] [Accepted: 09/01/2021] [Indexed: 01/03/2023] Open
Abstract
The mountains of subtropical China are an excellent system for investigating the processes driving the geographical distribution of biodiversity and radiation of plant populations in response to Pleistocene climate fluctuations. How the major mountain ranges in subtropical China have affected the evolution of plant species in the subtropical evergreen broadleaved forest is an issue with long-term concern. Here, we focused on Cercis chuniana, a woody species endemic to the southern mountain ranges in subtropical China, to elucidate its population dynamics. We used genotyping by sequencing (GBS) to investigate the spatial pattern of genetic variation among 11 populations. Geographical isolation was detected between the populations located in adjacent mountain ranges, thought to function as geographical barriers due to their complex physiography. Bayesian time estimation revealed that population divergence occurred in the middle Pleistocene, when populations in the Nanling Mts. separated from those to the east. The orientation and physiography of the mountain ranges of subtropical China appear to have contributed to the geographical pattern of genetic variation between the eastern and western populations of C. chuniana. Complex physiography plus long-term stable ecological conditions across glacial cycles facilitated the demographic expansion in the Nanling Mts., from which contemporary migration began. The Nanling Mts. are thus considered as a suitable area for preserving population diversity and large population sizes of C. chuniana compared with other regions. As inferred by ecological niche modeling and coalescent simulations, secondary contact occurred during the warm Lushan-Tali Interglacial period, with intensified East Asia summer monsoon and continuous habitat available for occupation. Our data support the strong influence of both climatic history and topographic characteristics on the high regional phytodiversity of the subtropical evergreen broadleaved forest in subtropical China.
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Affiliation(s)
- Wanzhen Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Jianguang Xie
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Hui Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Hanghui Kong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- Center of Conservation BiologyCore Botanical GardensChinese Academy of SciencesGuangzhouChina
| | - Gang Hao
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | | | - Wei Gong
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
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Chang M, Lee EJ, Kim JY, Lee H, Choe S, Moon S. A new minisatellite VNTR marker, Pscp1, discovered for the identification of opium poppy. Forensic Sci Int Genet 2021; 55:102581. [PMID: 34517229 DOI: 10.1016/j.fsigen.2021.102581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 08/18/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
Opium poppy, a member of the Papaveraceae family, is an ancient herbaceous plant and well-known medical resource in the pharmaceutical industry. However, opium poppies are grown worldwide for producing illicit drugs, significantly increasing the incidence of narcotic drug abuse. Since the narcotic poppy has not yet been genetically investigated, we characterized a novel variable number tandem repeat (VNTR) marker of forensically important poppy species based on the genetic analysis of 164 samples collected from two locations spanning the Jeolla province and Jeju island of South Korea. Comparing analysis of the chloroplast (cp) genome sequences for four representative species of Papaver (Papaver somniferum, Papaver somniferum subs. setigerum, Papaver orientale, and Papaver rhoeas) revealed a unique region with 1-3 repeats for 16 nucleotide motifs in the genome inverted repeat A (IRA, positions 128,651 to 128,698) region. For 16 nucleotide motifs, 3 repeats were found in P. somniferum, and 2 repeats were found in P. somniferum subs. setigerum. Therefore, 10 known and the 133 unknown, seized Papaver species were compared to determine whether the species could be identified via variations in the repeat units. The sizes of a novel VNTR ranged from 181 to 252 bp between the species. Phylogenetic analysis confirmed that a novel VNTR, which we named Pscp1, could clearly distinguish between the narcotic and non-narcotic types of Papaver species based on the patterns of sequence variation. Interestingly, we found that Pscp1 could also distinguish between P. somniferum and P. somniferum subs. setigerum. The regions of eight non-narcotic species displayed similar patterns and also differences were found due to the nucleotide substitution and deletion events. The structural differences of Pscp1 were observed within the two narcotic species or between the narcotic and non-narcotic species, suggesting that these variations may act as a genetic marker. We, therefore, developed a new Pscp1 PCR-capillary electrophoresis (CE) method that can reliably identify the narcotic type of Papaver species. Taken together, our findings suggest that the newly developed Pscp1 can be used as an identification marker of opium poppy, and establish that the Pscp1 genotyping method by PCR-CE is an effective primary screening tool that can also contribute to species discrimination in the field of forensic diagnosis and applications.
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Affiliation(s)
- Miwha Chang
- Forensic DNA Division, National Forensic Service, Wonju 26460, Republic of Korea
| | - Eun-Jung Lee
- Crime-scene DNA Section, Gwangju Institute, National Forensic Service, Gwangju 57231, Republic of Korea
| | - Joo-Young Kim
- Forensic DNA Division, National Forensic Service, Wonju 26460, Republic of Korea
| | - Haeyong Lee
- Forensic DNA Division, National Forensic Service, Wonju 26460, Republic of Korea
| | - Sanggil Choe
- Forensic Toxicology and Chemistry Division, Seoul Institute, National Forensic Service, Seoul 08036, Republic of Korea
| | - Seohyun Moon
- Forensic DNA Division, National Forensic Service, Wonju 26460, Republic of Korea.
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Cerna MF, Moreno MM, Fuertes BG, Iza ML, Medina GE, Recalde CG. Phylogeography of the neotropical epiphytic orchid, genus Dracula. AN ACAD BRAS CIENC 2021; 93:e20200297. [PMID: 34406285 DOI: 10.1590/0001-3765202120200297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/12/2020] [Indexed: 11/22/2022] Open
Abstract
The tropical Andes constitute a natural barrier between the Pacific Ocean and the Atlantic; in these mountains, are a great variety of Ecosystems, defined by factors such as orography, winds, humidity, temperature, among others. Some of these Ecosystems have different environmental conditions from tropical ones. In them, there is a great Biodiversity, in some cases endemic and associated with relatively small geographic areas. An example of this biodiversity is the orchids of the genus Dracula, about which discussions are currently generated due to the difficulty in classifying their members. The present work shows a study where DNA was isolated and sequenced from plant samples obtained from 52 species of orchids of the genus Dracula, which were analyzed using the MEGA7 software. Phylogenetic analysis of the DNA sequences showed a well-resolved topology that reflects a geographical pattern of several major clades of the Pacific and Atlantic watersheds. Geophysical conditions of the Andes have generated greater biodiversity of the genus Dracula on the side of the Pacific. Although the species Dracula cordobae and alessandroi reported on both sides of the study site belong to the same clade and show limited mobility through the drier area to the South of the mountain range.
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Affiliation(s)
- Marco F Cerna
- Universidad Politécnica Salesiana, Carrera de Biotecnología, Grupo de Investigación Nunkui Wakan, Isabel la Católica N23-52 y Madrid, 170525, Quito, Pichincha, Ecuador
| | - Mariela M Moreno
- Escuela Superior Politécnica de Chimborazo, Facultad de Ciencias, GEAA (Grupo de Energías Alternativas y Ambiente), Panamericana Sur Km 1 1/2, EC060155, Riobamba, Chimborazo, Ecuador
| | - Byron G Fuertes
- Universidad Politécnica Salesiana, Carrera de Biotecnología, Grupo de Investigación Nunkui Wakan, Isabel la Católica N23-52 y Madrid, 170525, Quito, Pichincha, Ecuador
| | - Mario L Iza
- Instituto Nacional de Investigaciones Agropecuarias, Departamento de Biotecnología, km 5 vía quevedo - el empalme. 70518, Mocache, Los Ríos, Ecuador
| | - Gerardo E Medina
- Universidad Estatal Amazónica, Km. 2. 1/2 vía Puyo a Tena (Paso Lateral), Tena, Napo, Ecuador
| | - Celso G Recalde
- Escuela Superior Politécnica de Chimborazo, Facultad de Ciencias, GEAA (Grupo de Energías Alternativas y Ambiente), Panamericana Sur Km 1 1/2, EC060155, Riobamba, Chimborazo, Ecuador
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Zhao B, Xiong C, Li J, Zhang D, Shi Y, Sun W, Duan X. Species Quantification in Complex Herbal Formulas-Vector Control Quantitative Analysis as a New Method. Front Pharmacol 2020; 11:488193. [PMID: 33324200 PMCID: PMC7725679 DOI: 10.3389/fphar.2020.488193] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/16/2020] [Indexed: 11/17/2022] Open
Abstract
Product mislabeling and/or species fraud in Traditional Chinese Medicine (TCM) not only decrease TCM quality, but also pose a potential health issue to the end user. Up to now, methods to control TCM quality have been developed to detect specific metabolites or identify the original species. However, species quantification in complex herbal formulas is rarely concerned. Here, we reported a simple Vector Control Quantitative Analysis (VCQA) method for flexible and accurate multiplex species quantification in traditional Chinese herbal formulas. We developed PCR-based strategy to quickly generate the integrated DNA fragments from multiple targeted species, which can be assembled into the quantitative vector in one round of cloning by Golden Gate ligation and Gateway recombination technique. With this method, we recruited the nuclear ribosomal DNA Internal Transcribed Spacer (ITS) region for the quantification of Ligusticum sinense “Chuanxiong,” Angelica dahurica (Hoffm.) Benth. & Hook.f. ex Franch. & Sav., Notopterygium incisum K. C. Ting ex H. T. Chang, Asarum sieboldii Miq., Saposhnikovia divaricata (Turcz.) Schischk., Nepeta cataria L., Mentha canadensis L., and Glycyrrhiza uralensis Fisch. ex DC. in ChuanXiong ChaTiao Wan, a classic Chinese herbal formula with very long historical background. We found that, firstly, VCQA method could eliminate the factors affecting such as the variations in DNA extracts when in combination with the use of universal and species-specific primers. Secondly, this method detected the limit of quantification of A. sieboldii Miq. in formula products down to 1%. Thirdly, the stability of quality of ChuanXiong ChaTiao Wan formula varies significantly among different manufacturers. In conclusion, VCQA method has the potential power and can be used as an alternative method for species quantification of complex TCM formulas.
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Affiliation(s)
- Bo Zhao
- College of Pharmacy, Guilin Medical University, Guilin, China.,Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chao Xiong
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.,School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Jingjian Li
- College of Pharmacy, Guilin Medical University, Guilin, China
| | - Deng Zhang
- Guangxi Institute of Botany, The Chinese Academy of Sciences, Guilin, China
| | - Yancai Shi
- Guangxi Institute of Botany, The Chinese Academy of Sciences, Guilin, China
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaoqun Duan
- College of Pharmacy, Guilin Medical University, Guilin, China
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Fritsch PW, Nowell CF, Leatherman LST, Gong W, Cruz BC, Burge DO, Delgado-Salinas A. Leaf adaptations and species boundaries in North American Cercis: implications for the evolution of dry floras. AMERICAN JOURNAL OF BOTANY 2018; 105:1577-1594. [PMID: 30207598 DOI: 10.1002/ajb2.1155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/08/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY The North American Cercis clade spans dry to mesic climates and exhibits complex morphological variation. We tested various proposed species classifications of this group and whether aspects of leaf morphology, particularly the "drip-tip" in some regional populations, are adaptive and/or linked with phylogeny. METHODS We made measurements on over 1100 herbarium specimens from throughout North America and analyzed the data with univariate and multivariate approaches. We analyzed phylogenetically DNA sequence data from nuclear ITS and three plastid regions from 40 samples, and estimated divergence times with a relaxed-clock Bayesian analysis. We used climate and geographic position data to predict the variation observed in leaf size and shape by using stepwise multiple linear regressions. KEY RESULTS Morphometric analyses yielded a pattern of continuous and often clinal character variation across North America, without correlated gaps in character states. Conversely, phylogenetic and divergence time analyses yielded distinct clades from California, the interior west, and eastern North America separated by between ~12 and 16 million years. Multiple regressions yielded highly significant correlations between leaf apex shape and precipitation of the warmest quarter. CONCLUSIONS Despite a pattern of continuous morphological character variation, the long period of geographic and presumably genetic isolation warrants the delimitation of three species. Predictive modeling supports the adaptive value of acuminate apices or "drip-tips" in mesic habitats. This suggests that Cercis leaves change more rapidly than inferred from parsimony reconstruction, which has implications for the evolution of the dry floras of North America and Eurasia.
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Affiliation(s)
- Peter W Fritsch
- Botanical Research Institute of Texas, 1700 University Drive, Fort Worth, TX, 76107-3400, USA
| | - Camille F Nowell
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118-4503, USA
- Department of Biology, San Francisco State University, 1600 Holloway Avenue, San Francisco, California, 94132, USA
| | - Lila S T Leatherman
- College of Forestry, Oregon State University, 1500 SW Jefferson Street, Corvallis, Oregon, 97331, USA
| | - Wei Gong
- College of Life Sciences, South China Agricultural University, Wushan, Tianhe, Guangzhou, 510642, China
| | - Boni C Cruz
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118-4503, USA
| | - Dylan O Burge
- University of British Columbia, 2329 West Mall, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Alfonso Delgado-Salinas
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Apartado Postal 70-233, 04510, CdMex., Mexico
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Liu W, Kong H, Zhou J, Fritsch PW, Hao G, Gong W. Complete Chloroplast Genome of Cercis chuniana (Fabaceae) with Structural and Genetic Comparison to Six Species in Caesalpinioideae. Int J Mol Sci 2018; 19:E1286. [PMID: 29693617 PMCID: PMC5983592 DOI: 10.3390/ijms19051286] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 04/16/2018] [Accepted: 04/19/2018] [Indexed: 11/17/2022] Open
Abstract
The subfamily Caesalpinioideae of the Fabaceae has long been recognized as non-monophyletic due to its controversial phylogenetic relationships. Cercis chuniana, endemic to China, is a representative species of Cercis L. placed within Caesalpinioideae in the older sense. Here, we report the whole chloroplast (cp) genome of C. chuniana and compare it to six other species from the Caesalpinioideae. Comparative analyses of gene synteny and simple sequence repeats (SSRs), as well as estimation of nucleotide diversity, the relative ratios of synonymous and nonsynonymous substitutions (dn/ds), and Kimura 2-parameter (K2P) interspecific genetic distances, were all conducted. The whole cp genome of C. chuniana was found to be 158,433 bp long with a total of 114 genes, 81 of which code for proteins. Nucleotide substitutions and length variation are present, particularly at the boundaries among large single copy (LSC), inverted repeat (IR) and small single copy (SSC) regions. Nucleotide diversity among all species was estimated to be 0.03, the average dn/ds ratio 0.3177, and the average K2P value 0.0372. Ninety-one SSRs were identified in C. chuniana, with the highest proportion in the LSC region. Ninety-seven species from the old Caesalpinioideae were selected for phylogenetic reconstruction, the analysis of which strongly supports the monophyly of Cercidoideae based on the new classification of the Fabaceae. Our study provides genomic information for further phylogenetic reconstruction and biogeographic inference of Cercis and other legume species.
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Affiliation(s)
- Wanzhen Liu
- College of Life Sciences, South China Agricultural University, Guangzhou 510614, China.
| | - Hanghui Kong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Juan Zhou
- College of Life Sciences, South China Agricultural University, Guangzhou 510614, China.
| | - Peter W Fritsch
- Botanical Research Institute of Texas, 1700 University Drive, Fort Worth, TX 76107, USA.
| | - Gang Hao
- College of Life Sciences, South China Agricultural University, Guangzhou 510614, China.
| | - Wei Gong
- College of Life Sciences, South China Agricultural University, Guangzhou 510614, China.
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Drew BT, Liu S, Bonifacino JM, Sytsma KJ. Amphitropical disjunctions in New World Menthinae: Three Pliocene dispersals to South America following late Miocene dispersal to North America from the Old World. AMERICAN JOURNAL OF BOTANY 2017; 104:1695-1707. [PMID: 29158343 DOI: 10.3732/ajb.1700225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 09/05/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY The subtribe Menthinae (Lamiaceae), with 35 genera and 750 species, is among the largest and most economically important subtribes within the mint family. Most genera of Menthinae are found exclusively in the New World, where the group has a virtually continuous distribution ranging from temperate North America to southern South America. In this study, we explored the presence, timing, and origin of amphitropical disjuncts within Menthinae. METHODS Our analyses were based on a data set consisting of 89 taxa and the nuclear ribosomal DNA markers ITS and ETS. Phylogenetic relationships were determined under maximum likelihood and Bayesian criteria, divergence times were estimated with the program BEAST, and ancestral range estimated with BioGeoBEARS. KEY RESULTS A North Atlantic Land Bridge migration event at about 10.6 Ma is inferred from western Eurasia to North America. New World Menthinae spread rapidly across North America, and then into Central and South America. Several of the large speciose genera are not monophyletic with nuclear rDNA, a finding mirrored with previous chloroplast DNA results. Three amphitropical disjunctions involving North and southern South America clades, one including a southeastern South American clade with several genera, were inferred to have occurred within the past 5 Myr. CONCLUSIONS Although three New World Menthinae genera occur in both North and South America, none exhibit an amphitropical disjunction. However, three clades exhibit amphitropical disjunctions, all dating to the early Pliocene, and all involve jump dispersals to either southeastern or southwestern South America from southeastern North America.
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Affiliation(s)
- Bryan T Drew
- Department of Biology, University of Nebraska-Kearney, NE Kearney 68849 USA
| | - Sitong Liu
- Department of Biology, University of Nebraska-Kearney, NE Kearney 68849 USA
| | - Jose M Bonifacino
- Laboratorio de Botánica, Facultad de Agronomía, Casilla de Correos 1238, Montevideo, Uruguay
| | - Kenneth J Sytsma
- Department of Botany, University of Wisconsin, Madison, Wisconsin 53706 USA
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Wang YH, Wang H, Yi TS, Wang YH. The complete chloroplast genomes of Adenolobus garipensis and Cercis glabra (Cercidoideae, Fabaceae). CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0744-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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13
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Cardoso D, Harris DJ, Wieringa JJ, São-Mateus WMB, Batalha-Filho H, Torke BM, Prenner G, Queiroz LPD. A molecular-dated phylogeny and biogeography of the monotypic legume genus Haplormosia, a missing African branch of the otherwise American-Australian Brongniartieae clade. Mol Phylogenet Evol 2016; 107:431-442. [PMID: 27965083 DOI: 10.1016/j.ympev.2016.12.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 12/02/2016] [Accepted: 12/09/2016] [Indexed: 11/17/2022]
Abstract
A comprehensively sampled reassessment of the molecular phylogeny of the genistoid legumes questions the traditional placement of Haplormosia, an African monotypic genus traditionally classified within tribe Sophoreae close to the Asian-American geographically disjunct genus Ormosia. Plastid matK sequences placed Haplormosia as sister to the American-Australian tribe Brongniartieae. Despite a superficial resemblance between Haplormosia and Ormosia, a re-examination of the morphology of Haplormosia corroborates the new phylogenetic result. The reciprocally monophyletic deep divergence of the Haplormosia stem lineage from the remaining Brongniartieae is dated to ca. 52Mya, thus supporting a signature of an old single long-distance dispersal during the early Eocene. Conversely, we estimated a relatively recent long-distance dispersal rooted in the Early Miocene for the Australian Brongniartieae clade emerging from within a grade of American Brongniartieae. The Bayesian ancestral area reconstruction revealed the coming and going of neotropical ancestors during the diversification history of the Brongniartieae legumes in Africa and all over the Americas and Australia.
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Affiliation(s)
- Domingos Cardoso
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, s.n., Ondina, 40170-115 Salvador, Bahia, Brazil; Programa de Pós-Graduação em Botânica, Universidade Estadual de Feira de Santana, Av. Transnordestina, s/n, Novo Horizonte, 44036-900 Feira de Santana, Bahia, Brazil.
| | - David J Harris
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Jan J Wieringa
- Naturalis Biodiversity Centre, Botany Section, Darwinweg 2, 2333 CR Leiden, The Netherlands
| | - Wallace M B São-Mateus
- Programa de Pós-Graduação em Sistemática e Evolução, Universidade Federal do Rio Grande do Norte, Campus Universitário Lagoa Nova, 59072-970 Natal, Rio Grande do Norte, Brazil
| | - Henrique Batalha-Filho
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, s.n., Ondina, 40170-115 Salvador, Bahia, Brazil
| | - Benjamin M Torke
- Institute of Systematic Botany, The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York 10458-5126, USA
| | - Gerhard Prenner
- Royal Botanic Gardens, Kew, Jodrell Laboratory, Richmond, Surrey TW9 3DS, UK
| | - Luciano Paganucci de Queiroz
- Programa de Pós-Graduação em Botânica, Universidade Estadual de Feira de Santana, Av. Transnordestina, s/n, Novo Horizonte, 44036-900 Feira de Santana, Bahia, Brazil
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Liu XQ, Ickert-Bond SM, Nie ZL, Zhou Z, Chen LQ, Wen J. Phylogeny of the Ampelocissus–Vitis clade in Vitaceae supports the New World origin of the grape genus. Mol Phylogenet Evol 2016; 95:217-28. [DOI: 10.1016/j.ympev.2015.10.013] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 07/31/2015] [Accepted: 10/13/2015] [Indexed: 01/29/2023]
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Lin Y, Wong WO, Shi G, Shen S, Li Z. Bilobate leaves of Bauhinia (Leguminosae, Caesalpinioideae, Cercideae) from the middle Miocene of Fujian Province, southeastern China and their biogeographic implications. BMC Evol Biol 2015; 15:252. [PMID: 26572133 PMCID: PMC4647482 DOI: 10.1186/s12862-015-0540-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 11/10/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Morphological and molecular phylogenetic studies suggest that the pantropical genus Bauhinia L. s.l. (Bauhiniinae, Cercideae, Leguminosae) is paraphyletic and may as well be subdivided into nine genera, including Bauhinia L. s.s. and its allies. Their leaves are usually characteristic bilobate and are thus easily recognized in the fossil record. This provides the opportunity to understand the early evolution, diversification, and biogeographic history of orchid trees from an historical perspective under the framework of morphological and molecular studies. RESULTS The taxonomy, distribution, and leaf architecture of Bauhinia and its allies across the world are summarized in detail, which formed the basis for classifying the bilobate leaf fossils and evaluating the fossil record and biogeography of Bauhinia. Two species of Bauhinia are described from the middle Miocene Fotan Group of Fujian Province, southeastern China. Bauhinia ungulatoides sp. nov. is characterized by shallowly to moderately bilobate, pulvinate leaves with shallowly cordate bases and acute apices on each lobe, as well as paracytic stomatal complexes. Bauhinia fotana F.M.B. Jacques et al. emend. possesses moderately bilobate, pulvinate leaves with moderately to deeply cordate bases and acute or slightly obtuse apices on each lobe. CONCLUSIONS Bilobate leaf fossils Bauhinia ungulatoides and B. fotana together with other late Paleogene - early Neogene Chinese record of the genus suggest that Bauhinia had been diverse in South China by the late Paleogene. Their great similarities to some species from South America and South Asia respectively imply that Bauhinia might have undergone extensive dispersals and diversification during or before the Miocene. The fossil record, extant species diversity, as well as molecular phylogenetic analyses demonstrate that the Bauhiniinae might have originated in the Paleogene of low-latitudes along the eastern Tethys Seaway. They dispersed southwards into Africa, migrated from Eurasia to North America via the North Atlantic Land Bridge or floating islands during the Oligocene. Then the genus spread into South America probably via the Isthmus of Panama since the Miocene onward, and underwent regional extinctions in the Boreotropics of mid-high-latitudes during the Neogene climatic cooling. Hence, Bauhinia presently exhibits a pantropical intercontinental disjunct distribution.
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Affiliation(s)
- Yanxiang Lin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P.R. China. .,University of Chinese Academy of Sciences, Beijing, 100049, P.R. China.
| | - William Oki Wong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P.R. China.
| | - Gongle Shi
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, 39 East Beijing Road, Nanjing, 210008, P.R. China.
| | - Si Shen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P.R. China.
| | - Zhenyu Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P.R. China.
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Manos PS, Meireles JE. Biogeographic analysis of the woody plants of the Southern Appalachians: Implications for the origins of a regional flora. AMERICAN JOURNAL OF BOTANY 2015; 102:780-804. [PMID: 26022491 DOI: 10.3732/ajb.1400530] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 04/21/2015] [Indexed: 06/04/2023]
Abstract
PREMISE OF THE STUDY We investigated the origins of 252 Southern Appalachian woody species representing 158 clades to analyze larger patterns of biogeographic connectivity around the northern hemisphere. We tested biogeographic hypotheses regarding the timing of species disjunctions to eastern Asia and among areas of North America. METHODS We delimited species into biogeographically informative clades, compiled sister-area data, and generated graphic representations of area connections across clades. We calculated taxon diversity within clades and plotted divergence times. KEY RESULTS Of the total taxon diversity, 45% were distributed among 25 North American endemic clades. Sister taxa within eastern North America and eastern Asia were proportionally equal in frequency, accounting for over 50% of the sister-area connections. At increasing phylogenetic depth, connections to the Old World dominated. Divergence times for 65 clades with intercontinental disjunctions were continuous, whereas 11 intracontinental disjunctions to western North America and nine to eastern Mexico were temporally congruent. CONCLUSIONS Over one third of the clades have likely undergone speciation within the region of eastern North America. The biogeographic pattern for the region is asymmetric, consisting of mostly mixed-aged, low-diversity clades connecting to the Old World, and a minority of New World clades. Divergence time data suggest that climate change in the Late Miocene to Early Pliocene generated disjunct patterns within North America. Continuous splitting times during the last 45 million years support the hypothesis that widespread distributions formed repeatedly during favorable periods, with serial cooling trends producing pseudocongruent area disjunctions between eastern North America and eastern Asia.
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Affiliation(s)
- Paul S Manos
- Department of Biology, Box 90338 Duke University, Durham, North Carolina 27708-0338 USA
| | - José Eduardo Meireles
- Department of Biology, Box 90338 Duke University, Durham, North Carolina 27708-0338 USA
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Choe S, Lee E, Jin GN, Lee YH, Kim SY, Choi H, Chung H, Hwang BY, Kim S. Genetic and chemical components analysis of Papaver setigerum naturalized in Korea. Forensic Sci Int 2012; 222:387-93. [PMID: 22921420 DOI: 10.1016/j.forsciint.2012.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 07/09/2012] [Accepted: 08/05/2012] [Indexed: 10/28/2022]
Abstract
Of the 110 species of genus Papaver, only Papaver somniferum and P. setigerum are controlled poppies in Korea. All poppy samples share similar morphology therefore it is important to check if they contain controlled substances such as morphine and codeine for forensic purpose. Since the alkaloid content of Papaver plants varies according to their growing stage, chemical components analysis alone is not enough to identify exact species. In 2010, hundreds of poppy plants suspected to be P. somniferum were found in Jeju Island, South Korea. They had a slightly different but overall similar appearance to P. somniferum. Using GC-MS analysis, codeine, rhoeadine, papaverine, protopine, noscapine, setigeridine and trace amounts of morphine were detected in these samples. Although their chemical components were different from what has been described in literatures for P. setigerum, they could be assumed to be P. setigerum based on their morphological features and GC-MS results. Also, chromosome numbers using their seeds showed 2n=44 and the numbers were in accordance with those of P. setigerum. Nucleotide substitution or insertion/deletion of ITS (internal transcribed spacer), 18S rRNA (ribosomal RNA), rbcL (large subunit of ribulose 1,5-bisphosphate carboxylase), trnL-trnF IGS (intergenic spacer), trnL intron and psbA-trnH were assessed as universal genetic markers for P. setigerum. Also, genetic analysis using six target genes involved in the biosynthesis of benzylisoquinoline alkaloids, including TYDC (tyrosine/dopa decarboxylase), SAT (salutaridinol-7-O-acetyltransferase), BBE (berberine bridge enzyme), COR (codeinone reductase), CYP80B1 ((S)-N-methylcoclaurine 3'-hydroxylase) and NCS (norcoclaurine synthase) were tested as Papaver-specific genetic markers by the existence of their PCR products. From the results, the sequences of the 6 universal genetic markers and 6 Papaver-specific genetic markers for P. setigerum were identified and then Genbank accession numbers of them were registered in NCBI. Also, the trnL intron and psbA-trnH nucleic acid sequences of the 7 Papaver species were identified and registered.
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Affiliation(s)
- Sanggil Choe
- Narcotics Analysis Division, National Forensic Service, Seoul, Republic of Korea
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Gong W, Duan T, Zhang D. Development of microsatellite markers from Cercis chinensis (Fabaceae). AMERICAN JOURNAL OF BOTANY 2012; 99:e337-e339. [PMID: 22837405 DOI: 10.3732/ajb.1200065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
PREMISE OF THE STUDY Microsatellite markers were developed to characterize the level of genetic diversity and population genetic structure of Cercis chinensis, a widely cultivated garden plant in China with congeneric species disjunctly distributed in East Asia, North America, and the Mediterranean. METHODS AND RESULTS Using the Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) protocol, eight microsatellite markers were developed in C. chinensis. Seven of the markers displayed polymorphism, with the number of alleles ranging from one to four in four populations of C. chinensis. Four to six microsatellite loci exhibited interspecific transferability in C. glabra, C. chuniana, and C. chingii. CONCLUSIONS These are the first microsatellite markers developed for C. chinensis, which will be further used in investigation of population genetic structure and phylogeographic pattern of C. chinensis and its congeneric species.
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Affiliation(s)
- Wei Gong
- College of Life Sciences, South China Agriculture University, Guangzhou, People's Republic of China
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