1
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Aran K, Giri P, Roy H, Uniyal PL. Taxonomic significance of megaspores in some species of Selaginella from Arunachal Pradesh in India. Microsc Res Tech 2024; 87:1413-1428. [PMID: 38385770 DOI: 10.1002/jemt.24513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/03/2024] [Accepted: 01/30/2024] [Indexed: 02/23/2024]
Abstract
The present study was carried out to record the color, size, and ornamentation of megaspores in 18 species of the family Selaginellaceae from Arunachal Pradesh using scanning electron microscope (SEM) and light microscope (LM). Electron microscopic study of the spore features revealed the type of ornamentation and microsculptural detail. SEM study on megaspore of Selaginella pentagona (S. pentagona), Selaginella tenuifolia, Selaginella semicordata, and Selaginella chrysorrhizos is presented for the first time. Variation in the megaspore ornamentation is noted at the interspecific level and intraspecific level in some cases. Examination of the megaspores under study found all the megaspores as trilete, with a size ranging from 116 to 560 μm in diameter. Taxonomic key is prepared to differentiate the species. Short descriptions of megaspores are provided and supported by photo plates. New features are recorded for seven species. The study contributes to the separation of species within the genus Selaginella based on the spore feature and brings forward the use of spore as a diagnostic tool in the taxonomy of the genus. These works contribute to the systematic of the family Selaginellaceae and provide useful information in the field of palynology. RESEARCH HIGHLIGHTS: Study on megaspore features of Selaginella species collected from Arunachal Pradesh, using SEM and LM. Taxonomic key is provided for each species based on megaspores features. New megaspore features are recorded for the seven species. The study brings forward the use of spore as a diagnostic tool in the taxonomy of the genus. These works provide useful information in the field of systematic and palynology.
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Affiliation(s)
- Khencha Aran
- Department of Botany, Cotton University, Guwahati, India
| | - Priti Giri
- Department of Botany, Delhi University, New Delhi, India
| | - Himu Roy
- Department of Botany, Cotton University, Guwahati, India
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2
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Kompoura V, Karapantzou I, Mitropoulou G, Parisis NA, Gkalpinos VK, Anagnostou VA, Tsiailanis AD, Vasdekis EP, Koutsaliaris IK, Tsouka AN, Karapetsi L, Madesis P, Letsiou S, Florou D, Koukkou AI, Barbouti A, Tselepis AD, Kourkoutas Y, Tzakos AG. Exploiting the beneficial effects of Salvia officinalis L. extracts in human health and assessing their activity as potent functional regulators of food microbiota. Food Chem 2024; 441:138175. [PMID: 38194793 DOI: 10.1016/j.foodchem.2023.138175] [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: 09/19/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 01/11/2024]
Abstract
Salvia officinalis L. has attracted scientific and industrial interest due to its pharmacological properties. However, its detailed phytochemical profile and its correlation with beneficial effects in the human microbiome and oxidative stress remained elusive. To unveil this, S. officinalis was collected from the region of Epirus and its molecular identity was verified with DNA barcoding. Phytochemical profile for both aqueous and ethanol-based extracts was determined by high-pressure liquid chromatography-tandem mass spectrometry and 103 phytochemicals were determined. The effect of S. officinalis extracts as functional regulators of food microbiota by stimulating the growth of Lacticaseibacillus rhamnosus strains and by suppressing evolution of pathogenic bacteria was verified. Furthermore, we recorded that both extracts exhibited a significant cellular protection against H2O2-induced DNA damage. Finally, both extracts exhibited strong inhibitory effect towards LDL oxidation. This study provides a comprehensive characterization of S. officinalis on its phytochemical components as also its potential impact in human microbiome and oxidative stress.
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Affiliation(s)
- Vasiliki Kompoura
- Laboratory of Applied Microbiology and Biotechnology, Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Ioanna Karapantzou
- Laboratory of Applied Microbiology and Biotechnology, Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Gregoria Mitropoulou
- Laboratory of Applied Microbiology and Biotechnology, Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Nikolaos A Parisis
- Department of Chemistry, Section of Organic Chemistry and Biochemistry, University of Ioannina, 45110 Ioannina, Greece
| | - Vasileios K Gkalpinos
- Department of Chemistry, Section of Organic Chemistry and Biochemistry, University of Ioannina, 45110 Ioannina, Greece
| | - Vasiliki A Anagnostou
- Department of Chemistry, Section of Organic Chemistry and Biochemistry, University of Ioannina, 45110 Ioannina, Greece
| | - Antonis D Tsiailanis
- Department of Chemistry, Section of Organic Chemistry and Biochemistry, University of Ioannina, 45110 Ioannina, Greece
| | | | - Ioannis K Koutsaliaris
- Department of Chemistry, Section of Organic Chemistry and Biochemistry, University of Ioannina, 45110 Ioannina, Greece; Atherothrombosis Research Centre/Laboratory of Biochemistry, Department of Chemistry, University of Ioannina, 45110, Ioannina, Greece
| | - Aikaterini N Tsouka
- Department of Chemistry, Section of Organic Chemistry and Biochemistry, University of Ioannina, 45110 Ioannina, Greece; Atherothrombosis Research Centre/Laboratory of Biochemistry, Department of Chemistry, University of Ioannina, 45110, Ioannina, Greece
| | - Lefkothea Karapetsi
- Laboratory of Molecular Biology of Plants, Department of Agriculture Crop Production and Rural Environment, University of Thessaly, Fytokou St., N. Ionia, 38446 Magnesia, Greece; Institute of Applied Biosciences (INAB), Centre for Research and Technology Hellas (CERTH), 6th Km Charilaou-Thermi Road, 57001 Thessaloniki, Greece
| | - Panagiotis Madesis
- Laboratory of Molecular Biology of Plants, Department of Agriculture Crop Production and Rural Environment, University of Thessaly, Fytokou St., N. Ionia, 38446 Magnesia, Greece; Institute of Applied Biosciences (INAB), Centre for Research and Technology Hellas (CERTH), 6th Km Charilaou-Thermi Road, 57001 Thessaloniki, Greece
| | - Stavroula Letsiou
- Department of Chemistry, Section of Organic Chemistry and Biochemistry, University of Ioannina, 45110 Ioannina, Greece
| | - Dimitra Florou
- Department of Forensic Medicine & Toxicology, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | - Anna-Irini Koukkou
- Department of Chemistry, Section of Organic Chemistry and Biochemistry, University of Ioannina, 45110 Ioannina, Greece
| | - Alexandra Barbouti
- Department of Anatomy-Histology-Embryology, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | - Alexandros D Tselepis
- Department of Chemistry, Section of Organic Chemistry and Biochemistry, University of Ioannina, 45110 Ioannina, Greece; Atherothrombosis Research Centre/Laboratory of Biochemistry, Department of Chemistry, University of Ioannina, 45110, Ioannina, Greece
| | - Yiannis Kourkoutas
- Laboratory of Applied Microbiology and Biotechnology, Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Andreas G Tzakos
- Department of Chemistry, Section of Organic Chemistry and Biochemistry, University of Ioannina, 45110 Ioannina, Greece; University Research Center of Ioannina, Institute of Materials Science and Computing, Ioannina, Greece.
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3
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Curd EE, Gal L, Gallego R, Silliman K, Nielsen S, Gold Z. rCRUX: A Rapid and Versatile Tool for Generating Metabarcoding Reference libraries in R. ENVIRONMENTAL DNA (HOBOKEN, N.J.) 2024; 6:e489. [PMID: 38370872 PMCID: PMC10871694 DOI: 10.1002/edn3.489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/19/2023] [Indexed: 02/20/2024]
Abstract
The sequencing revolution requires accurate taxonomic classification of DNA sequences. Key to making accurate taxonomic assignments are curated, comprehensive reference barcode databases. However, the generation and curation of such databases has remained challenging given the large and continuously growing volumes of both DNA sequence data and novel reference barcode targets. Monitoring and research applications require a greater diversity of specialized gene regions and targeted taxa then are currently curated by professional staff. Thus there is a growing need for an easy to implement computational tool that can generate comprehensive metabarcoding reference libraries for any bespoke locus. We address this need by reimagining CRUX from the Anacapa Toolkit and present the rCRUX package in R which, like it's predecessor, relies on sequence homology and PCR primer compatibility instead of keyword-searches to avoid limitations of user-defined metadata. The typical workflow involves searching for plausible seed amplicons (get_seeds_local() or get_seeds_remote()) by simulating in silico PCR to acquire a set of sequences analogous to PCR products containing a user-defined set of primer sequences. Next, these seeds are used to iteratively blast search seed sequences against a local copy of the National Center for Biotechnology Information (NCBI) formatted nt database using a taxonomic-rank based stratified random sampling approach ( blast_seeds() ). This results in a comprehensive set of sequence matches. This database is dereplicated and cleaned (derep_and_clean_db()) by identifying identical reference sequences and collapsing the taxonomic path to the lowest taxonomic agreement across all matching reads. This results in a curated, comprehensive database of primer-specific reference barcode sequences from NCBI. Databases can then be compared (compare_db()) to determine read and taxonomic overlap. We demonstrate that rCRUX provides more comprehensive reference databases for the MiFish Universal Teleost 12S, Taberlet trnl, fungal ITS, and Leray CO1 loci than CRABS, MetaCurator, RESCRIPt, and ecoPCR reference databases. We then further demonstrate the utility of rCRUX by generating 24 reference databases for 20 metabarcoding loci, many of which lack dedicated reference database curation efforts. The rCRUX package provides a simple to use tool for the generation of curated, comprehensive reference databases for user-defined loci, facilitating accurate and effective taxonomic classification of metabarcoding and DNA sequence efforts broadly.
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Affiliation(s)
- Emily E. Curd
- Vermont Biomedical Research Network, University of Vermont, VT, USA
| | - Luna Gal
- Landmark College, VT, USA
- California Cooperative Oceanic Fisheries Investigations (CalCOFI), Scripps Institution of Oceanography, University of California San Diego (UCSD), La Jolla, CA, USA
| | - Ramon Gallego
- Departamento de Biología, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Katherine Silliman
- Northern Gulf Institute, Mississippi State University, Starkville, MS, USA
- NOAA Atlantic Oceanographic and Meteorological Laboratory, Miami, FL, USA
| | | | - Zachary Gold
- California Cooperative Oceanic Fisheries Investigations (CalCOFI), Scripps Institution of Oceanography, University of California San Diego (UCSD), La Jolla, CA, USA
- NOAA Pacific Marine Environmental Laboratory, Seattle, WA, USA
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4
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Curd EE, Gal L, Gallego R, Nielsen S, Gold Z. rCRUX: A Rapid and Versatile Tool for Generating Metabarcoding Reference libraries in R. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.543005. [PMID: 37397980 PMCID: PMC10312559 DOI: 10.1101/2023.05.31.543005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Key to making accurate taxonomic assignments are curated, comprehensive reference barcode databases. However, the generation and curation of such databases has remained challenging given the large and continuously growing volumes of DNA sequence data and novel reference barcode targets. Monitoring and research applications require a greater diversity of specialized gene regions and targeted taxa to meet taxonomic classification goals then are currently curated by professional staff. Thus, there is a growing need for an easy to implement tool that can generate comprehensive metabarcoding reference libraries for any bespoke locus. We address this need by reimagining CRUX from the Anacapa Toolkit and present the rCRUX package in R. The typical workflow involves searching for plausible seed amplicons (get_seeds_local() or get_seeds_remote()) by simulating in silico PCR to acquire seed sequences containing a user-defined primer set. Next these seeds are used to iteratively blast search seed sequences against a local NCBI formatted database using a taxonomic rank based stratified random sampling approach (blast_seeds()) that results in a comprehensive set of sequence matches. This database is dereplicated and cleaned (derep_and_clean_db()) by identifying identical reference sequences and collapsing the taxonomic path to the lowest taxonomic agreement across all matching reads. This results in a curated, comprehensive database of primer specific reference barcode sequences from NCBI. We demonstrate that rCRUX provides more comprehensive reference databases for the MiFish Universal Teleost 12S, Taberlet trnl, and fungal ITS locus than CRABS, METACURATOR, RESCRIPt, and ECOPCR reference databases. We then further demonstrate the utility of rCRUX by generating 16 reference databases for metabarcoding loci that lack dedicated reference database curation efforts. The rCRUX package provides a simple to use tool for the generation of curated, comprehensive reference databases for user-defined loci, facilitating accurate and effective taxonomic classification of metabarcoding and DNA sequence efforts broadly.
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Affiliation(s)
- Emily E. Curd
- Vermont Biomedical Research Network, University of Vermont, VT, USA
| | - Luna Gal
- Landmark College, VT, USA
- California Cooperative Oceanic Fisheries Investigations (CalCOFI), Scripps Institution of Oceanography, University of California San Diego (UCSD), La Jolla, CA, USA
| | - Ramon Gallego
- Universidad Autónoma de Madrid - Unidad de Genética, Spain
| | | | - Zachary Gold
- California Cooperative Oceanic Fisheries Investigations (CalCOFI), Scripps Institution of Oceanography, University of California San Diego (UCSD), La Jolla, CA, USA
- NOAA Pacific Marine Environmental Laboratory, Seattle, WA, USA
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5
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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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6
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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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7
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Mustafa AA, Derise MR, Yong WTL, Rodrigues KF. A Concise Review of Dendrocalamus asper and Related Bamboos: Germplasm Conservation, Propagation and Molecular Biology. PLANTS 2021; 10:plants10091897. [PMID: 34579429 PMCID: PMC8468032 DOI: 10.3390/plants10091897] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 11/16/2022]
Abstract
Bamboos represent an emerging forest resource of economic significance and provide an avenue for sustainable development of forest resources. The development of the commercial bamboo industry is founded upon efficient molecular and technical approaches for the selection and rapid multiplication of elite germplasm for its subsequent propagation via commercial agro-forestry business enterprises. This review will delve into the micropropagation of Dendrocalamus asper, one of the most widely cultivated commercial varieties of bamboo, and will encompass the selection of germplasm, establishment of explants in vitro and micropropagation techniques. The currently available information pertaining to molecular biology, DNA barcoding and breeding, has been included, and potential areas for future research in the area of genetic engineering and gene regulation have been highlighted. This information will be of relevance to both commercial breeders and molecular biologists who have an interest in establishing bamboo as a crop of the future.
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8
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Kolter A, Gemeinholzer B. Internal transcribed spacer primer evaluation for vascular plant metabarcoding. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.68155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The unprecedented ongoing biodiversity decline necessitates scalable means of monitoring in order to fully understand the underlying causes. DNA metabarcoding has the potential to provide a powerful tool for accurate and rapid biodiversity monitoring. Unfortunately, in many cases, a lack of universal standards undermines the widespread application of metabarcoding. One of the most important considerations in metabarcoding of plants, aside from selecting a potent barcode marker, is primer choice. Our study evaluates published ITS primers in silico and in vitro, through mock communities and presents newly designed primers. We were able to show that a large proportion of previously available ITS primers have unfavourable attributes. Our combined results support the recommendation of the introduced primers ITS-3p62plF1 and ITS-4unR1 as the best current universal plant specific ITS2 primer combination. We also found that PCR optimisation, such as the addition of 5% DMSO, is essential to obtain meaningful results in ITS2 metabarcoding. Finally, we conclude that continuous quality assurance is indispensable for reliable metabarcoding results.
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Lin M, Simons AL, Harrigan RJ, Curd EE, Schneider FD, Ruiz-Ramos DV, Gold Z, Osborne MG, Shirazi S, Schweizer TM, Moore TN, Fox EA, Turba R, Garcia-Vedrenne AE, Helman SK, Rutledge K, Mejia MP, Marwayana O, Munguia Ramos MN, Wetzer R, Pentcheff ND, McTavish EJ, Dawson MN, Shapiro B, Wayne RK, Meyer RS. Landscape analyses using eDNA metabarcoding and Earth observation predict community biodiversity in California. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2021; 31:e02379. [PMID: 34013632 DOI: 10.5281/zenodo.4516670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/23/2020] [Accepted: 02/04/2021] [Indexed: 05/27/2023]
Abstract
Ecosystems globally are under threat from ongoing anthropogenic environmental change. Effective conservation management requires more thorough biodiversity surveys that can reveal system-level patterns and that can be applied rapidly across space and time. Using modern ecological models and community science, we integrate environmental DNA and Earth observations to produce a time snapshot of regional biodiversity patterns and provide multi-scalar community-level characterization. We collected 278 samples in spring 2017 from coastal, shrub, and lowland forest sites in California, a complex ecosystem and biodiversity hotspot. We recovered 16,118 taxonomic entries from eDNA analyses and compiled associated traditional observations and environmental data to assess how well they predicted alpha, beta, and zeta diversity. We found that local habitat classification was diagnostic of community composition and distinct communities and organisms in different kingdoms are predicted by different environmental variables. Nonetheless, gradient forest models of 915 families recovered by eDNA analysis and using BIOCLIM variables, Sentinel-2 satellite data, human impact, and topographical features as predictors, explained 35% of the variance in community turnover. Elevation, sand percentage, and photosynthetic activities (NDVI32) were the top predictors. In addition to this signal of environmental filtering, we found a positive relationship between environmentally predicted families and their numbers of biotic interactions, suggesting environmental change could have a disproportionate effect on community networks. Together, these analyses show that coupling eDNA with environmental predictors including remote sensing data has capacity to test proposed Essential Biodiversity Variables and create new landscape biodiversity baselines that span the tree of life.
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Affiliation(s)
- Meixi Lin
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Ariel Levi Simons
- Department of Marine and Environmental Biology, University of Southern California, Los Angeles, California, 90089, USA
- Institute of the Environment and Sustainability, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Ryan J Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Emily E Curd
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Fabian D Schneider
- Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California, 91009, USA
| | - Dannise V Ruiz-Ramos
- Columbia Environmental Research Center, U.S. Geological Survey, Columbia, Missouri, 65201, USA
- Department of Life & Environmental Sciences, University of California-Merced, Merced, California, 95343, USA
| | - Zack Gold
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Melisa G Osborne
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, 90089, USA
| | - Sabrina Shirazi
- Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, Santa Cruz, California, 95064, USA
| | - Teia M Schweizer
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Tiara N Moore
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
- School of Environmental and Forestry Sciences, University of Washington, Seattle, Washington, 98195, USA
| | - Emma A Fox
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Rachel Turba
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Ana E Garcia-Vedrenne
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Sarah K Helman
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Kelsi Rutledge
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Maura Palacios Mejia
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Onny Marwayana
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Bogor, 16911, Indonesia
| | - Miroslava N Munguia Ramos
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Regina Wetzer
- Research and Collections, Natural History Museum of Los Angeles County, Los Angeles, California, 90007, USA
- Biological Sciences, University of Southern California, Los Angeles, California, 90089, USA
| | - N Dean Pentcheff
- Research and Collections, Natural History Museum of Los Angeles County, Los Angeles, California, 90007, USA
| | - Emily Jane McTavish
- Department of Life & Environmental Sciences, University of California-Merced, Merced, California, 95343, USA
| | - Michael N Dawson
- Department of Life & Environmental Sciences, University of California-Merced, Merced, California, 95343, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, Santa Cruz, California, 95064, USA
- Howard Hughes Medical Institute, University of California-Santa Cruz, Santa Cruz, California, 95064, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Rachel S Meyer
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
- Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, Santa Cruz, California, 95064, USA
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10
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Lin M, Simons AL, Harrigan RJ, Curd EE, Schneider FD, Ruiz-Ramos DV, Gold Z, Osborne MG, Shirazi S, Schweizer TM, Moore TN, Fox EA, Turba R, Garcia-Vedrenne AE, Helman SK, Rutledge K, Mejia MP, Marwayana O, Munguia Ramos MN, Wetzer R, Pentcheff ND, McTavish EJ, Dawson MN, Shapiro B, Wayne RK, Meyer RS. Landscape analyses using eDNA metabarcoding and Earth observation predict community biodiversity in California. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2021; 31:e02379. [PMID: 34013632 PMCID: PMC9297316 DOI: 10.1002/eap.2379] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/23/2020] [Accepted: 02/04/2021] [Indexed: 05/15/2023]
Abstract
Ecosystems globally are under threat from ongoing anthropogenic environmental change. Effective conservation management requires more thorough biodiversity surveys that can reveal system-level patterns and that can be applied rapidly across space and time. Using modern ecological models and community science, we integrate environmental DNA and Earth observations to produce a time snapshot of regional biodiversity patterns and provide multi-scalar community-level characterization. We collected 278 samples in spring 2017 from coastal, shrub, and lowland forest sites in California, a complex ecosystem and biodiversity hotspot. We recovered 16,118 taxonomic entries from eDNA analyses and compiled associated traditional observations and environmental data to assess how well they predicted alpha, beta, and zeta diversity. We found that local habitat classification was diagnostic of community composition and distinct communities and organisms in different kingdoms are predicted by different environmental variables. Nonetheless, gradient forest models of 915 families recovered by eDNA analysis and using BIOCLIM variables, Sentinel-2 satellite data, human impact, and topographical features as predictors, explained 35% of the variance in community turnover. Elevation, sand percentage, and photosynthetic activities (NDVI32) were the top predictors. In addition to this signal of environmental filtering, we found a positive relationship between environmentally predicted families and their numbers of biotic interactions, suggesting environmental change could have a disproportionate effect on community networks. Together, these analyses show that coupling eDNA with environmental predictors including remote sensing data has capacity to test proposed Essential Biodiversity Variables and create new landscape biodiversity baselines that span the tree of life.
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Affiliation(s)
- Meixi Lin
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Ariel Levi Simons
- Department of Marine and Environmental Biology, University of Southern California, Los Angeles, California 90089 USA
- Institute of the Environment and Sustainability, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Ryan J. Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Emily E. Curd
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Fabian D. Schneider
- Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91009 USA
| | - Dannise V. Ruiz-Ramos
- Columbia Environmental Research Center, U.S. Geological Survey, Columbia, Missouri 65201 USA
- Department of Life & Environmental Sciences, University of California-Merced, Merced, California 95343 USA
| | - Zack Gold
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Melisa G. Osborne
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089 USA
| | - Sabrina Shirazi
- Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, Santa Cruz, California 95064 USA
| | - Teia M. Schweizer
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523 USA
| | - Tiara N. Moore
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
- School of Environmental and Forestry Sciences, University of Washington, Seattle, Washington 98195 USA
| | - Emma A. Fox
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Rachel Turba
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Ana E. Garcia-Vedrenne
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Sarah K. Helman
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Kelsi Rutledge
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Maura Palacios Mejia
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Onny Marwayana
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Bogor 16911 Indonesia
| | - Miroslava N. Munguia Ramos
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Regina Wetzer
- Research and Collections, Natural History Museum of Los Angeles County, Los Angeles, California 90007 USA
- Biological Sciences, University of Southern California, Los Angeles, California 90089 USA
| | - N. Dean Pentcheff
- Research and Collections, Natural History Museum of Los Angeles County, Los Angeles, California 90007 USA
| | - Emily Jane McTavish
- Department of Life & Environmental Sciences, University of California-Merced, Merced, California 95343 USA
| | - Michael N. Dawson
- Department of Life & Environmental Sciences, University of California-Merced, Merced, California 95343 USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, Santa Cruz, California 95064 USA
- Howard Hughes Medical Institute, University of California-Santa Cruz, Santa Cruz, California 95064 USA
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Rachel S. Meyer
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
- Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, Santa Cruz, California 95064 USA
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11
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Neeragunda Shivaraj Y, Plancot B, Ramdani Y, Gügi B, Kambalagere Y, Jogaiah S, Driouich A, Ramasandra Govind S. Physiological and biochemical responses involved in vegetative desiccation tolerance of resurrection plant Selaginella brachystachya. 3 Biotech 2021; 11:135. [PMID: 33680700 PMCID: PMC7897589 DOI: 10.1007/s13205-021-02667-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/27/2021] [Indexed: 12/30/2022] Open
Abstract
The vegetative desiccation tolerance of Selaginella brachystachya has been evaluated for its ability to revive from a desiccation (air dry) state and start normal functioning when rehydrated. In this study, S. brachystachya was identified by DNA barcoding. Experiments were conducted using the detached hydrated, desiccated and rehydrated fronds under laboratory conditions to understand the mechanism of revival upon the water availability. Scanning Electron Microscope images during desiccation showed closed stomata and inside curled leaves. Chlorophyll concentration decreased by 1.1 fold in desiccated state and recovered completely upon rehydration. However, the total carotenoid content decreased 4.5 fold while the anthocyanin concentration increased 5.98 fold and the CO2 exchange rate became negative during desiccation. Lipid peroxidation and superoxide radical production were enhanced during desiccation by 68.32 and 73.4%, respectively. Relative electrolyte leakage was found to be minimal during desiccation. Activities of antioxidant enzymes, namely peroxidase (158.33%), glutathione reductase (107.70%), catalase (92.95%) and superoxide dismutase (184.70%) were found to be higher in the desiccated state. The proline concentration increased by 1.4 fold, starch concentration decreased 3.9 fold and sucrose content increased 2.8 fold during desiccation. Upon rehydration, S. brachystachya recovered its original morphology, physiological and biochemical functions. Our results demonstrate that S. brachystachya minimizes desiccation stress through a range of morphological, physiological and biochemical mechanisms. These results provide useful insights into desiccation tolerance mechanisms for potential utilization in enhancing stress tolerance in crop plants. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02667-1.
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Affiliation(s)
- Yathisha Neeragunda Shivaraj
- Department of Studies and Research in Environmental Science, Kuvempu University, Shankaraghatta, Shimoga 577451 India
- Department of Studies and Research in Biotechnology and Microbiology, Tumkur University, Tumakuru, 57210 India
| | - Barbara Plancot
- Laboratoire de Glycobiologie Et Matrice Extracellulaire Végétale, Université de Rouen, 76000 Rouen, Normandie France
- Fédération de Recherche “Normandie-Végétal”-FED 4277, 76000 Rouen, France
| | - Yasmina Ramdani
- Laboratoire de Glycobiologie Et Matrice Extracellulaire Végétale, Université de Rouen, 76000 Rouen, Normandie France
- Fédération de Recherche “Normandie-Végétal”-FED 4277, 76000 Rouen, France
| | - Bruno Gügi
- Laboratoire de Glycobiologie Et Matrice Extracellulaire Végétale, Université de Rouen, 76000 Rouen, Normandie France
- Fédération de Recherche “Normandie-Végétal”-FED 4277, 76000 Rouen, France
| | - Yogendra Kambalagere
- Department of Studies and Research in Environmental Science, Kuvempu University, Shankaraghatta, Shimoga 577451 India
| | - Sudisha Jogaiah
- Department of Studies and Research in Biotechnology and Microbiology, Karnataka University, Dharwad, India
| | - Azeddine Driouich
- Laboratoire de Glycobiologie Et Matrice Extracellulaire Végétale, Université de Rouen, 76000 Rouen, Normandie France
- Fédération de Recherche “Normandie-Végétal”-FED 4277, 76000 Rouen, France
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12
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Dhivya S, Ashutosh S, Gowtham I, Baskar V, Harini AB, Mukunthakumar S, Sathishkumar R. Molecular identification and evolutionary relationships between the subspecies of Musa by DNA barcodes. BMC Genomics 2020; 21:659. [PMID: 32972362 PMCID: PMC7513480 DOI: 10.1186/s12864-020-07036-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 08/30/2020] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND The banana (Musa sp., AAA) genome is constantly increasing due to high-frequency of somaclonal variations. Due to its large diversity, a conventional numerical and morphological based taxonomic identification of banana cultivars is laborious, difficult and often leads to subject of disagreements. RESULTS Hence, in the present study, we used universal DNA barcode ITS2 region to identify and to find the genetic relationship between the cultivars and varieties of banana. Herein, a total of 16 banana cultivars were PCR amplified using ITS2 primer pair. In addition, 321 sequences which were retrieved from GenBank, USA, were used in this study. The sequences were then aligned using Clustal W and genetic distances were computed using MEGA V5.1. The study showed significant divergence between the intra- and inter-specific genetic distances in ITS2 region. BLAST1 and Distance methods proved that ITS2 DNA barcode region successfully identified and distinguished the cultivar and varieties of banana. CONCLUSION Thus, from the results of the present study, it is clear that ITS2 is not only an efficient DNA barcode to identify the banana species but also a potential candidate for enumerating the phylogenetic relationships between the subspecies and cultivars. This is the first comprehensive study to categorically distinguish the economically important banana subspecies and varieties using DNA barcodes and to understand its evolutionary relationship.
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Affiliation(s)
- S Dhivya
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641046, India
| | - S Ashutosh
- Technologico de Monterrey, Centre of Bioengineering, Epigmenio Gonzalez #500, Fracc. San Pablo, Campus Queretaro, Santiago de Querétaro, Queretaro, Mexico
| | - I Gowtham
- Plant Biofarming Laboratory, DRDO-BU Centre for Life Sciences, Bharathiar University, Coimbatore, 641046, India
| | - V Baskar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641046, India
| | - A Baala Harini
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641046, India
| | - S Mukunthakumar
- Biotechnology and Bioinformatics Division, Jawaharlal Nehru Tropical Botanic Garden & Research Institute, Palode, Thiruvananthapuram, Kerala, 695 562, India
| | - R Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641046, India.
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13
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Tan WH, Chai LC, Chin CF. Efficacy of DNA barcode internal transcribed spacer 2 (ITS 2) in phylogenetic study of Alpinia species from Peninsular Malaysia. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1889-1896. [PMID: 32943824 PMCID: PMC7468033 DOI: 10.1007/s12298-020-00868-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 08/01/2020] [Accepted: 08/14/2020] [Indexed: 05/20/2023]
Abstract
Alpinia belongs to a large genus with many species found in Peninsular Malaysia. Several species of Alpinia exhibit important medicinal potential. However, progressive studies on the genus Alpinia were hampered by difficulties encountered in species identification. With the advancement achieved in genomic technology, more sensitive tools such as DNA barcoding were developed, which can be used for species identification. Internal Transcribe Spacer 2 (ITS2) is a DNA barcode which has proven to be a promising tool for species identification. The criterions of ITS2 efficacy namely universality and efficacy for species identification were tested on Alpinia species collected from Peninsular Malaysia. The results showed that a success rate of 96.97% was achieved using ITS2 for screening 11 species of Alpinia and an outgroup sample (Zingiber specatabile). Combined with 15 additional sequences from the Genbank for five Alpinia species, ITS2 demonstrated high species identification efficacy with 88.2% of species identified using phylogenetic and distance analysis. The analysis was further improved with the use of ITS2 secondary structure. The results of both criterions demonstrated the ability of ITS2 to successfully discriminate Alpinia species, which will help to improve species identification of Alpinia species in Peninsular Malaysia.
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Affiliation(s)
- Wei Harn Tan
- University of Nottingham Malaysia Campus, Semenyih, Malaysia
| | - Li Chin Chai
- University of Nottingham Malaysia Campus, Semenyih, Malaysia
| | - Chiew Foan Chin
- University of Nottingham Malaysia Campus, Semenyih, Malaysia
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Abstract
INTRODUCTION In Saudi Arabia, Rhazya stricta is a widely used folkloric plant because of its various therapeutic properties. It is sold in herbal markets as a dried powder; however, the absence of visible phenotypic traits in the powder can mask its authenticity. Potential misidentification of this substance threatens consumer health. DNA barcoding could accurately identify this plant regardless of its physical state, however barcoding presents the challenge of variations in marker loci. OBJECTIVES The objective of this work was to assess barcode markers from the chloroplast and nuclear regions to determine their taxonomic accuracy in R. stricta barcoding, and select the best marker for this species that could fulfill the authentication test for its fresh and dried samples. METHOD In this study, we assessed seven barcode markers from the chloroplast (psbA-trnH, matK, rbcL, rpoB, and rpoC1) and nuclear regions (ITS1and ITS2). We compared DNA sequences of R. stricta from 50 fresh locally collected samples and 10 dried ground samples from the herbal market with the database sequences of R. stricta, R. orientalis, and eight other related species as controls. We utilized three methods (BLAST, nearest distance, and neighbor-joining tree) in this analysis. RESULT With the exception of psbA-trnH, all the chloroplast markers determined high similarity with other taxa. However, nuclear ITS2 best distinguished between R. stricta, R. orientalis, and other related species because of its secondary structures, which allowed for more accurate distinctions. A two-locus marker of ITS1 + ITS2 sequences also showed promising results. A two-dimensional image of our proposed marker was generated to more easily handle DNA barcoding applications. CONCLUSION Our study indicates that ITS2 is a cost-effective barcoding marker capable of verifying the authenticity of R. stricta and other medicinal plants in order to protect consumer health.
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15
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Gu W, Zhang A, Sun H, Gu Y, Chao J, Tian R, Duan JA. Identifying resurrection genes through the differentially expressed genes between Selaginella tamariscina (Beauv.) spring and Selaginella moellendorffii Hieron under drought stress. PLoS One 2019; 14:e0224765. [PMID: 31721818 PMCID: PMC6853609 DOI: 10.1371/journal.pone.0224765] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 10/21/2019] [Indexed: 02/06/2023] Open
Abstract
Selaginella tamariscina (Beauv.) spring, a primitive vascular resurrection plant, can survive extreme drought and recover when water becomes available. To identify drought-inducible genes and to clarify the molecular mechanism of drought tolerance, a comparative transcriptional pattern analysis was conducted between S. tamariscina and Selaginella moellendorffii Hieron (drought sensitive). 133 drought related genes were identified, including 72 functional genes and 61 regulatory genes. And several drought responsive reactions, such as antioxidant activity, osmotic balance, cuticle defense and signal transduction were highlighted in S. tamariscina under drought. Notably, besides peroxidase, catalase and L-ascorbate oxidase genes, DEGs associated with phenylalanine metabolism and polyamine catabolism could be alternative ways to enhance antioxidant ability in S. tamariscina. DEGs related to soluble carbohydrate metabolism, late embryogenesis abundant protein (LEA) and aquaporin protein (AQP) confirmed that osmotic adjustment could resist drought during desiccation. DEGs involved in xyloglucan metabolic process, pectin metabolic process and cutin biosynthesis may also contribute to drought tolerance of S. tamariscina by cuticle defense. Drought-responsive genes encoding protein kinases, calcium sensors, transcription factors (TFs) and plant hormones also help to drought resistance of S. tamariscina. The preliminary validation experiments were performed and the results were consistent with our hypothetical integrated regulatory network. The results of this study provide candidate resurrection genes and an integrated regulatory network for further studies on the molecular mechanisms of stress tolerance in S. tamariscina.
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Affiliation(s)
- Wei Gu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Aqin Zhang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Hongmei Sun
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuchen Gu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jianguo Chao
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Rong Tian
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jin-Ao Duan
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
- * E-mail:
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16
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Liu ZW, Gao YZ, Zhou J. Molecular Authentication of the Medicinal Species of Ligusticum (Ligustici Rhizoma et Radix, "Gao-ben") by Integrating Non-coding Internal Transcribed Spacer 2 (ITS2) and Its Secondary Structure. FRONTIERS IN PLANT SCIENCE 2019; 10:429. [PMID: 31024595 PMCID: PMC6465525 DOI: 10.3389/fpls.2019.00429] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 03/21/2019] [Indexed: 05/16/2023]
Abstract
Ligustici Rhizoma et Radix (LReR), an important Chinese medicine known as "Gao-ben," refers to Ligusticum sinense Oliv. or Ligusticum jeholense Nakai et Kitag. However, a number of other species are commonly sold as "Gao-ben" in the herbal medicine market, which may result in a series of quality control problems and inconsistent therapeutic effects. The "Gao-ben" is commonly sold sliced and dried, making traditional identification methods difficult. Here, the mini barcode ITS2 region was examined on 68 samples representing LReR and 7 potential adulterant or substitute species. The results showed 100% success rates of PCR and sequencing and the existence of a barcoding gap. The neighbor-joining (NJ) tree indicated that all the tested samples could be exactly identified. The ITS2 secondary structure revealed a clear difference between true "Gao-ben" and three adulterant species. We therefore recommend the use of ITS2 as a mini barcode for distinguishing between closely or distantly related plant species that may be used in Chinese medicine.
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Affiliation(s)
- Zhen-wen Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yu-zhen Gao
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, China
| | - Jing Zhou
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, China
- *Correspondence: Jing Zhou,
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17
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Kandlikar GS, Gold ZJ, Cowen MC, Meyer RS, Freise AC, Kraft NJB, Moberg-Parker J, Sprague J, Kushner DJ, Curd EE. ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations. F1000Res 2018; 7:1734. [PMID: 30613396 PMCID: PMC6305237 DOI: 10.12688/f1000research.16680.1] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/23/2018] [Indexed: 11/29/2022] Open
Abstract
Environmental DNA (eDNA) metabarcoding is becoming a core tool in ecology and conservation biology, and is being used in a growing number of education, biodiversity monitoring, and public outreach programs in which professional research scientists engage community partners in primary research. Results from eDNA analyses can engage and educate natural resource managers, students, community scientists, and naturalists, but without significant training in bioinformatics, it can be difficult for this diverse audience to interact with eDNA results. Here we present the R package ranacapa, at the core of which is a Shiny web app that helps perform exploratory biodiversity analyses and visualizations of eDNA results. The app requires a taxonomy-by-sample matrix and a simple metadata file with descriptive information about each sample. The app enables users to explore the data with interactive figures and presents results from simple community ecology analyses. We demonstrate the value of ranacapa to two groups of community partners engaging with eDNA metabarcoding results.
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Affiliation(s)
- Gaurav S Kandlikar
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Zachary J Gold
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Madeline C Cowen
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Rachel S Meyer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Amanda C Freise
- Department of Microbiology and Microbial Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Nathan J B Kraft
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jordan Moberg-Parker
- Department of Microbiology and Microbial Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Joshua Sprague
- Channel Islands National Park, National Park Service, Ventura, CA, USA
| | - David J Kushner
- Channel Islands National Park, National Park Service, Ventura, CA, USA
| | - Emily E Curd
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
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18
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Gong L, Qiu XH, Huang J, Xu W, Bai JQ, Zhang J, Su H, Xu CM, Huang ZH. Constructing a DNA barcode reference library for southern herbs in China: A resource for authentication of southern Chinese medicine. PLoS One 2018; 13:e0201240. [PMID: 30044868 PMCID: PMC6059470 DOI: 10.1371/journal.pone.0201240] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 07/11/2018] [Indexed: 11/19/2022] Open
Abstract
Southern Chinese Medicine (SCM) is an important sect of Traditional Chinese Medicine (TCM) with its own special cultural style. Species identification is essential for TCM quality control because authentic herbs are possibly substituted with adulterants that would threaten the health of the public or even cause death. Here, we provided the first local reference DNA barcode library based on the second internal transcribed spacer (ITS2) for the molecular identification of SCM. A total of 1512 specimens of southern herbs representing 359 species were collected under the instructions and identification of taxonomic experts. Genomic DNA was extracted, and the PCR reaction proceeded according to standard procedures. After Sanger sequencing, sequence assembling and annotation, a reliable ITS2 barcode library with 1276 sequences from 309 species of Southern herbs was constructed. The PCR efficiency of the whole samples was 84.39%. Characteristics of the ITS2 barcode were analyzed, including sequence lengths and GC contents in different taxa. Neighbor-joining trees based on Kimura 2-Parameter (K2P) genetic distances showed a 67.56% successful rate of species identification with ITS2 barcode. In addition, 96.57% of species could be successfully identified at the genus level by the BLAST method. Eleven plant species were discovered to be cryptic. In addition, we found that there is an incorrect sequence existing in the public database, making a reliable local DNA barcode reference more meaningful. ITS2 barcodes exhibit advantages in TCM identification. This DNA barcode reference library could be used in Southern Chinese Medicine quality control, thus contributing to protecting public health.
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Affiliation(s)
- Lu Gong
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
| | - Xiao Hui Qiu
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou, China
| | - Juan Huang
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
| | - Wen Xu
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
| | - Jun Qi Bai
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
| | - Jing Zhang
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
| | - He Su
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
| | - Chu Mei Xu
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
| | - Zhi Hai Huang
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
- * E-mail:
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19
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Xu Z, Xin T, Bartels D, Li Y, Gu W, Yao H, Liu S, Yu H, Pu X, Zhou J, Xu J, Xi C, Lei H, Song J, Chen S. Genome Analysis of the Ancient Tracheophyte Selaginella tamariscina Reveals Evolutionary Features Relevant to the Acquisition of Desiccation Tolerance. MOLECULAR PLANT 2018; 11:983-994. [PMID: 29777775 DOI: 10.1016/j.molp.2018.05.003] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 04/30/2018] [Accepted: 05/07/2018] [Indexed: 05/18/2023]
Abstract
Resurrection plants, which are the "gifts" of natural evolution, are ideal models for studying the genetic basis of plant desiccation tolerance. Here, we report a high-quality genome assembly of 301 Mb for the diploid spike moss Selaginella tamariscina, a primitive vascular resurrection plant. We predicated 27 761 protein-coding genes from the assembled S. tamariscina genome, 11.38% (2363) of which showed significant expression changes in response to desiccation. Approximately 60.58% of the S. tamariscina genome was annotated as repetitive DNA, which is an almost 2-fold increase of that in the genome of desiccation-sensitive Selaginella moellendorffii. Genomic and transcriptomic analyses highlight the unique evolution and complex regulations of the desiccation response in S. tamariscina, including species-specific expansion of the oleosin and pentatricopeptide repeat gene families, unique genes and pathways for reactive oxygen species generation and scavenging, and enhanced abscisic acid (ABA) biosynthesis and potentially distinct regulation of ABA signaling and response. Comparative analysis of chloroplast genomes of several Selaginella species revealed a unique structural rearrangement and the complete loss of chloroplast NAD(P)H dehydrogenase (NDH) genes in S. tamariscina, suggesting a link between the absence of the NDH complex and desiccation tolerance. Taken together, our comparative genomic and transcriptomic analyses reveal common and species-specific desiccation tolerance strategies in S. tamariscina, providing significant insights into the desiccation tolerance mechanism and the evolution of resurrection plants.
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Affiliation(s)
- Zhichao Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Tianyi Xin
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Dorothea Bartels
- Institute of Molecular Plant Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, 53115 Bonn, Germany
| | - Ying Li
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Wei Gu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Hui Yao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Sai Liu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Haoying Yu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Xiangdong Pu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Jianguo Zhou
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Caicai Xi
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Hetian Lei
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China.
| | - Shilin Chen
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China; Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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Zhang J, Hu X, Wang P, Huang B, Sun W, Xiong C, Hu Z, Chen S. Investigation on Species Authenticity for Herbal Products of Celastrus Orbiculatus and Tripterygum Wilfordii from Markets Using ITS2 Barcoding. Molecules 2018; 23:molecules23040967. [PMID: 29690494 PMCID: PMC6017776 DOI: 10.3390/molecules23040967] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 04/07/2018] [Accepted: 04/13/2018] [Indexed: 11/19/2022] Open
Abstract
Herbal material is both a medicine and a commodity. Accurate identification of herbal materials is necessary to ensure the safety and effectiveness of medication. With this work, we initiated an identification method to investigate the species authenticity for herbal products of Celastrus orbiculatus and Tripterygum wilfordii utilizing DNA barcoding technology. An ITS2 (internal transcribed spacer two) barcode database including 59 sequences was successfully established to estimate the reliability of species-level identification for Celastrus and Tripterygium. Our findings showed that ITS2 can effectively and clearly distinguish C. orbiculatus, T. wilfordii and its congeners. Then, we investigated the proportions and varieties of adulterant species in the herbal markets. The data from ITS2 region indicated that 13 (62%) of the 21 samples labeled as “Nan-she-teng” and eight (31%) of the 26 samples labeled as “Lei-gong-teng” were authentic; the remaining were adulterants. Of the 47 herbal products, approximately 55% of the product identity were not in accordance with the label. In summary, we support the efficacy of the ITS2 barcode for the traceability of C. orbiculatus and T. wilfordii, and the present study provides one method and reference for the identification of the herbal materials and adulterants in the medicinal markets.
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Affiliation(s)
- Jingjing Zhang
- College of Pharmacy, Hubei University of Chinese Medicine, No. 1 Huangjiahu West Road, Hongshan District, Wuhan 430065, China.
- Zhang Zhongjing Traditional Chinese Medicine College, Henan Key Laboratory of Zhang Zhongjing Formulae and Herbs for Immunoregulation, Nanyang Institute of Technology, No. 80 Changjiang Road, Wancheng District, Nanyang 473004, China.
| | - Xin Hu
- College of Pharmacy, Hubei University of Chinese Medicine, No. 1 Huangjiahu West Road, Hongshan District, Wuhan 430065, China.
| | - Ping Wang
- College of Pharmacy, Hubei University of Chinese Medicine, No. 1 Huangjiahu West Road, Hongshan District, Wuhan 430065, China.
| | - Bisheng Huang
- College of Pharmacy, Hubei University of Chinese Medicine, No. 1 Huangjiahu West Road, Hongshan District, Wuhan 430065, China.
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medicinal Sciences, No.16 Dongzhimenneinanxiaojie street, Dongcheng District, Beijing 100700, China.
| | - Chao Xiong
- College of Pharmacy, Hubei University of Chinese Medicine, No. 1 Huangjiahu West Road, Hongshan District, Wuhan 430065, China.
| | - Zhigang Hu
- College of Pharmacy, Hubei University of Chinese Medicine, No. 1 Huangjiahu West Road, Hongshan District, Wuhan 430065, China.
- Zhan Yahua National Famous Traditional Chinese Medicine Experts Inheritance Studio, No. 1 Huangjiahu West Road, Hongshan District, Wuhan 430065, China.
| | - Shilin Chen
- College of Pharmacy, Hubei University of Chinese Medicine, No. 1 Huangjiahu West Road, Hongshan District, Wuhan 430065, China.
- Institute of Chinese Materia Medica, China Academy of Chinese Medicinal Sciences, No.16 Dongzhimenneinanxiaojie street, Dongcheng District, Beijing 100700, China.
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Arshed MJC, Valdez MB, Alejandro GJD. Evaluating the Feasibility of Five Candidate DNA Barcoding Loci for Philippine Lasianthus Jack ( Lasiantheae: Rubiaceae). Pharmacogn Mag 2017; 13:553-558. [PMID: 29200712 PMCID: PMC5701390 DOI: 10.4103/pm.pm_1_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 02/01/2017] [Indexed: 11/04/2022] Open
Abstract
Introduction The pantropical genus Lasianthus Jack is identified for high phenotypic plasticity making traditional taxonomic identification difficult. Having some members with important medicinal properties, a precise complimentary identification through DNA barcoding is needed for species delineation. Materials and Methods In this study, 12 samples representing six Philippine Lasianthus species were used to determine the most efficient barcoding loci among the cpDNA markers (matK, rbcL, rps16, and trnT-F) and nrDNA (ITS) based on the criteria of universality, discriminatory power, and resolution of species. Results The results revealed that ITS has the recommended primer universality, greatest interspecific divergences, and average resolution of species. Among the cpDNA markers, matK and rbcL are recommended but with minimal resolution of species. While trnT-F showed moderate interspecific variations and resolution of Lasianthus species, rps16 has the lowest interspecific divergence and resolution of species. Conclusion Consequently, ITS is the potential ideal DNA barcode for Lasianthus species. SUMMARY ITS, matK, and rps16 markers have the excellent amplification and sequence qualityITS marker has the highest interspecific divergence with the maximum values, followed by matK, rbcL, trnT-F, and rps16, respectivelyAll markers except rps16 yielded average resolution to Lasianthus speciesITS marker is the most ideal locus in terms of excellent universality, high interspecific discriminatory ability, and average species resolution. Abbreviations used: ITS: Internal Transcribe Spacer, matK: maturase K, rbcL: ribulose-1,5-biphospahte-carboxylase, rps16: ribosomal protein 16 small subunit gene.
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Affiliation(s)
| | - Marcos B Valdez
- Department of Biological Sciences, Institute of Arts and Sciences, Far Eastern University, Nicanor Reyes Street, Sampaloc, 1008 Manila, Philippines
| | - Grecebio Jonathan D Alejandro
- The Graduate School and Research Center for the Natural and Applied Sciences, University of Santo Tomas, España Blvd, 1015 Manila, Philippines
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Yu N, Wei YL, Zhang X, Zhu N, Wang YL, Zhu Y, Zhang HP, Li FM, Yang L, Sun JQ, Sun AD. Barcode ITS2: a useful tool for identifying Trachelospermum jasminoides and a good monitor for medicine market. Sci Rep 2017; 7:5037. [PMID: 28698616 PMCID: PMC5506054 DOI: 10.1038/s41598-017-04674-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 05/18/2017] [Indexed: 01/31/2023] Open
Abstract
Trachelospermum jasminoides is commonly used in traditional Chinese medicine. However, the use of the plant's local alternatives is frequent, causing potential clinical problems. The T. jasminoides sold in the medicine market is commonly dried and sliced, making traditional identification methods difficult. In this study, the ITS2 region was evaluated on 127 sequences representing T. jasminoides and its local alternatives according to PCR and sequencing rates, intra- and inter-specific divergences, secondary structure, and discrimination capacity. Results indicated the 100% success rates of PCR and sequencing and the obvious presence of a barcoding gap. Results of BLAST 1, nearest distance and neighbor-joining tree methods showed that barcode ITS2 could successfully identify all the texted samples. The secondary structures of the ITS2 region provided another dimensionality for species identification. Two-dimensional images were obtained for better and easier identification. Previous studies on DNA barcoding concentrated more on the same family, genus, or species. However, an ideal barcode should be variable enough to identify closely related species. Meanwhile, the barcodes should also be conservative in identifying distantly related species. This study highlights the application of barcode ITS2 in solving practical problems in the distantly related local alternatives of medical plants.
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Affiliation(s)
- Ning Yu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Yu-Long Wei
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Xin Zhang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Ning Zhu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Yan-Li Wang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Yue Zhu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Hai-Ping Zhang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Fen-Mei Li
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Lan Yang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Jia-Qi Sun
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Ai-Dong Sun
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China.
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Shu JP, Shang H, Jin D, Wei HJ, Zhou XL, Liu HM, Gu YF, Wang Y, Wang FG, Shen H, Zhang R, Adjie B, Yan YH. Re-establishment of species from synonymies based on DNA barcoding and phylogenetic analysis using Diplopterygium simulans (Gleicheniaceae) as an example. PLoS One 2017; 12:e0164604. [PMID: 28296890 PMCID: PMC5351838 DOI: 10.1371/journal.pone.0164604] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Accepted: 07/21/2016] [Indexed: 11/19/2022] Open
Abstract
Because synonymy treatment traditionally relies on morphological judgments, it usually causes many problems in species delimitation and in the biodiversity catalogue. For example, Diplopterygium simulans, which belongs to the Gleicheniaceae family, has been considered to be synonymous with D. glaucum or D. giganteum based mainly on the morphology of its pinna rachis and blade. In the absence of molecular evidence, these revisions remain doubtful. DNA barcoding, which is considered to be a powerful method for species-level identification, was employed to assess the genetic distance among 9 members of the Diplopterygium genus. The results indicate that D. simulans is an independent species rather than a synonymy of D. glaucum or D. giganteum. Moreover, phylogenetic analysis uncovered the sisterhood of D. simulans and D. cantonense, which is supported by their geographical distributions and morphological traits. Incorrect synonymy treatment is prevalent in the characterization of biological diversity, and our study proposes a convenient and effective method for validating synonym treatments and discovering cryptic species.
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Affiliation(s)
- Jiang-Ping Shu
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Hui Shang
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Dongmei Jin
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Hong-Jin Wei
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Xi-Le Zhou
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Hong-Mei Liu
- Shenzhen Fairylake Botanical Garden, Chinese Academy of Sciences, Shenzhen, China
| | - Yu-Feng Gu
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Ying Wang
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Fa-Guo Wang
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Hui Shen
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Rui Zhang
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Bayu Adjie
- Bali Botanic Garden, Indonesian Institute of Science, Bali, Indonesia
| | - Yue-Hong Yan
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
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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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Yu B, Cai W, Zhang HH, Zhong YS, Fang J, Zhang WY, Mo L, Wang LC, Yu CH. Selaginella uncinata flavonoids ameliorated ovalbumin-induced airway inflammation in a rat model of asthma. JOURNAL OF ETHNOPHARMACOLOGY 2017; 195:71-80. [PMID: 27916586 DOI: 10.1016/j.jep.2016.11.049] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 11/06/2016] [Accepted: 11/30/2016] [Indexed: 06/06/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Selaginella uncinata (Desv.) Spring, known as "Cuiyuncao", is a perennial herb widely distributed in the Southeast Asian countries. In the folk medicine, the local minority commonly use it to treat cough and asthma for centuries. AIM OF THE STUDY This study was carried out to investigate the protective mechanisms of total flavonoids from S. uncinata (SUF) on airway hyperresponsiveness, cytokine release and bitter taste receptors (T2Rs) signaling with emphasis on inflammatory responses in a rat model of ovalbumin (OVA)-induced asthma. MATERIALS AND METHODS Rats were sensitized and challenged with OVA to induce typical asthmatic reactions. Pathological changes of lung tissue were examined by HE staining. The serum levels of T cell-associated cytokines (IFN-γ, IL-4, IL-5 and IL-13), total IgE and OVA-specific IgE were determined by enzyme-linked immunosorbent assay (ELISA). Gene expressions of T2R10, IP3R1 and Orai1 in lung tissue were assayed by fluorescence quantitative real-time polymerase chain reaction (FQ-PCR) while protein expressions of NFAT1 and c-Myc were assayed by western blot analysis. The activation of SUF was investigated on tansgentic T2R10-GFP HEK293 cells. RESULTS SUF treatment attenuated airway hyperresponsiveness and goblet cell hyperplasia compared with OVA-challenged asthmatic rats. The serum levels of IL-4, IL-5 and IL-13 as well as total and OVA-specific IgE were decreased while serum IFN-γ was increased in SUF-treated rats. SUF treatment significantly up-regulated T2R10 gene expression, down-regulated IP3R1 and Orai1 gene expression. SUF further suppressed eotaxin, NFAT1 and c-Myc protein expression in lung tissues of OVA-challenged rats. CONCLUSIONS These results imply that SUF exerts anti-inflammatory function through the T2R10/IP3R1/NFAT1 dependent signaling pathway, and may warrant further evaluation as a possible agent for the treatment of asthma.
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Affiliation(s)
- Bing Yu
- College of Pharmacy, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Wei Cai
- Department of Traditional Chinese Medicine, Zhejiang Pharmaceutical College, Ningbo 315100, China
| | - Huan-Huan Zhang
- Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou 310013, China
| | - Yu-Sen Zhong
- Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou 310013, China
| | - Jie Fang
- Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou 310013, China
| | - Wen-You Zhang
- Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou 310013, China
| | - Li Mo
- College of Pharmacy, Zhejiang Chinese Medical University, Hangzhou 310053, China; Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou 310013, China
| | - Lu-Chen Wang
- College of Pharmacy, Zhejiang Chinese Medical University, Hangzhou 310053, China; Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou 310013, China
| | - Chen-Huan Yu
- Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou 310013, China.
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Poovitha S, Stalin N, Balaji R, Parani M. Multi-locus DNA barcoding identifies matK as a suitable marker for species identification in Hibiscus L. Genome 2016; 59:1150-1156. [DOI: 10.1139/gen-2015-0205] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genus Hibiscus L. includes several taxa of medicinal value and species used for the extraction of natural dyes. These applications require the use of authentic plant materials. DNA barcoding is a molecular method for species identification, which helps in reliable authentication by using one or more DNA barcode marker. In this study, we have collected 44 accessions, representing 16 species of Hibiscus, distributed in the southern peninsular India, to evaluate the discriminatory power of the two core barcodes rbcLa and matK together with the suggested additional regions trnH-psbA and ITS2. No intraspecies divergence was observed among the accessions studied. Interspecies divergence was 0%–9.6% with individual markers, which increased to 0%–12.5% and 0.8%–20.3% when using two- and three-marker combinations, respectively. Differentiation of all the species of Hibiscus was possible with the matK DNA barcode marker. Also, in two-marker combinations, only those combinations with matK differentiated all the species. Though all the three-marker combinations showed 100% species differentiation, species resolution was consistently better when the matK marker formed part of the combination. These results clearly showed that matK is more suitable when compared to rbcLa, trnH-psbA, and ITS2 for species identification in Hibiscus.
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Affiliation(s)
- Sundar Poovitha
- Centre for DNA Barcoding, Department of Genetic Engineering, SRM University, Kattankulathur, Tamil Nadu, India
- Centre for DNA Barcoding, Department of Genetic Engineering, SRM University, Kattankulathur, Tamil Nadu, India
| | - Nithaniyal Stalin
- Centre for DNA Barcoding, Department of Genetic Engineering, SRM University, Kattankulathur, Tamil Nadu, India
- Centre for DNA Barcoding, Department of Genetic Engineering, SRM University, Kattankulathur, Tamil Nadu, India
| | - Raju Balaji
- Centre for DNA Barcoding, Department of Genetic Engineering, SRM University, Kattankulathur, Tamil Nadu, India
- Centre for DNA Barcoding, Department of Genetic Engineering, SRM University, Kattankulathur, Tamil Nadu, India
| | - Madasamy Parani
- Centre for DNA Barcoding, Department of Genetic Engineering, SRM University, Kattankulathur, Tamil Nadu, India
- Centre for DNA Barcoding, Department of Genetic Engineering, SRM University, Kattankulathur, Tamil Nadu, India
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Zhang W, Zhang M, Wang Z, Cheng Y, Liu H, Zhou Z, Han B, Chen B, Yao H, Chao J. Neogambogic acid prevents silica-induced fibrosis via inhibition of high-mobility group box 1 and MCP-1-induced protein 1. Toxicol Appl Pharmacol 2016; 309:129-40. [PMID: 27616297 DOI: 10.1016/j.taap.2016.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/13/2016] [Accepted: 09/06/2016] [Indexed: 12/26/2022]
Abstract
BACKGROUND Silicosis is a systemic disease caused by inhaling silicon dioxide (SiO2); early stages are characterized by alveolar inflammation, and later stages are characterized by progressive lung fibrosis. Mounting evidence indicates that high-mobility group box 1 (HMGB1) is involved in pulmonary fibrosis. Whether neogambogic acid (NGA) inhibits macrophage and fibroblast activation induced by SiO2 by targeting HMGB1 remains unclear. METHODS AND RESULTS Experiments using cultured mouse macrophages (RAW264.7 cells) demonstrated that SiO2 treatment induces the expression of HMGB1 in a time- and dose-dependent manner via mitogen-activated protein kinases (MAPKs) and the phosphatidylinositol 3-kinase (PI3K)/Akt pathway; in turn, this expression causes macrophage apoptosis and fibroblast activation. Pretreating macrophages with NGA inhibited the HMGB1 expression induced by SiO2 and attenuated both macrophage apoptosis and fibroblast activation. Moreover, NGA directly inhibited MCP-1-induced protein 1 (MCPIP1) expression, as well as markers of fibroblast activation and migration induced by SiO2. Furthermore, the effects of NGA on macrophages and fibroblasts were confirmed in vivo by exposing mice to SiO2. CONCLUSION NGA can prevent SiO2-induced macrophage activation and apoptosis via HMGB1 inhibition and SiO2-induced fibrosis via the MCPIP1 pathway. Targeting HMGB1 and MCPIP1 with NGA could provide insights into the potential development of a therapeutic approach for alleviating the inflammation and fibrosis induced by SiO2.
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Affiliation(s)
- Wei Zhang
- Department of Physiology, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China; Department of Pharmacology, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China; Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China; Department of Respiration, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China
| | - Mei Zhang
- Department of Respiration, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China.
| | - Zhongjiang Wang
- Department of Radiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China
| | - Yusi Cheng
- Department of Physiology, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China
| | - Haijun Liu
- Department of Physiology, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China
| | - Zewei Zhou
- Department of Physiology, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China; Department of Pharmacology, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China
| | - Bing Han
- Department of Pharmacology, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China
| | - Baoan Chen
- Department of Hematology and Oncology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China
| | - Honghong Yao
- Department of Pharmacology, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China; Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China.
| | - Jie Chao
- Department of Physiology, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China; Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China; Department of Respiration, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China.
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Feng S, Jiang M, Shi Y, Jiao K, Shen C, Lu J, Ying Q, Wang H. Application of the Ribosomal DNA ITS2 Region of Physalis (Solanaceae): DNA Barcoding and Phylogenetic Study. FRONTIERS IN PLANT SCIENCE 2016; 7:1047. [PMID: 27486467 PMCID: PMC4949264 DOI: 10.3389/fpls.2016.01047] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 07/04/2016] [Indexed: 05/15/2023]
Abstract
Recently, commercial interest in Physalis species has grown worldwide due to their high nutritional value, edible fruit, and potential medicinal properties. However, many Physalis species have similar shapes and are easily confused, and consequently the phylogenetic relationships between Physalis species are poorly understood. This hinders their safe utilization and genetic resource conservation. In this study, the nuclear ribosomal ITS2 region was used to identify species and phylogenetically examine Physalis. Eighty-six ITS2 regions from 45 Physalis species were analyzed. The ITS2 sequences were aligned using Clustal W and genetic distances were calculated using MEGA V6.0. The results showed that ITS2 regions have significant intra- and inter-specific divergences, obvious barcoding gaps, and higher species discrimination rates (82.2% for both the BLASTA1 and nearest distance methods). In addition, the secondary structure of ITS2 provided another way to differentiate species. Cluster analysis based on ITS2 regions largely concurred with the relationships among Physalis species established by many previous molecular analyses, and showed that most sections of Physalis appear to be polyphyletic. Our results demonstrated that ITS2 can be used as an efficient and powerful marker in the identification and phylogenetic study of Physalis species. The technique provides a scientific basis for the conservation of Physalis plants and for utilization of resources.
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Affiliation(s)
- Shangguo Feng
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Mengying Jiang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Yujun Shi
- School of Foreign Languages, Zhejiang Gongshang UniversityHangzhou, China
| | - Kaili Jiao
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Chenjia Shen
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Jiangjie Lu
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Qicai Ying
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Huizhong Wang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
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Wang X, Zhang Y, Zhang W, Liu H, Zhou Z, Dai X, Cheng Y, Fang S, Zhang Y, Yao H, Chao J. MCPIP1 Regulates Alveolar Macrophage Apoptosis and Pulmonary Fibroblast Activation After in vitro Exposure to Silica. Toxicol Sci 2016; 151:126-38. [PMID: 26865670 DOI: 10.1093/toxsci/kfw029] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Silicosis is a fatal and fibrotic pulmonary disease caused by the inhalation of silica. After arriving at the alveoli, silica is ingested by alveolar macrophages (AMOs), in which monocyte chemotactic protein-induced protein 1 (MCPIP1) plays an essential role in controlling macrophage-mediated inflammatory responses. However, the mechanism of action of MCPIP1 in silicosis is poorly understood. METHODS Primary rat AMOs were isolated and treated with SiO2 (50 µg/cm(2)). MCPIP1 and AMO activation/apoptosis markers were detected by immunoblotting. MCPIP1 was down-regulated using siRNA in AMOs. The effects of AMOs on fibroblast activation and migration were evaluated using a gel contraction assay, a scratch assay, and a nested collagen matrix migration model. RESULTS After exposure to SiO2, MCPIP1 was significantly increased in rat AMOs. Activation and apoptosis markers in AMOs were up-regulated after exposure to SiO2 Following siRNA-mediated silencing of MCPIP1 mRNA, the markers of AMO activation and apoptosis were significantly decreased. Rat pulmonary fibroblasts (PFBs) cultured in conditional medium from AMOs treated with MCPIP1 siRNA and SiO2 showed significantly less activation and migration compared with those cultured in conditional medium from AMOs treated with control siRNA and SiO2 CONCLUSION: Our data suggest a vital role for MCPIP1 in AMO apoptosis and PFB activation/migration induced by SiO2.
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Affiliation(s)
- Xingang Wang
- *Department of Physiology, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China Department of Pharmacology, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China
| | - Yuxia Zhang
- *Department of Physiology, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China
| | - Wei Zhang
- *Department of Physiology, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China
| | - Haijun Liu
- *Department of Physiology, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China Neurobiology Laboratory, New Drug Screening Centre, China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Zewei Zhou
- *Department of Physiology, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China Department of Pharmacology, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China
| | - Xiaoniu Dai
- *Department of Physiology, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China
| | - Yusi Cheng
- *Department of Physiology, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China
| | - Shencun Fang
- Nine Department of Respiratory Medicine, Nanjing Chest Hospital, Nanjing, Jiangsu 210029, China
| | - Yingming Zhang
- Nine Department of Respiratory Medicine, Nanjing Chest Hospital, Nanjing, Jiangsu 210029, China
| | - Honghong Yao
- Department of Pharmacology, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Jie Chao
- *Department of Physiology, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China, Department of Respiration, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China
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Wu L, Wang B, Zhao M, Liu W, Zhang P, Shi Y, Xiong C, Wang P, Sun W, Chen S. Rapid Identification of Officinal Akebiae Caulis and Its Toxic Adulterant Aristolochiae Manshuriensis Caulis (Aristolochia manshuriensis) by Loop-Mediated Isothermal Amplification. FRONTIERS IN PLANT SCIENCE 2016; 7:887. [PMID: 27379153 PMCID: PMC4913086 DOI: 10.3389/fpls.2016.00887] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 06/06/2016] [Indexed: 05/07/2023]
Abstract
Mu-tong (Akebiae Caulis) is a traditional Chinese medicine commonly used as a diuretic and antiphlogistic. A common adulterant of Mu-tong is Guan-mu-tong (Aristolochiae Manshuriensis Caulis), which is derived from the stem of Aristolochia manshuriensis Komarov, and contains carcinogenic aristolochic acids. We used an alternative technique, loop-mediated isothermal amplification (LAMP), to differentiate Mu-tong from Guan-mu-tong because LAMP is quick, highly sensitive, and specific. We designed a set of four common primers (G-F3, G-B3, G-FIP, and G-BIP) and a loop primer (G-LB) for LAMP based on the internal transcribed spacer 2 sequence of Ar. manshuriensis. We successfully amplified the LAMP assays and visual detection occurred within 60 min at isothermal conditions of 65°C. The LAMP reaction exhibited a tenfold increase in detection (4.22 pg/μl DNA) over conventional polymerase chain reaction demonstrating that LAMP is a useful technique to detect Guan-mu-tong. We conclude that the LAMP technique is a potentially valuable safety control method for simple and efficient discrimination of Mu-tong from its adulterant Guan-mu-tong.
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Affiliation(s)
- Lan Wu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
- College of Pharmacy, Hubei University of Chinese MedicineWuhan, China
| | - Bo Wang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Mingming Zhao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Wei Liu
- Institute of Disease Control and Prevention, Academy of Military Medical SciencesBeijing, China
| | - Peng Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Yuhua Shi
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Chao Xiong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Ping Wang
- College of Pharmacy, Hubei University of Chinese MedicineWuhan, China
| | - Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
- *Correspondence: Wei Sun, ; Shilin Chen,
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
- College of Pharmacy, Hubei University of Chinese MedicineWuhan, China
- *Correspondence: Wei Sun, ; Shilin Chen,
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Zhao S, Chen X, Song J, Pang X, Chen S. Internal transcribed spacer 2 barcode: a good tool for identifying Acanthopanacis cortex. FRONTIERS IN PLANT SCIENCE 2015; 6:840. [PMID: 26500674 PMCID: PMC4597102 DOI: 10.3389/fpls.2015.00840] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/24/2015] [Indexed: 05/02/2023]
Abstract
Acanthopanacis cortex has been used in clinical applications for a long time. Considering some historical and geographical factors, Acanthopanacis cortex is easily confused with other herbs in medicine markets, thereby causing potential safety issues. In this study, we used the internal transcribed spacer 2 (ITS2) barcode to identify 69 samples belonging to six species, including Acanthopanacis cortex and its adulterants. The nearest distance, single-nucleotide polymorphisms (SNPs), and neighbor-joining (NJ) tree methods were used to evaluate the identification ability of the ITS2 barcode. According to the kimura-2-parameter model, the intraspecific distance of Eleutherococcus nodiflorus ITS2 sequences ranged from 0 to 0.0132. The minimum interspecific distance between E. nodiflorus and E. giraldii was 0.0221, which was larger than the maximum intraspecific distance of E. nodiflorus. Three stable SNPs in ITS2 can be used to distinguish Acanthopanacis cortex and its closely related species. The NJ tree indicated that the Acanthopanacis cortex samples clustered into one clade, which can be distinguished clearly from the adulterants of this herb. A secondary structure of ITS2 provided another dimensionality to identify species. In conclusion, the ITS2 barcode effectively identifies Acanthopanacis cortex, and DNA barcoding is a convenient tool for medicine market supervision.
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Affiliation(s)
- Sha Zhao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
| | - Xiaochen Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
| | - Jingyuan Song
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
| | - Xiaohui Pang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
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Feng S, Jiang Y, Wang S, Jiang M, Chen Z, Ying Q, Wang H. Molecular Identification of Dendrobium Species (Orchidaceae) Based on the DNA Barcode ITS2 Region and Its Application for Phylogenetic Study. Int J Mol Sci 2015; 16:21975-88. [PMID: 26378526 PMCID: PMC4613292 DOI: 10.3390/ijms160921975] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/26/2015] [Accepted: 08/27/2015] [Indexed: 11/22/2022] Open
Abstract
The over-collection and habitat destruction of natural Dendrobium populations for their commercial medicinal value has led to these plants being under severe threat of extinction. In addition, many Dendrobium plants are similarly shaped and easily confused during the absence of flowering stages. In the present study, we examined the application of the ITS2 region in barcoding and phylogenetic analyses of Dendrobium species (Orchidaceae). For barcoding, ITS2 regions of 43 samples in Dendrobium were amplified. In combination with sequences from GenBank, the sequences were aligned using Clustal W and genetic distances were computed using MEGA V5.1. The success rate of PCR amplification and sequencing was 100%. There was a significant divergence between the inter- and intra-specific genetic distances of ITS2 regions, while the presence of a barcoding gap was obvious. Based on the BLAST1, nearest distance and TaxonGAP methods, our results showed that the ITS2 regions could successfully identify the species of most Dendrobium samples examined; Second, we used ITS2 as a DNA marker to infer phylogenetic relationships of 64 Dendrobium species. The results showed that cluster analysis using the ITS2 region mainly supported the relationship between the species of Dendrobium established by traditional morphological methods and many previous molecular analyses. To sum up, the ITS2 region can not only be used as an efficient barcode to identify Dendrobium species, but also has the potential to contribute to the phylogenetic analysis of the genus Dendrobium.
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Affiliation(s)
- Shangguo Feng
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310018, China.
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha 410128, China.
| | - Yan Jiang
- Zhejiang Institute of Chinese Meteria Medica, Hangzhou 310023, China.
| | - Shang Wang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310018, China.
| | - Mengying Jiang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310018, China.
| | - Zhe Chen
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310018, China.
| | - Qicai Ying
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310018, China.
| | - Huizhong Wang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310018, China.
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Zhou XM, Rothfels CJ, Zhang L, He ZR, Le Péchon T, He H, Lu NT, Knapp R, Lorence D, He XJ, Gao XF, Zhang LB. A large-scale phylogeny of the lycophyte genusSelaginella(Selaginellaceae: Lycopodiopsida) based on plastid and nuclear loci. Cladistics 2015; 32:360-389. [DOI: 10.1111/cla.12136] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2015] [Indexed: 11/30/2022] Open
Affiliation(s)
- Xin-Mao Zhou
- Chengdu Institute of Biology; Chinese Academy of Sciences; PO Box 416 Chengdu Sichuan 610041 China
- School of Life Sciences; Sichuan University; Chengdu Sichuan 610064 China
| | - Carl J. Rothfels
- Department of Zoology; University of British Columbia; #4200-6270 University Blvd Vancouver BC V6T 1Z4 Canada
- University Herbarium and Department of Integrative Biology; University of California; Berkeley CA 94720-2465 USA
| | - Liang Zhang
- Chengdu Institute of Biology; Chinese Academy of Sciences; PO Box 416 Chengdu Sichuan 610041 China
| | - Zhao-Rong He
- School of Life Science; Yunnan University; Kunming Yunnan 650091 China
| | - Timothée Le Péchon
- Chengdu Institute of Biology; Chinese Academy of Sciences; PO Box 416 Chengdu Sichuan 610041 China
- School of Life Sciences; University of KwaZulu-Natal; Private Bag X01 Scottsville Pietermaritzburg 3209 South Africa
| | - Hai He
- Department of Biology; Chongqing Normal University; Shapingba, Chongqing 400047 China
| | - Ngan Thi Lu
- Department of Botany, Vietnam National Museum of Nature; Vietnam Academy of Science and Technology; 18th Hoang Quoc Viet Road Cau Giay, Ha Noi Viet Nam
| | - Ralf Knapp
- Correspondent of the Muséum national d'Histoire naturelle (MNHN, Paris, France); Steigestrasse 78 69412 Eberbach Germany
| | - David Lorence
- National Tropical Botanical Garden; 3530 Papalina Road Kalaheo HI 96741 USA
| | - Xing-Jin He
- School of Life Sciences; Sichuan University; Chengdu Sichuan 610064 China
| | - Xin-Fen Gao
- Chengdu Institute of Biology; Chinese Academy of Sciences; PO Box 416 Chengdu Sichuan 610041 China
| | - Li-Bing Zhang
- Missouri Botanical Garden; PO Box 299 St Louis MO 63166-0299 USA
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Vassou SL, Kusuma G, Parani M. DNA barcoding for species identification from dried and powdered plant parts: A case study with authentication of the raw drug market samples of Sida cordifolia. Gene 2015; 559:86-93. [DOI: 10.1016/j.gene.2015.01.025] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 01/09/2015] [Accepted: 01/11/2015] [Indexed: 11/28/2022]
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Sarwat M, Yamdagni MM. DNA barcoding, microarrays and next generation sequencing: recent tools for genetic diversity estimation and authentication of medicinal plants. Crit Rev Biotechnol 2014; 36:191-203. [PMID: 25264574 DOI: 10.3109/07388551.2014.947563] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
DNA barcoding, microarray technology and next generation sequencing have emerged as promising tools for the elucidation of plant genetic diversity and its conservation. They are proving to be immensely helpful in authenticating the useful medicinal plants for herbal drug preparations. These newer versions of molecular markers utilize short genetic markers in the genome to characterize the organism to a particular species. This has the potential not only to classify the known and yet unknown species but also has a promising future to link the medicinally important plants according to their properties. The newer trends being followed in DNA chips and barcoding pave the way for a future with many different possibilities. Several of these possibilities might be: characterization of unknown species in a considerably less time than usual, identification of newer medicinal properties possessed by the species and also updating the data of the already existing but unnoticed properties. This can assist us to cure many different diseases and will also generate novel opportunities in medicinal drug delivery and targeting.
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Affiliation(s)
- Maryam Sarwat
- a Pharmaceutical Biotechnology, Amity Institute of Pharmacy, Amity University , NOIDA , Uttar Pradesh , India
| | - Manu Mayank Yamdagni
- a Pharmaceutical Biotechnology, Amity Institute of Pharmacy, Amity University , NOIDA , Uttar Pradesh , India
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Wang XC, Liu C, Huang L, Bengtsson-Palme J, Chen H, Zhang JH, Cai D, Li JQ. ITS1: a DNA barcode better than ITS2 in eukaryotes? Mol Ecol Resour 2014; 15:573-86. [PMID: 25187125 DOI: 10.1111/1755-0998.12325] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 08/27/2014] [Indexed: 11/30/2022]
Abstract
A DNA barcode is a short piece of DNA sequence used for species determination and discovery. The internal transcribed spacer (ITS/ITS2) region has been proposed as the standard DNA barcode for fungi and seed plants and has been widely used in DNA barcoding analyses for other biological groups, for example algae, protists and animals. The ITS region consists of both ITS1 and ITS2 regions. Here, a large-scale meta-analysis was carried out to compare ITS1 and ITS2 from three aspects: PCR amplification, DNA sequencing and species discrimination, in terms of the presence of DNA barcoding gaps, species discrimination efficiency, sequence length distribution, GC content distribution and primer universality. In total, 85 345 sequence pairs in 10 major groups of eukaryotes, including ascomycetes, basidiomycetes, liverworts, mosses, ferns, gymnosperms, monocotyledons, eudicotyledons, insects and fishes, covering 611 families, 3694 genera, and 19 060 species, were analysed. Using similarity-based methods, we calculated species discrimination efficiencies for ITS1 and ITS2 in all major groups, families and genera. Using Fisher's exact test, we found that ITS1 has significantly higher efficiencies than ITS2 in 17 of the 47 families and 20 of the 49 genera, which are sample-rich. By in silico PCR amplification evaluation, primer universality of the extensively applied ITS1 primers was found superior to that of ITS2 primers. Additionally, shorter length of amplification product and lower GC content was discovered to be two other advantages of ITS1 for sequencing. In summary, ITS1 represents a better DNA barcode than ITS2 for eukaryotic species.
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Affiliation(s)
- Xin-Cun Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, 151 MaLianWa North Road, Beijing, 100193, China
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A renaissance in herbal medicine identification: from morphology to DNA. Biotechnol Adv 2014; 32:1237-1244. [PMID: 25087935 DOI: 10.1016/j.biotechadv.2014.07.004] [Citation(s) in RCA: 162] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 07/13/2014] [Accepted: 07/16/2014] [Indexed: 02/08/2023]
Abstract
Numerous adverse reactions have arisen following the use of inaccurately identified medicinal plant ingredients, resulting in conditions such as aristolochic acid nephropathy and herb-induced poisoning. This problem has prompted increased global concern over the safety of herbal medicines. DNA barcoding, a technique aiming at detecting species-specific differences in a short region of DNA, provides a powerful new tool for addressing this problem. A preliminary system for DNA barcoding herbal materials has been established based on a two-locus combination of ITS2+psbA-trnH barcodes. There are 78,847 sequences belonging to 23,262 species in the system, which include more than 95% of crude herbal drugs in pharmacopeia, such as those of China, Japan, Korea, India, USA, and Europe. The system has been widely used in traditional herbal medicine enterprises. This review summarizes recent key advances in the DNA barcoding of medicinal plant ingredients (herbal materia medica) as a contribution towards safe and efficacious herbal medicines.
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