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Karbarz M, Szlachcikowska D, Zapał A, Leśko A. Unlocking the Genetic Identity of Endangered Paphiopedilum Orchids: A DNA Barcoding Approach. Genes (Basel) 2024; 15:689. [PMID: 38927625 PMCID: PMC11202981 DOI: 10.3390/genes15060689] [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: 04/15/2024] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
Orchids of the genus Paphiopedilum, also called slippers, are among the most valued representatives of the Orchidaceae family due to their aesthetic qualities. Due to overexploitation, deforestation, and illegal trade in these plants, especially in the vegetative phase, Paphiopedilum requires special protection. This genus is listed in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora. Their precise identification is of great importance for the preservation of genetic resources and biodiversity of the orchid family (Orchidaceae). Therefore, the main objective of the study was to investigate the usefulness of the DNA barcoding technique for the identification of endangered orchids of the genus Paphiopedilum and to determine the effectiveness of five loci: matK, rbcL, ITS2, atpF-atpH and trnH-psbA as potential molecular markers for species of this genus. Among single locus barcodes, matK was the most effective at identifying species (64%). Furthermore, matK, ITS2, matK + rbcL, and matK + trnH-psbA barcodes can be successfully used as a complementary tool to identify Paphiopedilum orchids while supporting morphological data provided by taxonomists.
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Affiliation(s)
| | - Dominika Szlachcikowska
- Department of Biotechnology and Cell Biology, Medical College, University of Information Technology and Management in Rzeszow, 35-225 Rzeszów, Poland
| | - Angelika Zapał
- Institute of Biology, University of Rzeszow, 35-959 Rzeszów, Poland
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Gutiérrez-Ortega JS, Pérez-Farrera MA, Matsuo A, Sato MP, Suyama Y, Calonje M, Vovides AP, Kajita T, Watano Y. The phylogenetic reconstruction of the Neotropical cycad genus Ceratozamia (Zamiaceae) reveals disparate patterns of niche evolution. Mol Phylogenet Evol 2024; 190:107960. [PMID: 37918683 DOI: 10.1016/j.ympev.2023.107960] [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: 05/12/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023]
Abstract
The cycad genus Ceratozamia comprises 40 species from Mexico, Guatemala, Belize, and Honduras, where cycads occur throughout climatically varied montane habitats. Ceratozamia has the potential to reveal the history and processes of species diversification across diverse Neotropical habitats in this region. However, the species relationships within Ceratozamia and the ecological trends during its evolution remain unclear. Here, we aimed to clarify the phylogenetic relationships, the timing of clade and species divergences, and the niche evolution throughout the phylogenetic history of Ceratozamia. Genome-wide DNA sequences were obtained with MIG-seq, and multiple data-filtering steps were used to optimize the dataset used to construct an ultrametric species tree. Divergence times among branches and ancestral niches were estimated. The niche variation among species was evaluated, summarized into two principal components, and their ancestral states were reconstructed to test whether niche shifts among branches can be explained by random processes, under a Brownian Motion model. Ceratozamia comprises three main clades, and most species relationships within the clades were resolved. Ceratozamia has diversified since the Oligocene, with major branching events occurring during the Miocene. This timing is consistent with fossil evidence, the timing estimated for other Neotropical plant groups, and the major geological events that shaped the topographic and climatic variation in Mexico. Patterns of niche evolution in the genus do not accord with the Brownian Motion model. Rather, non-random evolution with shifts towards more seasonal environments at high latitudes, or shifts towards humid or dry environments at low latitudes explain the diversification of Ceratozamia. We present a comprehensive phylogenetic reconstruction for Ceratozamia and identify for the first time the environmental factors involved in clade and species diversification within the genus. This study alleviates the controversies regarding the species relationships in the genus and provides the first evidence that latitude-associated environmental factors may influence processes of niche evolution in cycads.
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Affiliation(s)
| | - Miguel Angel Pérez-Farrera
- Herbario Eizi Matuda, Laboratorio de Ecología Evolutiva, Instituto de Ciencias Biológicas, Universidad de Ciencias y Artes de Chiapas, Tuxtla Gutiérrez 29039, Mexico.
| | - Ayumi Matsuo
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
| | - Mitsuhiko P Sato
- Kazusa DNA Research Institute, 2-6-7 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Yoshihisa Suyama
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
| | | | - Andrew P Vovides
- Departamento de Biología Evolutiva, Instituto de Ecología, A.C., 91070 Xalapa, Mexico
| | - Tadashi Kajita
- Iriomote Station, Tropical Biosphere Research Center, University of the Ryukyus, Uehara, Yaeyama, Okinawa 907-1541, Japan
| | - Yasuyuki Watano
- Department of Biology, Graduate School of Science, Chiba University, Chiba 263-8522, Japan
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Tnah LH, Lee SL, Lee CT, Ng KKS, Ng CH, Zawiah N. DNA barcode identification of cultivated and wild tropical fruit species. 3 Biotech 2024; 14:7. [PMID: 38074292 PMCID: PMC10703749 DOI: 10.1007/s13205-023-03848-w] [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: 01/25/2023] [Accepted: 11/08/2023] [Indexed: 01/19/2024] Open
Abstract
With the rapid growth of the fruit industry worldwide, it is important to assess adulteration to ensure the authenticity and the safety of fruit products. The DNA barcoding approach offers a quick and accurate way of identifying and authenticating species. In this study, we developed reference DNA barcodes (rbcL, ITS2, and trnH-psbA) for 70 cultivated and wild tropical fruit species, representing 43 genera and 26 families. In terms of species recoverability, rbcL has a greater recoverability (100%) than ITS2 (95.7%) and trnH-psbA (88.6%). We evaluated the performance of these barcodes in species discrimination using similarity BLAST, phylogenetic tree, and barcoding gap analyses. The efficiency of rbcL, ITS2, and trnH-psbA in discriminating species was 80%, 100%, and 93.6%, respectively. We employed a multigene-tiered approach for species identification, with the rbcL region used for primary differentiation and ITS2 or trnH-psbA used for secondary differentiation. The two-locus barcodes rbcL + ITS2 and rbcL + trnH-psbA demonstrated robustness, achieving species discrimination rates of 100% and 94.3% respectively. Beyond the conventional species identification method based on plant morphology, the developed reference barcodes will aid the fruit agroindustry and trade, by making fruit-based product authentication possible. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03848-w.
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Affiliation(s)
- Lee Hong Tnah
- Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan Malaysia
| | - Soon Leong Lee
- Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan Malaysia
| | - Chai Ting Lee
- Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan Malaysia
| | - Kevin Kit Siong Ng
- Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan Malaysia
| | - Chin Hong Ng
- Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan Malaysia
| | - Ngah Zawiah
- Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan Malaysia
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Li Y, Cui M, Le X, Gong J, Jiang K, Tong X, Zhang Q, Li J, Li H, Lu L, Zou J, Wang R, Chen X. Genetic structure shows the presence of small-scale management units in a relict tree species. Ecol Evol 2023; 13:e10500. [PMID: 37706160 PMCID: PMC10495812 DOI: 10.1002/ece3.10500] [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: 02/09/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/15/2023] Open
Abstract
Identifying conservation units is crucial for the effective conservation of threatened species. Previous cases are almost exclusively based on large-scale but coarse sampling for genetic structure analyses. Significant genetic structure can occur within a small range, and thus multiple conservation units may exist in narrowly distributed plants. However, small-scale genetic structure is often overlooked in conservation planning especially for wind-pollinated and wind-dispersed trees, largely due to the absence of dense and elaborate sampling. In this study, we focused on a representative endangered relict plant, Metasequoia glyptostroboides. Using both nuclear microsatellites (nSSRs) and chloroplast DNA (cpDNA) fragments, we sampled across the narrow distribution range of this species and determined its conservation units by exploring its genetic structure and historical demography. cpDNA haplotypes were classified into two groups, but mixed in space, suggesting that the existent wild trees of M. glyptostroboides cannot be divided into different evolutionarily significant units. However, using nSSRs, we detected strong spatial genetic structure, with significant genetic differentiation and weak gene flow between the samples in the east of the species' distribution range and other samples. The divergence between the two nSSR groups was dated to the Last Glacial Maximum (c. 19.6 kya), suggesting that such spatial genetic structure has been maintained for a long term. Therefore, these two nSSR groups should be considered as different conservation units, that is, management units, to protect intergroup genetic variations, which is likely to be the outputs of local adaptation. Our findings highlight the necessity to reveal small-scale genetic structure and population demography to improve the conservation strategies of evolutionary potential of endangered plants.
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Affiliation(s)
- Yuan‐Yuan Li
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration, School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
- Institute of Eco‐Chongming (IEC)ShanghaiChina
| | - Min‐Yan Cui
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration, School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
| | - Xiao‐Wei Le
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration, School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
| | - Jun Gong
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration, School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
| | - Kai Jiang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration, School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
- Eastern China Conservation Centre for Wild Endangered Plant ResourcesShanghai Chenshan Botanical GardenShanghaiChina
| | - Xin Tong
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration, School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
- Eastern China Conservation Centre for Wild Endangered Plant ResourcesShanghai Chenshan Botanical GardenShanghaiChina
| | - Qian Zhang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration, School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of BotanyChinese Academy of SciencesBeijingChina
| | - Jia‐Hui Li
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration, School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
| | - Hong‐Yue Li
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration, School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
| | - Ling Lu
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration, School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
| | - Jie Zou
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration, School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
| | - Rong Wang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration, School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
- Shanghai Engineering Research Center of Sustainable Plant InnovationShanghaiChina
- Shanghai Institute of Pollution Control and Ecological SecurityShanghaiChina
| | - Xiao‐Yong Chen
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration, School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
- Shanghai Engineering Research Center of Sustainable Plant InnovationShanghaiChina
- Shanghai Institute of Pollution Control and Ecological SecurityShanghaiChina
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DNA Barcoding, Phylogenetic Analysis and Secondary Structure Predictions of Nepenthes ampullaria, Nepenthes gracilis and Nepenthes rafflesiana. Genes (Basel) 2023; 14:genes14030697. [PMID: 36980969 PMCID: PMC10048361 DOI: 10.3390/genes14030697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/02/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
Nepentheceae, the most prominent carnivorous family in the Caryophyllales order, comprises the Nepenthes genus, which has modified leaf trap characteristics. Although most Nepenthes species have unique morphologies, their vegetative stages are identical, making identification based on morphology difficult. DNA barcoding is seen as a potential tool for plant identification, with small DNA segments amplified for species identification. In this study, three barcode loci; ribulose-bisphosphate carboxylase (rbcL), intergenic spacer 1 (ITS1) and intergenic spacer 2 (ITS2) and the usefulness of the ITS1 and ITS2 secondary structure for the molecular identification of Nepenthes species were investigated. An analysis of barcodes was conducted using BLASTn, pairwise genetic distance and diversity, followed by secondary structure prediction. The findings reveal that PCR and sequencing were both 100% successful. The present study showed the successful amplification of all targeted DNA barcodes at different sizes. Among the three barcodes, rbcL was the least efficient as a DNA barcode compared to ITS1 and ITS2. The ITS1 nucleotide analysis revealed that the ITS1 barcode had more variations compared to ITS2. The mean genetic distance (K2P) between them was higher for interspecies compared to intraspecies. The results showed that the DNA barcoding gap existed among Nepenthes species, and differences in the secondary structure distinguish the Nepenthes. The secondary structure generated in this study was found to successfully discriminate between the Nepenthes species, leading to enhanced resolutions.
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Habib S, Gong Y, Dong S, Lindstrom A, Stevenson DW, Wu H, Zhang S. Phylotranscriptomics Shed Light on Intrageneric Relationships and Historical Biogeography of Ceratozamia (Cycadales). PLANTS (BASEL, SWITZERLAND) 2023; 12:478. [PMID: 36771563 PMCID: PMC9921377 DOI: 10.3390/plants12030478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/10/2023] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Ceratozamia Brongn. is one of the species-rich genera of Cycadales comprising 38 species that are mainly distributed in Mexico, with a few species reported from neighboring regions. Phylogenetic relationships within the genus need detailed investigation based on extensive datasets and reliable systematic approaches. Therefore, we used 30 of the known 38 species to reconstruct the phylogeny based on transcriptome data of 3954 single-copy nuclear genes (SCGs) via coalescent and concatenated approaches and three comparative datasets (nt/nt12/aa). Based on all these methods, Ceratozamia is divided into six phylogenetic subclades within three major clades. There were a few discrepancies regarding phylogenetic position of some species within these subclades. Using these phylogenetic trees, biogeographic history and morphological diversity of the genus are explored. Ceratozamia originated from ancestors in southern Mexico since the mid-Miocene. There is a distinct distribution pattern of species through the Trans-Mexican Volcanic Belt (TMVB), that act as a barrier for the species dispersal at TMVB and its southern and northern part. Limited dispersal events occurred during the late Miocene, and maximum diversification happened during the Pliocene epoch. Our study provides a new insight into phylogenetic relationships, the origin and dispersal routes, and morphological diversity of the genus Ceratozamia. We also explain how past climatic changes affected the diversification of this Mesoamerica-native genus.
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Affiliation(s)
- Sadaf Habib
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen 518004, China
| | - Yiqing Gong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen 518004, China
| | - Shanshan Dong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen 518004, China
| | - Anders Lindstrom
- Global Biodiversity Conservancy 144/124 Moo 3, Soi Bua Thong, Bangsalae, Sattahip, Chonburi 20250, Thailand
| | | | - Hong Wu
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Shouzhou Zhang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen 518004, China
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Primananda E, Sumeru Rinandio D, Rifqi Hariri M, Nurul Zulkarnaen R, Arifiani D, Robiansyah I. Rediscovery and Conservation of Actinodaphne quercina Blume (Lauraceae), an Endemic and Critically Endangered Tree Last Collected in 1841. J Nat Conserv 2023. [DOI: 10.1016/j.jnc.2023.126349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Molecular Characterization of Wild and Cultivated Strawberry (Fragaria × ananassa) through DNA Barcode Markers. Genet Res (Camb) 2022; 2022:9249561. [PMID: 36299683 PMCID: PMC9578897 DOI: 10.1155/2022/9249561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/16/2022] [Accepted: 09/27/2022] [Indexed: 12/02/2022] Open
Abstract
Background DNA barcoding is a useful technique for the identification, conservation, and diversity estimation at the species level in plants. The current research work was carried out to characterize selected Fragaria species from northern Pakistan using DNA barcode markers. Methodology. Initially, the efficacy of eight DNA barcode markers was analyzed based on the amplification and sequencing of the genome of selected Fragaria species. The resultant sequences were analyzed using BLAST, MEGA 7.0, and Bio Edit software. The phylogenetic tree was constructed by using Fragaria current species sequences and reference sequences through the neighbor-joining method or maximum likelihood method. Results Among eight DNA barcode markers, only two (ITS2 and rbclC) were amplified, and sequences were obtained. ITS2 sequence was BLAST in NCBI for related reference species which ranged from 89.79% to 90.05% along with Fragaria vesca (AF163517.1) which have 99.05% identity. Similarly, the rbclC sequence of Fragaria species was ranged from 96% to 99.58% along with Fragaria × ananassa (KY358226.1) which had 99.58% identity. Conclusion It is recommended that DNA barcode markers are a useful tool to identify the genetic diversity of a species. Moreover, this study could be helpful for the identification of the Fragaria species cultivated in other regions of the world.
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Wang J, Yan Z, Zhong P, Shen Z, Yang G, Ma L. Screening of universal DNA barcodes for identifying grass species of Gramineae. FRONTIERS IN PLANT SCIENCE 2022; 13:998863. [PMID: 36161013 PMCID: PMC9490308 DOI: 10.3389/fpls.2022.998863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
There is currently international interest in applying DNA barcoding as a tool for plant species discrimination and identification. In this study, we evaluated the utility of four candidate plant DNA barcoding regions [rbcL, matK, trnL-F, and internal transcribed spacer (ITS)] in seven genera of Gramineae including Agropyron, Bromus, Elymus, Elytrigia, Festuca, Leymus, and Lolium. Fourteen accessions were analyzed, and matK and ITS showed the highest species, subspecies, and variety discriminatory power, each resolving 11 accessions. Species discrimination using rbcL and trnL-F was lower, resolving 7 and 8 accessions, respectively. Subspecies and variety discrimination using rbcL and trnL-F could not identify 4 accessions of Agropyron. A technical system can be established using the proposed DNA barcode to rapidly and reliably identify the seven genera of Gramineae. This study serves as a "useful reference" for identifying the genetic diversity of grass germplasm resources. DNA barcoding can be utilized to uncover the relatives of different species within the same family or between different families. It can also be used to determine the related groups of important herbage, turfgrass, and crops and provide crucial background information for discovering excellent genes and improving existing crop varieties.
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Affiliation(s)
- Jianli Wang
- Pratacultural Science Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Zhenfei Yan
- College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Peng Zhong
- Branch of Animal Husbandry and Veterinary, Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Zhongbao Shen
- Pratacultural Science Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Guofeng Yang
- College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Lichao Ma
- College of Grassland Science, Qingdao Agricultural University, Qingdao, China
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Yao R, Guo R, Liu Y, Kou Z, Shi B. Identification and phylogenetic analysis of the genus Syringa based on chloroplast genomic DNA barcoding. PLoS One 2022; 17:e0271633. [PMID: 35853031 PMCID: PMC9295972 DOI: 10.1371/journal.pone.0271633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 07/05/2022] [Indexed: 11/25/2022] Open
Abstract
DNA barcoding is a supplementary tool in plant systematics that is extensively used to resolve species-level controversies. This study assesses the significance of using two DNA barcoding loci (e.g., psbA-trnH and trnC-petN) in distinguishing 33 plant samples of the genus Syringa. Results showed that the average genetic distance K2P of psbA-trnH DNA marker was 0.0521, which is much higher than that of trnC-petN, which is 0.0171. A neighbor-joining phylogenetic tree based on psbA-trnH and trnC-petN indicated that the identification rate of psbA-trnH and trnC-petN alone were 75% and 62.5%, respectively. The barcode combination of psbA-trnH+trnC-petN could identify 33 samples of the genus Syringa accurately and effectively with an identification rate of 87.5%. The 33 Syringa samples were divided into four groups: Group I is series Syringa represented by Syringa oblata; Group II is series Villosae represented by Syringa villosa; Group III is series Pubescentes represented by Syringa meyeri; and Group IV is section Ligustrina represented by Syringa reticulata subsp. pekinensis. These research results provided strong evidence that the combinatorial barcode of psbA-trnH+trnC-petN had high-efficiency identification ability and application prospects in species of the genus Syringa.
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Affiliation(s)
- Ruihong Yao
- College of Landscape Architecture and Tourism, Hebei Agricultural University, Baoding, P. R. China
| | - Runfang Guo
- Department of Bioengineering, Hebei Agricultural University, Baoding, P. R. China
| | - Yuguang Liu
- College of Landscape Architecture and Tourism, Hebei Agricultural University, Baoding, P. R. China
| | - Ziqian Kou
- College of Landscape Architecture and Tourism, Hebei Agricultural University, Baoding, P. R. China
| | - Baosheng Shi
- College of Landscape Architecture and Tourism, Hebei Agricultural University, Baoding, P. R. China
- * E-mail:
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Pinya T, Intharuksa A, Yanaso S, Kamnuan S, Phrutivorapongkul A. Conventional and molecular pharmacognostic characters integrated with chemical profiles of five Piper plants in the Thai herbal pharmacopoeia and their admixture/adulteration/substitution situations in Thailand. J Nat Med 2022; 76:605-620. [PMID: 35201516 DOI: 10.1007/s11418-022-01607-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/31/2022] [Indexed: 11/28/2022]
Abstract
The morphological and microscopy were combined with DNA-barcoding, together with rapid TLC for the characterization of Piper betle (PB), P. nigrum (PN), P. retrofractum (PR), P. sarmentosum (PS), and P. wallichii (PW), five medicinal Piper plants announced in the Thai Herbal Pharmacopoeia (THP). The authentic plants collected from various locations and voucher Piper products bought from commercial sites in Thailand were studied. The reproductive parts of authentic plants were subjected to ensure their morphological characters. Using sequencing analysis and genetic divergence for analyzing discriminatory performance, ITS2 was selected from eight candidate DNA markers to authenticate the origin of Piper crude drugs together with microscopic and TLC profiles for examining their characters, admixtures, adulterants, and substituents. PB and PR exhibited unique characters of the species, with no admixture, adulteration, and substitution. PN showed no variable characters of morphology and genetics. However, the microscopy could illustrate some commercial products of PN sold in Thailand have been adulterated with rice starch and roasted rice. In the herbal trade, PS has been sold in the form of mixed leaf, root, and stem more than the isolated part, but there is no variable character of the species. PW has shown more than one character of species explained by microscopic, chemical components, and genetic data. In conclusion, the conventional and molecular pharmacognostic data combined with chemical profile of authentic five Piper plants could be applied to indicate the plant origin and clarify the situations of admixture, adulteration, and substitution of the commercial Piper products launched in Thailand.
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Affiliation(s)
- Thawanratn Pinya
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Mueang, Chiang Mai, 50200, Thailand
| | - Aekkhaluck Intharuksa
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Mueang, Chiang Mai, 50200, Thailand
| | - Suthira Yanaso
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Mueang, Chiang Mai, 50200, Thailand.,Department of Pharmaceutical Chemistry and Pharmacognosy, Faculty of Pharmaceutical Sciences, Huachiew Chalermprakiet University, Bang Chalong, Bang Phli, Samutprakan, 10540, Thailand
| | - Suthiwat Kamnuan
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Mueang, Chiang Mai, 50200, Thailand
| | - Ampai Phrutivorapongkul
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Mueang, Chiang Mai, 50200, Thailand.
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12
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DNA Barcoding Medicinal Plant Species from Indonesia. PLANTS 2022; 11:plants11101375. [PMID: 35631799 PMCID: PMC9147630 DOI: 10.3390/plants11101375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 11/17/2022]
Abstract
Over the past decade, plant DNA barcoding has emerged as a scientific breakthrough and is often used to help with species identification or as a taxonomical tool. DNA barcoding is very important in medicinal plant use, not only for identification purposes but also for the authentication of medicinal products. Here, a total of 61 Indonesian medicinal plant species from 30 families and a pair of ITS2, matK, rbcL, and trnL primers were used for a DNA barcoding study consisting of molecular and sequence analyses. This study aimed to analyze how the four identified DNA barcoding regions (ITS2, matK, rbcL, and trnL) aid identification and conservation and to investigate their effectiveness for DNA barcoding for the studied species. This study resulted in 212 DNA barcoding sequences and identified new ones for the studied medicinal plant species. Though there is no ideal or perfect region for DNA barcoding of the target species, we recommend matK as the main region for Indonesian medicinal plant identification, with ITS2 and rbcL as alternative or complementary regions. These findings will be useful for forensic studies that support the conservation of medicinal plants and their national and global use.
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13
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Li F, Xie X, Huang R, Tian E, Li C, Chao Z. Chloroplast genome sequencing based on genome skimming for identification of Eriobotryae Folium. BMC Biotechnol 2021; 21:69. [PMID: 34895202 PMCID: PMC8666020 DOI: 10.1186/s12896-021-00728-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 12/06/2021] [Indexed: 12/02/2022] Open
Abstract
Background Whole chloroplast genome (cpDNA) sequence is becoming widely used in the phylogenetic studies of plant and species identification, but in most cases the cpDNA were acquired from silica gel dried fresh leaves. So far few reports have been available to describe cpDNA acquisition from crude drugs derived from plant materials, the DNA of which usually was seriously damaged during their processing. In this study, we retrieved cpDNA from the commonly used crude drug Eriobotryae Folium (Pipaye in Chinese, which is the dried leaves of Eriobotrya japonica, PPY) using genome skimming technique. Results We successfully recovered cpDNA sequences and rDNA sequences from the crude drug PPY, and bioinformatics analysis showed a high overall consistency between the cpDNA obtained from the crude drugs and fresh samples. In the ML tree, each species formed distinct monophyletic clades based on cpDNA sequence data, while the phylogenetic relationships between Eriobotrya species were poorly resolved based on ITS and ITS2. Conclusion Our results demonstrate that both cpDNA and ITS/ITS2 are effective for identifying PPY and its counterfeits derived from distantly related species (i.e. Dillenia turbinata and Magnolia grandiflora), but cpDNA is more effective for distinguishing the counterfeits derived from the close relatives of Eriobotrya japonica, suggesting the potential of genome skimming for retrieving cpDNA from crude drugs used in Traditional Chinese Medicine for their identification. Supplementary Information The online version contains supplementary material available at 10.1186/s12896-021-00728-0.
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Affiliation(s)
- Fang Li
- Department of Pharmacy, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China.,Faculty of Medicinal Plants and Pharmacognosy, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Xuena Xie
- Faculty of Medicinal Plants and Pharmacognosy, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Rong Huang
- Faculty of Medicinal Plants and Pharmacognosy, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Enwei Tian
- Faculty of Medicinal Plants and Pharmacognosy, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Chan Li
- Faculty of Medicinal Plants and Pharmacognosy, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Zhi Chao
- Faculty of Medicinal Plants and Pharmacognosy, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China. .,Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou, 510515, China.
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14
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Abstract
Growing popularity of herbal medicine has increased the demand of medicinal orchids in the global markets leading to their overharvesting from natural habitats for illegal trade. To stop such illegal trade, the correct identification of orchid species from their traded products is a foremost requirement. Different species of medicinal orchids are traded as their dried or fresh parts (tubers, pseudobulbs, stems), which look similar to each other making it almost impossible to identify them merely based on morphological observation. To overcome this problem, DNA barcoding could be an important method for accurate identification of medicinal orchids. Therefore, this research evaluated DNA barcoding of medicinal orchids in Asia where illegal trade of medicinal orchids has long existed. Based on genetic distance, similarity-based and tree-based methods with sampling nearly 7,000 sequences from five single barcodes (ITS, ITS2, matK, rbcL, trnH-psbA and their seven combinations), this study revealed that DNA barcoding is effective for identifying medicinal orchids. Among single locus, ITS performed the best barcode, whereas ITS + matK exhibited the most efficient barcode among multi-loci. A barcode library as a resource for identifying medicinal orchids has been established which contains about 7,000 sequences of 380 species (i.e. 90%) of medicinal orchids in Asia.
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15
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Philippe F, Dubrulle N, Marteaux B, Bonnet B, Choisy P, Berthon JY, Garnier L, Leconte N, Milesi S, Morvan PY, Saunois A, Sun JS, Weber S, Giraud N. Combining DNA Barcoding and Chemical fingerprints to authenticate Lavender raw material. Int J Cosmet Sci 2021; 44:91-102. [PMID: 34860432 PMCID: PMC9305429 DOI: 10.1111/ics.12757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/19/2021] [Accepted: 12/01/2021] [Indexed: 11/30/2022]
Abstract
Objective This study was initiated and conducted by several laboratories, 3 of the main cosmetic ingredient suppliers and 4 brands of cosmetics in France. Its objective is to show the interest and robustness of coupling chemical and genetic analyses in the identification of plant species. In this study, the Lavandula genus was used. Methods In this study, we used two analytical methods. Chemical analysis from UHPLC (ultra‐high‐performance liquid chromatography) and genetic analysis from barcoding with genetic markers. Results Eleven lavender species were selected (botanically authenticated) and analysed. The results show that three chemical compounds (coumaric acid hexoside, ferulic acid hexoside and rosmarinic acid) and three genetic markers (RbcL, trnH‐psbA and ITS) are of interest for the differentiation of species of the genus lavandula. Conclusion The results show that the combination of complementary analytical methods is a relevant system to prove the botanical identification of lavender species. This first study, carried out on a plant of interest for cosmetics, demonstrates the need for authentication using a tool combining genetic and chemical analysis as an advance over traditional investigation methods used alone, in terms of identification and authentication reliability.
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Affiliation(s)
- Florian Philippe
- DNA Gensee, 17 rue du lac saint andré, Le Bourget du Lac, 73370, France
| | - Nelly Dubrulle
- DNA Gensee, 17 rue du lac saint andré, Le Bourget du Lac, 73370, France
| | - Benjamin Marteaux
- DNA Gensee, 17 rue du lac saint andré, Le Bourget du Lac, 73370, France
| | | | | | | | | | | | | | | | | | - Jian-Sheng Sun
- Structure et Instabilite des Génomes, Muséum national d'Histoire naturelle, CNRS, INSERM, 43 rue Cuvier, Paris, 75005, France
| | | | - Nicole Giraud
- DNA Gensee, 17 rue du lac saint andré, Le Bourget du Lac, 73370, France
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16
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Alkaraki AK, Aldmoor MA, Lahham JN, Awad M. DNA Barcoding of Two Thymelaeaceae Species: Daphne mucronata Royle and Thymelaea hirsuta (L.) Endl. PLANTS 2021; 10:plants10102199. [PMID: 34686008 PMCID: PMC8537861 DOI: 10.3390/plants10102199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/30/2021] [Accepted: 10/11/2021] [Indexed: 11/16/2022]
Abstract
Daphne mucronata Royle and Thymelaea hirsuta (L.) Endl both belong to the Thymelaeaceae family. Both species are used traditionally to treat several diseases along with various daily applications by Jordanian Bedouins. Traditionally, those species are identified through personal proficiency, which could be misleading due to human errors or lack of expertise. This study aims to investigate an effective DNA barcoding method to identify and characterize Daphne mucronata Royle and Thymelaea hirsuta plant species at the molecular level. Daphne mucronata Royle and Thymelaea hirsuta were collected from the ancient city of Petra in the Southern part of Jordan. Sequences of candidate DNA barcodes were amplified (rbcL, matK, and rpoC1), sequenced, and aligned to the blastn database. Moreover, the obtained sequences were compared with available sequences of related species at the GenBank database. Our results showed that DNA barcoding successfully identifies the two plant species using any of chloroplast genes (rbcL, matK, or rpoC1). The results emphasize the ability of DNA barcoding for identifying and characterizing different plant species through the recruitment of different barcode loci in molecular identification.
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Affiliation(s)
- Almuthanna K. Alkaraki
- Department of Biological Sciences, Faculty of Science, Yarmouk University, Irbid 21163, Jordan; (M.A.A.); (J.N.L.)
- Correspondence:
| | - Maisam A. Aldmoor
- Department of Biological Sciences, Faculty of Science, Yarmouk University, Irbid 21163, Jordan; (M.A.A.); (J.N.L.)
| | - Jamil N. Lahham
- Department of Biological Sciences, Faculty of Science, Yarmouk University, Irbid 21163, Jordan; (M.A.A.); (J.N.L.)
| | - Mohammed Awad
- Department of Biotechnology, Faculty of Agriculture, Al-Azhar University, Cairo 11651, Egypt;
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17
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Azizi MMF, Lau HY, Abu-Bakar N. Integration of advanced technologies for plant variety and cultivar identification. J Biosci 2021. [DOI: 10.1007/s12038-021-00214-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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18
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Egydio Brandão APM, Yamaguchi LF, Tepe EJ, Salatino A, Kato MJ. Evaluation of DNA markers for molecular identification of three Piper species from Brazilian Atlantic Rainforest. PLoS One 2020; 15:e0239056. [PMID: 33075070 PMCID: PMC7571689 DOI: 10.1371/journal.pone.0239056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 08/28/2020] [Indexed: 01/08/2023] Open
Abstract
Piper is one of two large genera in the Piperaceae, and with ca. 2600 species, is one of the largest plant genera in the world. Species delimitation and evaluation of genetic diversity among populations are important requisites for conservation and adequate exploitation of economically important species. DNA barcoding has been used as a powerful tool and a practical method for species characterization and delimitation. The present work aims to evaluate molecular markers for barcoding three Piper species native to Brazil: P. gaudichaudianum (“jaborandi” or “pariparoba”), P. malacophyllum (“pariparoba-murta”) and P. regnellii (“caapeba” or “pariparoba”). A reference DNA barcode library was developed using sequences of three candidate regions: ITS2, trnH-psbA and rbcL. Transferability of the microsatellite (SSR) primers Psol 3, Psol 6 and Psol 10, designed originally for Piper solmsianum, to the three Piper species was also evaluated. The discriminatory power of the markers was based on the determination of inter- and intraspecific distances, phylogenetic reconstruction, and clustering analysis, as well as BLASTn comparison. Sequences of ITS2 enabled efficient species identification by means of the BLASTn procedure. Based on these sequences, intraspecific divergence was lower than interspecific variation. Maximum Parsimony analyses based on ITS2 sequences provided three resolved clades, each corresponding to one of the three analysed species. Sequences of trnH-psbA and rbcL had lower discriminatory value. Analyses combining sequences of these regions were less effective toward the attainment of resolved and strongly supported clades of all species. In summary, robustly supported clades of P. regnellii were obtained in most of the analyses, based either on isolated or combined sequences. The SSRs primers Psol 3, Psol 6 and Psol 10 were shown to be transferable to P. gaudichaudianum and P. regnellii, but not to P. malacophyllum. Preliminary cluster analyses based on the polymorphism of the amplified products suggested that Psol 3 has lower potential than Psol 6 and Psol 10 for discrimination of Piper species.
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Affiliation(s)
| | - Lydia F. Yamaguchi
- Institute of Chemistry, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Eric J. Tepe
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Antonio Salatino
- Department of Botany, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Massuo J. Kato
- Institute of Chemistry, University of São Paulo, São Paulo, São Paulo, Brazil
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19
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Kurian A, Dev SA, Sreekumar VB, Muralidharan EM. The low copy nuclear region, RPB2 as a novel DNA barcode region for species identification in the rattan genus Calamus (Arecaceae). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1875-1887. [PMID: 32943823 PMCID: PMC7468035 DOI: 10.1007/s12298-020-00864-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 07/30/2020] [Accepted: 08/10/2020] [Indexed: 06/11/2023]
Abstract
Taxonomic complexities, like environmental plasticity and homoplasy, make precise identification challenging in Calamus, the genus of spiny climbing palms of the subfamily Calamoideae (Arecaceae). In the present study, the species discriminatory power of twelve potential DNA barcode regions (rbcL, matK, psbA-trnH, rpoC, rpoB, psbK-psbI, atpF-atpH, psbZ-trnfM, ITS1, ITS2, PRK, and RPB2) were evaluated in 21 species of Calamus from the Western Ghats region of India, using distance, tree, and similarity based statistical methods. Except for the low copy nuclear region, RPB2, none of the tested plastid loci or nuclear loci ITS, either singly or in combinations, could discriminate all the species of Calamus due to low substitution rate of plastid regions and multiple copies of ITS respectively. The RPB2 locus showed highest species resolution with 96% accuracy in similarity based analysis, indicating its potential and efficiency as a barcode locus for the genus. The putative "Calamus gamblei complex" based on overlapping morphology was successfully resolved as six distinct, though closely related, species. The analysis also indicates that C. delessertianus is a morphological variant of C. dransfieldii. In spite of being a low copy nuclear gene region, RPB2 provided an efficient barcode to delineate Calamus species and has the potential to further extend its use as a prospective barcode to other Palm genera.
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Affiliation(s)
- Anoja Kurian
- Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala 680653 India
| | - Suma Arun Dev
- Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala 680653 India
| | | | - E. M. Muralidharan
- Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala 680653 India
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20
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Ismail M, Ahmad A, Nadeem M, Javed MA, Khan SH, Khawaish I, Sthanadar AA, Qari SH, Alghanem SM, Khan KA, Khan MF, Qamer S. Development of DNA barcodes for selected Acacia species by using rbcL and matK DNA markers. Saudi J Biol Sci 2020; 27:3735-3742. [PMID: 33304185 PMCID: PMC7715041 DOI: 10.1016/j.sjbs.2020.08.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/28/2020] [Accepted: 08/11/2020] [Indexed: 12/13/2022] Open
Abstract
Acacia species are very important tree species in tropical and subtropical countries of the World for their economic and medicinal benefits. Precise identification of Acacia is very important to distinguish the invasive species from rare species however, it is difficult to differentiate Acacia species based on morphological charcters. In addition, precise identification is also important for wood charcterization in the forest industry as these species are declining due to illegal logging and deforestation. To overcome thsese limitations of morphological identification, DNA barcoding is being used as an efficient and quick approach for precise identification of tree species. In this study, we selected two chloroplast and plastid base DNA markers (rbcL and matK) for the identification of five selected tree species of Acacia (A. albida, A. ampliceps, A. catechu, A. coriacea and A. tortilis). The genomic DNA of the selected Acacia species was extracted, amplified through PCR using specific primers and subsequently sequenced through Sanger sequencing. In matK DNA marker the average AT nucleotide contents were higher (59.46%) and GC contents were lower (40.44%) as compared to the AT (55.40%) and GC content (44.54%) in rbcL marker. The means genetic distance K2P between the Acacia species was higher in matK (0.704%) as compared to rbcL (0.230%). All Acacia species could be identified based on unique SNPs profile. Based on SNP data profiles, DNA sequence based scannable QR codes were developed for accurate identification of Acacia species. The phylogenetic analysis based on both markers (rbcL and matK) showed that both A. coriacea and A. tortilis were closely related with each other and clustered in the same group while other two species A. albida and A. catechu were grouped together. The specie A. ampliceps remained ungrouped distantly, compared with other four species. These finding highlights the potential of DNA barcoding for efficient and reproducible identification of Acacia species.
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Affiliation(s)
- Muhammad Ismail
- Department of Forestry and Range Management, Faculty of Agriculture, University of Agriculture Faisalabad, Pakistan
| | - Aftab Ahmad
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad, Pakistan.,Department of Biochemistry, Faculty of Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Nadeem
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad, Pakistan.,Department of Biochemistry, Faculty of Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Asif Javed
- Department of Forestry and Range Management, Faculty of Agriculture, University of Agriculture Faisalabad, Pakistan.,Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad, Pakistan
| | - Sultan Habibullah Khan
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad, Pakistan.,Center for Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Iqra Khawaish
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad, Pakistan.,Department of Biochemistry, Faculty of Sciences, University of Agriculture, Faisalabad, Pakistan
| | | | - Sameer H Qari
- Biology Department, Aljumum, University College, Umm Al-Qura University, Saudi Arabia
| | - Suliman M Alghanem
- Biology Department, Faculty of Science, Tabuk University, Tabuk 71491, Saudi Arabia
| | - Khalid Ali Khan
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia.,Unit of Bee Research and Honey Production, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia.,Biology Department, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | | | - Samina Qamer
- Department of Zoology, Government College University, Faisalabad, Pakistan
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21
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DNA barcodes for delineating Clerodendrum species of North East India. Sci Rep 2020; 10:13490. [PMID: 32778674 PMCID: PMC7417596 DOI: 10.1038/s41598-020-70405-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/06/2020] [Indexed: 01/06/2023] Open
Abstract
The diversified genus of Clerodendrum with its complex evolutionary history leads to taxonomic mystification. Unlike traditional taxonomic methods, DNA barcoding could be a promising tool for the identification and conservation of Clerodendrum species. This study was attempted to develop an efficient barcode locus in Clerodendrum species of North East India. We evaluated four barcode candidates (ITS2, matK, rbcL, ycf1) and its combinations in different Clerodendrum species. The reliability of barcodes to distinguish the species were calculated using genetic pairwise distances, intra- and inter-specific diversity, barcode gap, and phylogenetic tree-based methods. The results exemplify that matK posse’s maximum number of variables and parsimony-informative sites (103/100), intra- (0.021 ± 0.001) and inter- (0.086 ± 0.005) specific divergences and species resolution rate (89.1%) followed by ITS2, ycf1, and rbcL. Among the combinatorial locus, ITS2 + matK showed the best species discrimination with distinctive barcode gaps. Therefore, we tentatively suggest that the combination of ITS2 + matK as core barcode for Clerodendrum and converted into quick response (QR) code. Hence, this finding indicates that DNA barcoding could provide consistent resources for species discrimination and resolve taxonomic controversies of the genus as well as set a preliminary assessment toward its biodiversity.
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22
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Mir RA, Bhat KA, Rashid G, Ebinezer LB, Masi A, Rakwal R, Shah AA, Zargar SM. DNA barcoding: a way forward to obtain deep insights about the realistic diversity of living organisms. THE NUCLEUS 2020. [DOI: 10.1007/s13237-020-00330-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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23
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Gostel MR, Zúñiga JD, Kress WJ, Funk VA, Puente-Lelievre C. Microfluidic Enrichment Barcoding (MEBarcoding): a new method for high throughput plant DNA barcoding. Sci Rep 2020; 10:8701. [PMID: 32457375 PMCID: PMC7250904 DOI: 10.1038/s41598-020-64919-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 04/20/2020] [Indexed: 11/24/2022] Open
Abstract
DNA barcoding is a valuable tool to support species identification with broad applications from traditional taxonomy, ecology, forensics, food analysis, and environmental science. We introduce Microfluidic Enrichment Barcoding (MEBarcoding) for plant DNA Barcoding, a cost-effective method for high-throughput DNA barcoding. MEBarcoding uses the Fluidigm Access Array to simultaneously amplify targeted regions for 48 DNA samples and hundreds of PCR primer pairs (producing up to 23,040 PCR products) during a single thermal cycling protocol. As a proof of concept, we developed a microfluidic PCR workflow using the Fluidigm Access Array and Illumina MiSeq. We tested 96 samples for each of the four primary DNA barcode loci in plants: rbcL, matK, trnH-psbA, and ITS. This workflow was used to build a reference library for 78 families and 96 genera from all major plant lineages - many currently lacking in public databases. Our results show that this technique is an efficient alternative to traditional PCR and Sanger sequencing to generate large amounts of plant DNA barcodes and build more comprehensive barcode databases.
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Affiliation(s)
- Morgan R Gostel
- Botanical Research Institute of Texas, Fort Worth, Texas, 76107-3400, USA.
| | - Jose D Zúñiga
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, 20892, USA
| | - W John Kress
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Vicki A Funk
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013-7012, USA
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24
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Duan H, Wang W, Zeng Y, Guo M, Zhou Y. The screening and identification of DNA barcode sequences for Rehmannia. Sci Rep 2019; 9:17295. [PMID: 31754140 PMCID: PMC6872558 DOI: 10.1038/s41598-019-53752-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 11/04/2019] [Indexed: 11/09/2022] Open
Abstract
In this study, ITS, ITS2, matK, rbcL and psbA-trnH in Rehmannia were successfully amplified and sequenced, but some ITS sequences need to be proofread according to ITS2 sequences. Compared with rbcL, matK and psbA-trnH, ITS and ITS2 had higher mutation rate and more information sites, and ITS2 had higher interspecific diversity and lower intraspecific variation in Rehmannia, but the interspecific genetic variation of rbcL and matK was lower. Furthermore, the obvious barcoding gap was found in psbA-trnH or ITS2 + psbA-trnH, and the overlap between interspecific and intraspecific variation of ITS, ITS2 or matK was less. In addition, the phylogenetic tree based on ITS or ITS2 indicated that R. glutinosa, R. chingii or R. henryi with obvious monophyly could be successfully identified, but R. piasezkii and R. elata were clustered into one branch, R. solanifolia could not be distinguished from R. glutinosa, and R. chingii was closer to R. henryi. In phylogenetic tree based on psbA-trnH or ITS2 + psbA-trnH, cultivars and wild varieties of R. glutinosa could be distinguished, were clearly separated from other Rehmannia species, and cultivars or wild varieties of R. glutinosa could be also distinguished by matK. Taken together, ITS2 has great potential in systematic study and species identification of Rehmannia, the combination of ITS2 and psbA-trnH might be the most suitable DNA barcode for Rehmannia species.
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Affiliation(s)
- Hongying Duan
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Wanshen Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Yunpeng Zeng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Mengmeng Guo
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Yanqing Zhou
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China.
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25
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Valente Valente D, Aguiar Saraiva Câmara PE, Peralta DF, Stech M. Molecular tools to identify tropical mosses: a case study of the Brazilian species of Schlotheimia Brid. (Bryophyta, Orthotrichaceae). SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2019.1655110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Daiane Valente Valente
- Universidade de Brasília (UnB), Departamento de Botânica, Laboratório de Criptógamas, Brasília, DF, Brazil
| | | | | | - Michael Stech
- Naturalis Biodiversity Center, Leiden, the Netherlands
- Leiden University, Leiden, the Netherlands
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26
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Santamaria M, Fosso B, Licciulli F, Balech B, Larini I, Grillo G, De Caro G, Liuni S, Pesole G. ITSoneDB: a comprehensive collection of eukaryotic ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences. Nucleic Acids Res 2019; 46:D127-D132. [PMID: 29036529 PMCID: PMC5753230 DOI: 10.1093/nar/gkx855] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 09/18/2017] [Indexed: 01/21/2023] Open
Abstract
A holistic understanding of environmental communities is the new challenge of metagenomics. Accordingly, the amplicon-based or metabarcoding approach, largely applied to investigate bacterial microbiomes, is moving to the eukaryotic world too. Indeed, the analysis of metabarcoding data may provide a comprehensive assessment of both bacterial and eukaryotic composition in a variety of environments, including human body. In this respect, whereas hypervariable regions of the 16S rRNA are the de facto standard barcode for bacteria, the Internal Transcribed Spacer 1 (ITS1) of ribosomal RNA gene cluster has shown a high potential in discriminating eukaryotes at deep taxonomic levels. As metabarcoding data analysis rely on the availability of a well-curated barcode reference resource, a comprehensive collection of ITS1 sequences supplied with robust taxonomies, is highly needed. To address this issue, we created ITSoneDB (available at http://itsonedb.cloud.ba.infn.it/) which in its current version hosts 985 240 ITS1 sequences spanning over 134 000 eukaryotic species. Each ITS1 is mapped on the NCBI reference taxonomy with its start and end positions precisely annotated. ITSoneDB has been developed in agreement to the FAIR guidelines by enabling the users to query and download its content through a simple web-interface and access relevant metadata by cross-linking to European Nucleotide Archive.
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Affiliation(s)
- Monica Santamaria
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari 70126, Italy
| | - Bruno Fosso
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari 70126, Italy
| | - Flavio Licciulli
- Institute of Biomedical Technologies, Consiglio Nazionale delle Ricerche, Bari 70126, Italy
| | - Bachir Balech
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari 70126, Italy
| | - Ilaria Larini
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari 'A. Moro', Bari 70126, Italy
| | - Giorgio Grillo
- Institute of Biomedical Technologies, Consiglio Nazionale delle Ricerche, Bari 70126, Italy
| | - Giorgio De Caro
- Institute of Biomedical Technologies, Consiglio Nazionale delle Ricerche, Bari 70126, Italy
| | - Sabino Liuni
- Institute of Biomedical Technologies, Consiglio Nazionale delle Ricerche, Bari 70126, Italy
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari 70126, Italy.,Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari 'A. Moro', Bari 70126, Italy
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Yang J, Feng L, Yue M, He YL, Zhao GF, Li ZH. Species delimitation and interspecific relationships of the endangered herb genus Notopterygium inferred from multilocus variations. Mol Phylogenet Evol 2019; 133:142-151. [PMID: 30639766 DOI: 10.1016/j.ympev.2019.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 12/28/2018] [Accepted: 01/01/2019] [Indexed: 01/29/2023]
Abstract
Species identification and discrimination is the basis of biodiversity research. In general, it is considered that numerous nucleotide variations (e.g., whole chloroplast genomes) can identify species with higher resolution than a few loci, e.g., partial chloroplast or nuclear gene fragments. In this study, we tested this hypothesis by sampling population genetics samples of the endangered herb genus Notopterygium. We sequenced the complete plastomes, five nuclear gene regions, three chloroplast DNA fragments, and a nuclear internal transcribed spacer (nrITS) region for 18 populations sampled throughout most of the geographic ranges of all six Notopterygium species. Species identification analysis showed that four DNA barcodes (matK, rbcL, trnS-trnG, and nrITS) and/or combinations of these markers achieved Notopterygium species discrimination at higher resolution than the general plastomes and nuclear gene sequences. In particular, nrITS had the highest discriminatory power among all of the individual markers. Molecular data sets and morphological evidence indicated that all six Notopterygium species could be reclassified unambiguously to four putative species clades. N. oviforme and N. franchetii had the closest relationship. Molecular dating showed that the origin and divergence of Notopterygium species was significantly associated with geological and climatic fluctuations during the middle of the Pliocene. In conclusion, our results suggest that a few nucleotide variations can achieve species discrimination with higher resolution than numerous plastomes and general nuclear gene fragments when discerning related Notopterygium species.
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Affiliation(s)
- Jiao Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Li Feng
- School of Pharmacy, Xi'an Jiaotong University, Xi'an 710061, China
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Yan-Ling He
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Gui-Fang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
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DNA Barcoding Analysis and Phylogenetic Relation of Mangroves in Guangdong Province, China. FORESTS 2019. [DOI: 10.3390/f10010056] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Mangroves are distributed in the transition zone between sea and land, mostly in tropical and subtropical areas. They provide important ecosystem services and are therefore economically valuable. DNA barcoding is a useful tool for species identification and phylogenetic reconstruction. To evaluate the effectiveness of DNA barcoding in identifying mangrove species, we sampled 135 individuals representing 23 species, 22 genera, and 17 families from Zhanjiang, Shenzhen, Huizhou, and Shantou in the Guangdong province, China. We tested the universality of four DNA barcodes, namely rbcL, matK, trnH-psbA, and the internal transcribed spacer of nuclear ribosomal DNA (ITS), and examined their efficacy for species identification and the phylogenetic reconstruction of mangroves. The success rates for PCR amplification of rbcL, matK, trnH-psbA, and ITS were 100%, 80.29% ± 8.48%, 99.38% ± 1.25%, and 97.18% ± 3.25%, respectively, and the rates of DNA sequencing were 100%, 75.04% ± 6.26%, 94.57% ± 5.06%, and 83.35% ± 4.05%, respectively. These results suggest that both rbcL and trnH–psbA are universal in mangrove species from the Guangdong province. The highest success rate for species identification was 84.48% ± 12.09% with trnH-psbA, followed by rbcL (82.16% ± 9.68%), ITS (66.48% ± 5.97%), and matK (65.09% ± 6.00%), which increased to 91.25% ± 9.78% with the addition of rbcL. Additionally, the identification rate of mangroves was not significantly different between rbcL + trnH-psbA and other random fragment combinations. In conclusion, rbcL and trnH-psbA were the most suitable DNA barcode fragments for species identification in mangrove plants. When the phylogenetic relationships were constructed with random fragment combinations, the optimal evolutionary tree with high supporting values (86.33% ± 4.16%) was established using the combination of matK + rbcL + trnH-psbA + ITS in mangroves. In total, the 476 newly acquired sequences in this study lay the foundation for a DNA barcode database of mangroves.
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A Systematic Study on DNA Barcoding of Medicinally Important Genus Epimedium L. (Berberidaceae). Genes (Basel) 2018; 9:genes9120637. [PMID: 30563021 PMCID: PMC6316794 DOI: 10.3390/genes9120637] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 12/05/2018] [Accepted: 12/10/2018] [Indexed: 01/28/2023] Open
Abstract
Genus Epimedium consists of approximately 50 species in China, and more than half of them possess medicinal properties. The high similarity of species’ morphological characteristics complicates the identification accuracy, leading to potential risks in herbal efficacy and medical safety. In this study, we tested the applicability of four single loci, namely, rbcL, psbA-trnH, internal transcribed spacer (ITS), and ITS2, and their combinations as DNA barcodes to identify 37 Epimedium species on the basis of the analyses, including the success rates of PCR amplifications and sequencing, specific genetic divergence, distance-based method, and character-based method. Among them, character-based method showed the best applicability for identifying Epimedium species. As for the DNA barcodes, psbA-trnH showed the best performance among the four single loci with nine species being correctly differentiated. Moreover, psbA-trnH + ITS and psbA-trnH + ITS + rbcL exhibited the highest identification ability among all the multilocus combinations, and 17 species, of which 12 are medicinally used, could be efficiently discriminated. The DNA barcode data set developed in our study contributes valuable information to Chinese resources of Epimedium. It provides a new means for discrimination of the species within this medicinally important genus, thus guaranteeing correct and safe usage of Herba Epimedii.
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Li S, Qian X, Zheng Z, Shi M, Chang X, Li X, Liu J, Tu T, Zhang D. DNA barcoding the flowering plants from the tropical coral islands of Xisha (China). Ecol Evol 2018; 8:10587-10593. [PMID: 30464830 PMCID: PMC6238132 DOI: 10.1002/ece3.4545] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 07/19/2018] [Accepted: 08/09/2018] [Indexed: 12/14/2022] Open
Abstract
AIM DNA barcoding has been widely applied to species diversity assessment in various ecosystems, including temperate forests, subtropical forests, and tropical rain forests. However, tropical coral islands have never been barcoded before due to the difficulties in field exploring. This study aims at barcoding the flowering plants from a unique ecosystem of the tropical coral islands in the Pacific Ocean and supplying valuable evolutionary information for better understanding plant community assembly of those particular islands in the future. LOCATION Xisha Islands, China. METHODS This study built a DNA barcode database for 155 plant species from the Xisha Islands using three DNA markers (ITS, rbcL, and matK). We applied the sequence similarity method and a phylogenetic-based method to assess the barcoding resolution. RESULTS All the three DNA barcodes showed high levels of PCR success (96%-99%) and sequencing success (98%-100%). ITS performed the highest rate of species resolution (>95%) among the three markers, while plastid markers delivered a relatively poor species resolution (85%-90%). Our analyses obtained a marginal increase in species resolution when combining the three DNA barcodes. MAIN CONCLUSIONS This study provides the first plant DNA barcode data for the unique ecosystem of tropical coral islands and considerably supplements the DNA barcode library for the flowering plants on the oceanic islands. Based on the PCR and sequencing success rates, and the discriminatory power of the three DNA regions, we recommend ITS as the most successful DNA barcode to identify the flowering plants from Xisha Islands. Due to its high sequence variation and low fungal contamination, ITS could be a preferable candidate of DNA barcode for plants from other tropical coral islands as well. Our results also shed lights on the importance of biodiversity conservation of tropical coral islands.
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Affiliation(s)
- Shengchun Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xin Qian
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zexin Zheng
- South China Agricultural UniversityGuangzhouChina
| | - Miaomiao Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
| | - Xiaoyu Chang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
| | - Xiaojuan Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Junfang Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Tieyao Tu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
| | - Dianxiang Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
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Nadarajan J, Benson EE, Xaba P, Harding K, Lindstrom A, Donaldson J, Seal CE, Kamoga D, Agoo EMG, Li N, King E, Pritchard HW. Comparative Biology of Cycad Pollen, Seed and Tissue - A Plant Conservation Perspective. THE BOTANICAL REVIEW; INTERPRETING BOTANICAL PROGRESS 2018; 84:295-314. [PMID: 30174336 PMCID: PMC6105234 DOI: 10.1007/s12229-018-9203-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Cycads are the most endangered of plant groups based on IUCN Red List assessments; all are in Appendix I or II of CITES, about 40% are within biodiversity 'hotspots,' and the call for action to improve their protection is long-standing. We contend that progress in this direction will not be made until there is better understanding of cycad pollen, seed and tissue biology, which at the moment is limited to relatively few (<10%) species. We review what is known about germplasm (seed and pollen) storage and germination, together with recent developments in the application of contemporary technologies to tissues, such as isotype labelling, biomolecular markers and tissue culture. Whilst progress is being made, we conclude that an acceleration of comparative studies is needed to facilitate the integration of in situ and ex situ conservation programmes to better safeguard endangered cycads.
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Affiliation(s)
- J. Nadarajan
- Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, West Sussex RH17 6TN UK
- Present Address: The New Zealand Institute for Plant & Food Research Ltd, Private Bag 11600, Palmerston North, 4442 New Zealand
| | - E. E. Benson
- Damar Research Scientists, Damar, Cuparmuir, Fife, KY15 5RJ UK
| | - P. Xaba
- South African National Biodiversity Institute, Kirstenbosch National Botanical Garden, Cape Town, Republic of South Africa
| | - K. Harding
- Damar Research Scientists, Damar, Cuparmuir, Fife, KY15 5RJ UK
| | - A. Lindstrom
- Nong Nooch Tropical Botanical Garden, Chonburi, 20250 Thailand
| | - J. Donaldson
- South African National Biodiversity Institute, Kirstenbosch National Botanical Garden, Cape Town, Republic of South Africa
| | - C. E. Seal
- Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, West Sussex RH17 6TN UK
| | - D. Kamoga
- Joint Ethnobotanical Research Advocacy, P.O.Box 27901, Kampala, Uganda
| | | | - N. Li
- Fairy Lake Botanic Garden, Shenzhen, Guangdong People’s Republic of China
| | - E. King
- UNEP-World Conservation Monitoring Centre, Cambridge, UK
| | - H. W. Pritchard
- Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, West Sussex RH17 6TN UK
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Divide and conquer! Data-mining tools and sequential multivariate analysis to search for diagnostic morphological characters within a plant polyploid complex (Veronica subsect. Pentasepalae, Plantaginaceae). PLoS One 2018; 13:e0199818. [PMID: 29958275 PMCID: PMC6025878 DOI: 10.1371/journal.pone.0199818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 06/14/2018] [Indexed: 11/19/2022] Open
Abstract
This study exhaustively explores leaf features seeking diagnostic characters to aid the classification (assigning cases to groups, i.e. populations to taxa) in a polyploid plant-species complex. A challenging case study was selected: Veronica subsection Pentasepalae, a taxonomically intricate group. The “divide and conquer” approach was implemented—that is, a difficult primary dataset was split into more manageable subsets. Three techniques were explored: two data-mining tools (artificial neural networks and decision trees) and one unsupervised discriminant analysis. However, only the decision trees and discriminant analysis were finally used to select diagnostic traits. A previously established classification hypothesis based on other data sources was used as a starting point. A guided discriminant analysis (i.e. involving manual character selection) was used to produce a grouping scheme fitting this hypothesis so that it could be taken as a reference. Sequential unsupervised multivariate analysis enabled the recognition of all species and infraspecific taxa; however, a suboptimal classification rate was achieved. Decision trees resulted in better classification rates than unsupervised multivariate analysis, but three complete taxa were misidentified (not present in terminal nodes). The variable selection led to a different grouping scheme in the case of decision trees. The resulting groups displayed low misclassification rates when analyzed using artificial neural networks. The decision trees as well as the discriminant analysis are recommended in the search of diagnostic characters. Due to the high sensitivity that artificial neural networks have to the combination of input/output layers, they are proposed as evaluation tools for morphometric studies. The “divide and conquer” principle is a promising strategy, providing success in the present case study.
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Zhao L, Feng S, Tian J, Wei A, Yang T. Internal transcribed spacer 2 (ITS2) barcodes: A useful tool for identifying Chinese Zanthoxylum. APPLICATIONS IN PLANT SCIENCES 2018; 6:e01157. [PMID: 30131899 PMCID: PMC6025816 DOI: 10.1002/aps3.1157] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 03/30/2018] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY The genus Zanthoxylum in the Rutaceae family of trees and shrubs has a long history of domestication and cultivation in Asia for both economic and medicinal purposes. However, many Zanthoxylum species are morphologically similar and are easily confused. This often leads to false authentication of source materials and confusion in herbal markets, hindering their safe utilization and genetic resource conservation. DNA barcoding is a promising tool for identifying plant taxa. METHODS We used three candidate DNA barcoding regions (ITS2, ETS, and trnH-psbA) to identify 69 accessions representing 13 Chinese Zanthoxylum species. The discriminatory capabilities of these regions were evaluated in terms of PCR amplification success, intra- and interspecific divergence, DNA barcoding gaps, and identification efficiency using the BLAST and tree-building methods. RESULTS ITS2 proved the most useful for discriminating Chinese Zanthoxylum species, with a correct identification rate of 100%, and this region also exhibited significantly higher intra- and interspecific divergence. DISCUSSION Phylogenetic analysis confirmed that ITS2 has a powerful discriminatory ability both at and below the species level. We confirmed that ITS2 is a powerful barcoding region for identifying Chinese Zanthoxylum species, and will be useful for analyzing and managing Chinese Zanthoxylum germplasm collections.
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Affiliation(s)
- Li‐Li Zhao
- College of ForestryNorthwest A&F UniversityYanglingShaanxi712100People's Republic of China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry AdministrationYanglingShaanxi712100People's Republic of China
| | - Shi‐Jing Feng
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry AdministrationYanglingShaanxi712100People's Republic of China
- College of Life ScienceNorthwest A&F UniversityYanglingShaanxi712100People's Republic of China
| | - Jie‐Yun Tian
- College of ForestryNorthwest A&F UniversityYanglingShaanxi712100People's Republic of China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry AdministrationYanglingShaanxi712100People's Republic of China
| | - An‐Zhi Wei
- College of ForestryNorthwest A&F UniversityYanglingShaanxi712100People's Republic of China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry AdministrationYanglingShaanxi712100People's Republic of China
| | - Tu‐Xi Yang
- College of ForestryNorthwest A&F UniversityYanglingShaanxi712100People's Republic of China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry AdministrationYanglingShaanxi712100People's Republic of China
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Osathanunkul M, Osathanunkul R, Madesis P. Species identification approach for both raw materials and end products of herbal supplements from Tinospora species. BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2018; 18:111. [PMID: 29587839 PMCID: PMC5870811 DOI: 10.1186/s12906-018-2174-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 03/15/2018] [Indexed: 02/08/2023]
Abstract
Background Nowadays herbal products used in traditional medicine are sold in processed forms and thus morphological authentication is almost impossible. With herbal industry rapidly growing size, consumer safety becomes an important issue that requires special attention. Identification of herbal species in the products is therefore needed. Methods Sequences from the selected regions (matK, rbcL, trnL and ITS1) were retrieved and analysed. Then the most suitable barcode was assessed for discrimination of T. crispa from closely related species by HRM analysis and used in authentication of commercial products. Results The ITS1 barcode was found to be the suitable primer as melting data from the HRM assay proved to be capable of distinguishing T. crispa from its related species. The developed protocol was then employed to authenticate medicinal products in powdered form. HRM analysis of all tested samples here revealed that five out of eight products contained not only the indicated species T. crispa but also other Tinospora, that have a high level of morphological similarity. Conclusion Misrepresentation, poor packaging and inappropriate labeling of the tested medicinal herbal products are thought to be the reason of the results here. Using Bar-HRM with the ITS marker lead to success in authenticating the tested herbal products. Electronic supplementary material The online version of this article (10.1186/s12906-018-2174-0) contains supplementary material, which is available to authorized users.
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Osathanunkul M, Dheeranupattana S, Rotarayanont S, Sookkhee S, Osathanunkul K, Madesis P. Evaluation of suitable DNA regions for molecular identification of high value medicinal plants in genus Kaempferia. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2017; 36:726-735. [PMID: 29215948 DOI: 10.1080/15257770.2017.1391393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
DNA barcoding coupled high resolution melting (Bar-HRM) is an emerging method for species discrimination based on DNA dissociation kinetics. The aim of this work was to evaluate the suitability of different primer sets, derived from selected DNA regions, for Bar-HRM analysis of species in Kaempferia (Zingiberaceae). Four primer pairs were evaluated (rbcL, rpoC, trnL and ITS1). It was observed that the ITS1 barcode was the most useful DNA barcoding region overall for species discrimination out of all of the regions and primers assessed. Thus, the primer pair derived from the ITS1 region was the single most effective region for the identification of the tested species, whereas the rbcL primer pair gave the lowest resolution. Our Bar-HRM developed here would not only be useful for identification of Kaempferia plant specimens lacking essential parts for morphological identification but will be useful for authenticating products in powdered form of a high value medicinal species Kaempferia parviflora, in particular.
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Affiliation(s)
- Maslin Osathanunkul
- a Department of Biology, Faculty of Science , Chiang Mai University , Chiang Mai , Thailand.,b Center of Excellence in Bioresources for Agriculture, Industry and Medicine , Chiang Mai University , Chiang Mai , Thailand
| | | | - Siriphron Rotarayanont
- a Department of Biology, Faculty of Science , Chiang Mai University , Chiang Mai , Thailand
| | - Siriwoot Sookkhee
- c Department of Microbiology, Faculty of Medicine , Chiang Mai University , Chiang Mai , Thailand
| | - Khukrit Osathanunkul
- d Department of Information Technology , International College, Payap University , Chiang Mai , Thailand
| | - Panagiotis Madesis
- e Institute of Applied Biosciences , Centre for Research & Technology Hellas (CERTH) , Thessaloniki , Greece
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Osathanunkul M, Ounjai S, Osathanunkul R, Madesis P. Evaluation of a DNA-based method for spice/herb authentication, so you do not have to worry about what is in your curry, buon appetito! PLoS One 2017; 12:e0186283. [PMID: 29020084 PMCID: PMC5636142 DOI: 10.1371/journal.pone.0186283] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 09/28/2017] [Indexed: 12/27/2022] Open
Abstract
It is long believed that some spices may help protect against certain chronic conditions. Spices are usually parts of plants that have been powdered into small pieces. Have you ever wondered what the curry powder in your dish is made of? The aim of this work was to develop an appropriate DNA-based method for assessment of spice identity. Selecting the best marker for species recognition in the Zingiberaceae family. Six DNA regions were investigated in silico, including ITS, matK, rbcL, rpoC, trnH-psbA and trnL. Then, only four regions (ITS, matK, rbcL and trnH-psbA) were included in the simulated HRM (High-resolution Melting) analysis as the results from previous analysis showed that rpoC and trnL may not be suitable to be used to identify Zingiberaceae species in HRM analysis based on both the percentage of nucleotide variation and GC content. Simulated HRM analysis was performed to test the feasibility of Bar-HRM. We found that ITS2 is the most effective region to be used for identification of the studied species and thus was used in laboratory HRM analysis. All seven tested Zingiberaceae plants were then able to be distinguished using the ITS2 primers in laboratory HRM. Most importantly the melting curves gained from fresh and dried tissue overlapped, which is a crucial outcome for the applicability of the analysis. The method could be used in an authentication test for dried products. In the authentication test, only one of seven store-sold Zingiberaceae products that were tested contained the species listed on their labels, while we found substitution/contamination of the tested purchased products in the rest.
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Affiliation(s)
- Maslin Osathanunkul
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand
- * E-mail:
| | - Sarawut Ounjai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | | | - Panagiotis Madesis
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
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Cryptic diversity, sympatry, and other integrative taxonomy scenarios in the Mexican Ceratozamia miqueliana complex (Zamiaceae). ORG DIVERS EVOL 2017. [DOI: 10.1007/s13127-017-0341-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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DNA barcoding analysis and phylogenetic relationships of tree species in tropical cloud forests. Sci Rep 2017; 7:12564. [PMID: 28970548 PMCID: PMC5624878 DOI: 10.1038/s41598-017-13057-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 09/18/2017] [Indexed: 11/08/2022] Open
Abstract
DNA barcoding is a useful tool for species identification and phylogenetic construction. But present studies have far reached a consistent result on the universality of DNA barcoding. We tested the universality of tree species DNA barcodes including rbcL, matK, trnH-psbA and ITS, and examined their abilities of species identification and phylogenetic construction in three tropical cloud forests. Results showed that the success rates of PCR amplification of rbcL, matK, trnH-psbA and ITS were 75.26% ± 3.65%, 57.24% ± 4.42%, 79.28% ± 7.08%, 50.31% ± 6.64%, and the rates of DNA sequencing were 63.84% ± 4.32%, 50.82% ± 4.36%, 72.87% ± 11.37%, 45.15% ± 8.91% respectively, suggesting that both rbcL and trnH-psbA are universal for tree species in the tropical cloud forests. The success rates of species identification of the four fragments were higher than 41.00% (rbcL: 41.50% ± 2.81%, matK: 42.88% ± 2.59%, trnH-psbA: 46.16% ± 5.11% and ITS: 47.20% ± 5.76%), demonstrating that these fragments have potentiality in species identification. When the phylogenetic relationships were built with random fragment combinations, optimal evolutionary tree with high supporting values were established using the combinations of rbcL + matK + trnH-psbA in tropical cloud forests.
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Hosein FN, Austin N, Maharaj S, Johnson W, Rostant L, Ramdass AC, Rampersad SN. Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad. Ecol Evol 2017; 7:7311-7333. [PMID: 28944019 PMCID: PMC5606854 DOI: 10.1002/ece3.3220] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 05/17/2017] [Accepted: 06/12/2017] [Indexed: 02/06/2023] Open
Abstract
The islands of the Caribbean are considered to be a "biodiversity hotspot." Collectively, a high level of endemism for several plant groups has been reported for this region. Biodiversity conservation should, in part, be informed by taxonomy, population status, and distribution of flora. One taxonomic impediment to species inventory and management is correct identification as conventional morphology-based assessment is subject to several caveats. DNA barcoding can be a useful tool to quickly and accurately identify species and has the potential to prompt the discovery of new species. In this study, the ability of DNA barcoding to confirm the identities of 14 endangered endemic vascular plant species in Trinidad was assessed using three DNA barcodes (matK, rbcL, and rpoC1). Herbarium identifications were previously made for all species under study. matK, rbcL, and rpoC1 markers were successful in amplifying target regions for seven of the 14 species. rpoC1 sequences required extensive editing and were unusable. rbcL primers resulted in cleanest reads, however, matK appeared to be superior to rbcL based on a number of parameters assessed including level of DNA polymorphism in the sequences, genetic distance, reference library coverage based on BLASTN statistics, direct sequence comparisons within "best match" and "best close match" criteria, and finally, degree of clustering with moderate to strong bootstrap support (>60%) in neighbor-joining tree-based comparisons. The performance of both markers seemed to be species-specific based on the parameters examined. Overall, the Trinidad sequences were accurately identified to the genus level for all endemic plant species successfully amplified and sequenced using both matK and rbcL markers. DNA barcoding can contribute to taxonomic and biodiversity research and will complement efforts to select taxa for various molecular ecology and population genetics studies.
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Affiliation(s)
- Fazeeda N. Hosein
- Faculty of Science and TechnologyDepartment of Life SciencesThe University of the West IndiesSt. AugustineTrinidad and Tobago – West Indies
| | - Nigel Austin
- Faculty of Science and TechnologyDepartment of Life SciencesThe University of the West IndiesSt. AugustineTrinidad and Tobago – West Indies
| | - Shobha Maharaj
- Faculty of Science and TechnologyDepartment of Life SciencesThe University of the West IndiesSt. AugustineTrinidad and Tobago – West Indies
| | - Winston Johnson
- Faculty of Science and TechnologyDepartment of Life SciencesThe University of the West IndiesSt. AugustineTrinidad and Tobago – West Indies
| | - Luke Rostant
- Faculty of Science and TechnologyDepartment of Life SciencesThe University of the West IndiesSt. AugustineTrinidad and Tobago – West Indies
| | - Amanda C. Ramdass
- Faculty of Science and TechnologyDepartment of Life SciencesThe University of the West IndiesSt. AugustineTrinidad and Tobago – West Indies
| | - Sephra N. Rampersad
- Faculty of Science and TechnologyDepartment of Life SciencesThe University of the West IndiesSt. AugustineTrinidad and Tobago – West Indies
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Suesatpanit T, Osathanunkul K, Madesis P, Osathanunkul M. Should DNA sequence be incorporated with other taxonomical data for routine identifying of plant species? BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2017; 17:437. [PMID: 28859638 PMCID: PMC5580213 DOI: 10.1186/s12906-017-1937-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 08/18/2017] [Indexed: 12/13/2022]
Abstract
Background A variety of plants in Acanthaceae have long been used in traditional Thai ailment and commercialised with significant economic value. Nowadays medicinal plants are sold in processed forms and thus morphological authentication is almost impossible. Full identification requires comparison of the specimen with some authoritative sources, such as a full and accurate description and verification of the species deposited in herbarium. Intake of wrong herbals can cause adverse effects. Identification of both raw materials and end products is therefore needed. Methods Here, the potential of a DNA-based identification method, called Bar-HRM (DNA barcoding coupled with High Resolution Melting analysis), in raw material species identification is investigated. DNA barcode sequences from five regions (matK, rbcL, trnH-psbA spacer region, trnL and ITS2) of Acanthaceae species were retrieved for in silico analysis. Then the specific primer pairs were used in HRM assay to generate unique melting profiles for each plants species. Results The method allows identification of samples lacking necessary morphological parts. In silico analyses of all five selected regions suggested that ITS2 is the most suitable marker for Bar-HRM in this study. The HRM analysis on dried samples of 16 Acanthaceae medicinal species was then performed using primer pair derived from ITS2 region. 100% discrimination of the tested samples at both genus and species level was observed. However, two samples documented as Clinacanthus nutans and Clinacanthus siamensis were recognised as the same species from the HRM analysis. Further investigation reveals that C. siamensis is now accepted as C. nutans. Conclusions The results here proved that Bar-HRM is a promising technique in species identification of the studied medicinal plants in Acanthaceae. In addition, molecular biological data is currently used in plant taxonomy and increasingly popular in recent years. Here, DNA barcode sequence data should be incorporated with morphological characters in the species identification.
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Mishra P, Kumar A, Nagireddy A, Shukla AK, Sundaresan V. Evaluation of single and multilocus DNA barcodes towards species delineation in complex tree genus Terminalia. PLoS One 2017; 12:e0182836. [PMID: 28829803 PMCID: PMC5567895 DOI: 10.1371/journal.pone.0182836] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 07/25/2017] [Indexed: 11/19/2022] Open
Abstract
DNA barcoding is used as a universal tool for delimiting species boundaries in taxonomically challenging groups, with different plastid and nuclear regions (rbcL, matK, ITS and psbA-trnH) being recommended as primary DNA barcodes for plants. We evaluated the feasibility of using these regions in the species-rich genus Terminalia, which exhibits various overlapping morphotypes with pantropical distribution, owing to its complex taxonomy. Terminalia bellerica and T. chebula are ingredients of the famous Ayurvedic Rasayana formulation Triphala, used for detoxification and rejuvenation. High demand for extracted phytochemicals as well as the high trade value of several species renders mandatory the need for the correct identification of traded plant material. Three different analytical methods with single and multilocus barcoding regions were tested to develop a DNA barcode reference library from 222 individuals representing 41 Terminalia species. All the single barcodes tested had a lower discriminatory power than the multilocus regions, and the combination of matK+ITS had the highest resolution rate (94.44%). The average intra-specific variations (0.0188±0.0019) were less than the distance to the nearest neighbour (0.106±0.009) with matK and ITS. Distance-based Neighbour Joining analysis outperformed the character-based Maximum Parsimony method in the identification of traded species such as T. arjuna, T. chebula and T. tomentosa, which are prone to adulteration. rbcL was shown to be a highly conservative region with only 3.45% variability between all of the sequences. The recommended barcode combination, rbcL+matK, failed to perform in the genus Terminalia. Considering the complexity of resolution observed with single regions, the present study proposes the combination of matK+ITS as the most successful barcode in Terminalia.
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Affiliation(s)
- Priyanka Mishra
- Plant Biology and Systematics, CSIR—Central Institute of Medicinal and Aromatic Plants, Research Center, Bengaluru, Karnataka, India
| | - Amit Kumar
- Plant Biology and Systematics, CSIR—Central Institute of Medicinal and Aromatic Plants, Research Center, Bengaluru, Karnataka, India
| | - Akshitha Nagireddy
- Plant Biology and Systematics, CSIR—Central Institute of Medicinal and Aromatic Plants, Research Center, Bengaluru, Karnataka, India
| | - Ashutosh K. Shukla
- Biotechnology Division, CSIR—Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India
| | - Velusamy Sundaresan
- Plant Biology and Systematics, CSIR—Central Institute of Medicinal and Aromatic Plants, Research Center, Bengaluru, Karnataka, India
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Discriminatory power of rbcL barcode locus for authentication of some of United Arab Emirates (UAE) native plants. 3 Biotech 2017; 7:144. [PMID: 28597155 DOI: 10.1007/s13205-017-0746-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 02/06/2017] [Indexed: 12/18/2022] Open
Abstract
DNA barcoding of United Arab Emirates (UAE) native plants is of high practical and scientific value as the plants adapt to very harsh environmental conditions that challenge their identification. Fifty-one plant species belonged to 22 families, 2 monocots, and 20 eudicots; a maximum number of species being legumes and grasses were collected. To authenticate the morphological identification of the wild plant taxa, rbcL and matK regions were used in the study. The primer universality and discriminatory power of rbcL is 100%, while it is 35% for matK locus for these plant species. The sequences were submitted to GenBank; accession numbers were obtained for all the rbcL sequences and for 6 of matK sequences. We suggest rbcL as a promising barcode locus for the tested group of 51 plants. In the present study, an inexpensive, simple method of identification of rare desert plant taxa through rbcL barcode is being reported.
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Parveen I, Singh HK, Malik S, Raghuvanshi S, Babbar SB. Evaluating five different loci (rbcL, rpoB, rpoC1, matK, and ITS) for DNA barcoding of Indian orchids. Genome 2017; 60:665-671. [PMID: 28514600 DOI: 10.1139/gen-2016-0215] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Orchidaceae, one of the largest families of angiosperms, is represented in India by 1600 species distributed in diverse habitats. Orchids are in high demand owing to their beautiful flowers and therapeutic properties. Overexploitation and habitat destruction have made many orchid species endangered. In the absence of effective identification methods, illicit trade of orchids continues unabated. Considering DNA barcoding as a potential identification tool, species discrimination capability of five loci, ITS, matK, rbcL, rpoB, and rpoC1, was tested in 393 accessions of 94 Indian orchid species belonging to 47 genera, including one listed in Appendix I of CITES and 26 medicinal species. ITS provided the highest species discrimination rate of 94.9%. While, among the chloroplast loci, matK provided the highest species discrimination rate of 85.7%. None of the tested loci individually discriminated 100% of the species. Therefore, multi-locus combinations of up to five loci were tested for their species resolution capability. Among two-locus combinations, the maximum species resolution (86.7%) was provided by ITS+matK. ITS and matK sequences of the medicinal orchids were species specific, thus providing unique molecular identification tags for their identification and detection. These observations emphasize the need for the inclusion of ITS in the core barcode for plants, whenever required and available.
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Affiliation(s)
- Iffat Parveen
- a Department of Botany, University of Delhi, Delhi 110007, India.,b National Centre for Natural Products Research, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA
| | - Hemant K Singh
- a Department of Botany, University of Delhi, Delhi 110007, India
| | - Saloni Malik
- a Department of Botany, University of Delhi, Delhi 110007, India
| | - Saurabh Raghuvanshi
- c Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Shashi B Babbar
- a Department of Botany, University of Delhi, Delhi 110007, India
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Ghorbani A, Saeedi Y, de Boer HJ. Unidentifiable by morphology: DNA barcoding of plant material in local markets in Iran. PLoS One 2017; 12:e0175722. [PMID: 28419161 PMCID: PMC5395179 DOI: 10.1371/journal.pone.0175722] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 03/30/2017] [Indexed: 11/24/2022] Open
Abstract
Local markets provide a rapid insight into the medicinal plants growing in a region as well as local traditional health concerns. Identification of market plant material can be challenging as plants are often sold in dried or processed forms. In this study, three approaches of DNA barcoding-based molecular identification of market samples are evaluated, two objective sequence matching approaches and an integrative approach that coalesces sequence matching with a priori and a posteriori data from other markers, morphology, ethnoclassification and species distribution. Plant samples from markets and herbal shops were identified using morphology, descriptions of local use, and vernacular names with relevant floras and pharmacopoeias. DNA barcoding was used for identification of samples that could not be identified to species level using morphology. Two methods based on BLAST similarity-based identification, were compared with an integrative identification approach. Integrative identification combining the optimized similarity-based approach with a priori and a posteriori information resulted in a 1.67, 1.95 and 2.00 fold increase for ITS, trnL-F spacer, and both combined, respectively. DNA barcoding of traded plant material requires objective strategies to include data from multiple markers, morphology, and traditional knowledge to optimize species level identification success.
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MESH Headings
- Amaranthus
- Cell Nucleus/genetics
- DNA Barcoding, Taxonomic/methods
- DNA, Chloroplast/chemistry
- DNA, Chloroplast/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Plants, Medicinal/anatomy & histology
- Plants, Medicinal/classification
- Plants, Medicinal/genetics
- RNA, Transfer/genetics
- Reproducibility of Results
- Sequence Analysis, DNA
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Affiliation(s)
- Abdolbaset Ghorbani
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Traditional Medicine and Materia Medica Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Yousef Saeedi
- Traditional Medicine and Materia Medica Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hugo J. de Boer
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Naturalis Biodiversity Center, Leiden, The Netherlands
- The Natural History Museum, University of Oslo, Oslo, Norway
- * E-mail:
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Identification of Traditional She Medicine Shi-Liang Tea Species and Closely Related Species Using the ITS2 Barcode. APPLIED SCIENCES-BASEL 2017. [DOI: 10.3390/app7030195] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Identification of newly established Spodoptera littoralis cell lines by two DNA barcoding markers. In Vitro Cell Dev Biol Anim 2017; 53:288-292. [DOI: 10.1007/s11626-016-0118-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 11/29/2016] [Indexed: 10/20/2022]
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Enan MR, Palakkott AR, Ksiksi TS. DNA barcoding of selected UAE medicinal plant species: a comparative assessment of herbarium and fresh samples. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:221-227. [PMID: 28250597 PMCID: PMC5313416 DOI: 10.1007/s12298-016-0412-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 12/28/2016] [Indexed: 05/24/2023]
Abstract
It is commonly difficult to extract and amplify DNA from herbarium samples as they are old and preserved using different compounds. In addition, such samples are subjected to the accumulation of intrinsically produced plant substances over long periods (up to hundreds of years). DNA extraction from desert flora may pause added difficulties as many contain high levels of secondary metabolites. Herbarium samples from the Biology Department (UAE University) plant collection and fresh plant samples, collected from around Al-Ain (UAE), were used in this study. The three barcode loci for the coding genes matK, rbcL and rpoC1-were amplified. Our results showed that T. terresteris, H. robustum,T. pentandrus and Z. qatarense were amplified using all three primers for both fresh and herbaium samples. Both fresh and herbarium samples of C. comosum, however, were not amplified at all, using the three primers. Herbarium samples from A. javanica, C. imbricatum, T. aucherana and Z. simplex were not amplified with any of the three primers. For fresh samples 90, 90 and 80% of the samples were amplified using matK, rbcL and rpoC1, respectively. In short, fresh samples were significantly better amplified than those from herbarium sources, using the three primers. Both fresh and herbarium samples from one species (C. comosum), however, were not successfully amplified. It is also concluded that the rbcL regions showed real potentials to distinguish the UAE species under investigation into the appropriate family and genus.
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Ghorbani A, Gravendeel B, Selliah S, Zarré S, de Boer H. DNA barcoding of tuberous Orchidoideae: a resource for identification of orchids used in Salep. Mol Ecol Resour 2016; 17:342-352. [DOI: 10.1111/1755-0998.12615] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 08/26/2016] [Accepted: 09/06/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Abdolbaset Ghorbani
- Department of Organismal Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-75236 Uppsala Sweden
- Traditional Medicine and Materia Medica Research Center; Shahid Beheshti University of Medical Sciences; No 19, Tavanir Street, Hemmat Highway P.O. Box 14155-6153 Tehran Iran
| | - Barbara Gravendeel
- Naturalis Biodiversity Center; Darwinweg 2 2333 CR Leiden The Netherlands
- University of Applied Sciences Leiden; Zernikedreef 11 2333 CK Leiden The Netherlands
| | - Sugirthini Selliah
- The Natural History Museum; University of Oslo; P.O. Box 1172 Blindern 0318 Oslo Norway
| | - Shahin Zarré
- Department of Plant Sciences; School of Biology; College of Science; University of Tehran; 14155-6455 Tehran Iran
| | - Hugo de Boer
- Department of Organismal Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-75236 Uppsala Sweden
- Naturalis Biodiversity Center; Darwinweg 2 2333 CR Leiden The Netherlands
- The Natural History Museum; University of Oslo; P.O. Box 1172 Blindern 0318 Oslo Norway
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Williamson J, Maurin O, Shiba S, van der Bank H, Pfab M, Pilusa M, Kabongo R, van der Bank M. Exposing the illegal trade in cycad species (Cycadophyta:Encephalartos) at two traditional medicine markets in South Africa using DNA barcoding. Genome 2016; 59:771-81. [DOI: 10.1139/gen-2016-0032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Species in the cycad genus Encephalartos are listed in CITES Appendix I and as Threatened or Protected Species in terms of South Africa’s National Environmental Management: Biodiversity Act (NEM:BA) of 2004. Despite regulations, illegal plant harvesting for medicinal trade has continued in South Africa and resulted in declines in cycad populations and even complete loss of sub-populations. Encephalartos is traded at traditional medicine markets in South Africa in the form of bark strips and stem sections; thus, determining the species traded presents a major challenge due to a lack of characteristic plant parts. Here, a case study is presented on the use of DNA barcoding to identify cycads sold at the Faraday and Warwick traditional medicine markets in Johannesburg and Durban, respectively. Market samples were sequenced for the core DNA barcodes (rbcLa and matK) as well as two additional regions: nrITS and trnH-psbA. The barcoding database for cycads at the University of Johannesburg was utilized to assign query samples to known species. Three approaches were followed: tree-based, similarity-based, and character-based (BRONX) methods. Market samples identified were Encephalartos ferox (Near Threatened), Encephalartos lebomboensis (Endangered), Encephalartos natalensis (Near Threatened), Encephalartos senticosus (Vulnerable), and Encephalartos villosus (Least Concern). Results from this study are crucial for making appropriate assessments and decisions on how to manage these markets.
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Affiliation(s)
- J. Williamson
- The African Centre for DNA Barcoding, Department of Botany & Plant Biotechnology, University of Johannesburg, APK Campus, P.O. Box 524, Auckland Park, 2006, South Africa
| | - O. Maurin
- The African Centre for DNA Barcoding, Department of Botany & Plant Biotechnology, University of Johannesburg, APK Campus, P.O. Box 524, Auckland Park, 2006, South Africa
| | - S.N.S. Shiba
- The African Centre for DNA Barcoding, Department of Botany & Plant Biotechnology, University of Johannesburg, APK Campus, P.O. Box 524, Auckland Park, 2006, South Africa
| | - H. van der Bank
- The African Centre for DNA Barcoding, Department of Zoology, University of Johannesburg, APK Campus, P.O. Box 524, Auckland Park, 2006, South Africa
| | - M. Pfab
- South African National Biodiversity Institute, Pretoria National Botanical Garden, P/Bag X101, Silverton, 0184, South Africa
| | - M. Pilusa
- The African Centre for DNA Barcoding, Department of Botany & Plant Biotechnology, University of Johannesburg, APK Campus, P.O. Box 524, Auckland Park, 2006, South Africa
| | - R.M. Kabongo
- The African Centre for DNA Barcoding, Department of Botany & Plant Biotechnology, University of Johannesburg, APK Campus, P.O. Box 524, Auckland Park, 2006, South Africa
| | - M. van der Bank
- The African Centre for DNA Barcoding, Department of Botany & Plant Biotechnology, University of Johannesburg, APK Campus, P.O. Box 524, Auckland Park, 2006, South Africa
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Jiang GF, Hinsinger DD, Strijk JS. Comparison of intraspecific, interspecific and intergeneric chloroplast diversity in Cycads. Sci Rep 2016; 6:31473. [PMID: 27558458 PMCID: PMC4997344 DOI: 10.1038/srep31473] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 07/20/2016] [Indexed: 11/18/2022] Open
Abstract
Cycads are among the most threatened plant species. Increasing the availability of genomic information by adding whole chloroplast data is a fundamental step in supporting phylogenetic studies and conservation efforts. Here, we assemble a dataset encompassing three taxonomic levels in cycads, including ten genera, three species in the genus Cycas and two individuals of C. debaoensis. Repeated sequences, SSRs and variations of the chloroplast were analyzed at the intraspecific, interspecific and intergeneric scale, and using our sequence data, we reconstruct a phylogenomic tree for cycads. The chloroplast was 162,094 bp in length, with 133 genes annotated, including 87 protein-coding, 37 tRNA and 8 rRNA genes. We found 7 repeated sequences and 39 SSRs. Seven loci showed promising levels of variations for application in DNA-barcoding. The chloroplast phylogeny confirmed the division of Cycadales in two suborders, each of them being monophyletic, revealing a contradiction with the current family circumscription and its evolution. Finally, 10 intraspecific SNPs were found. Our results showed that despite the extremely restricted distribution range of C. debaoensis, using complete chloroplast data is useful not only in intraspecific studies, but also to improve our understanding of cycad evolution and in defining conservation strategies for this emblematic group.
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Affiliation(s)
- Guo-Feng Jiang
- Plant Ecophysiology and Evolution Group, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and College of Forestry, Guangxi University, Nanning, Guangxi 530004, China
| | - Damien Daniel Hinsinger
- Plant Ecophysiology and Evolution Group, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and College of Forestry, Guangxi University, Nanning, Guangxi 530004, China
| | - Joeri Sergej Strijk
- Plant Ecophysiology and Evolution Group, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and College of Forestry, Guangxi University, Nanning, Guangxi 530004, China
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