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Ye H, Chen W, Huang T, Xu J, Wang X. Establishment of rapid extraction and sensitive detection system of trace corn syrup DNA in honey. FOOD CHEMISTRY. MOLECULAR SCIENCES 2024; 8:100206. [PMID: 38694166 PMCID: PMC11061233 DOI: 10.1016/j.fochms.2024.100206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/17/2024] [Accepted: 04/20/2024] [Indexed: 05/04/2024]
Abstract
Honey adulteration with exogenous syrup has become a common phenomenon, and current detection techniques that require large instruments are cumbersome and time-consuming. In this study, a simple and efficient method was developed by integrating the rapid extraction of nucleic acids (REMD) and recombinase polymerase amplification (RPA), known as REMD-RPA, for the rapid screening of syrup adulteration in honey. First, a rapid extraction method was developed to rapidly extract corn syrup DNA in five minutes to meet the requirements of PCR and RPA assays. Then, the RPA method for detecting endogenous maize genes (ZssIIb) was established, which could detect 12 copies/μL of the endogenous maize gene within 30 min without cross-reacting with other plant-derived genes. This indicated that the RPA technique exhibited high sensitivity and specificity. Finally, the REMD-RPA detection platform was used to detect different concentrations of corn syrup adulteration, and 1 % adulteration could be detected within 30 min. The 22 commercially available samples were tested to validate the efficacy of this method, and the established RPA was able to detect seven adulterated samples in less than 30 min. Overall, the developed method is rapid, sensitive, and specific, providing technical support for the rapid field detection of honey adulteration and can serve as a reference for developing other field test methods.
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Affiliation(s)
- Huixing Ye
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, P.R.China, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Wenqiang Chen
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Tao Huang
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Junfeng Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, P.R.China, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaofu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, P.R.China, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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2
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Mück F, Scotti F, Mauvisseau Q, Thorbek BLG, Wangensteen H, de Boer HJ. Three-tiered authentication of herbal traditional Chinese medicine ingredients used in women's health provides progressive qualitative and quantitative insight. Front Pharmacol 2024; 15:1353434. [PMID: 38375033 PMCID: PMC10875096 DOI: 10.3389/fphar.2024.1353434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 01/16/2024] [Indexed: 02/21/2024] Open
Abstract
Traditional Chinese Medicine (TCM) herbal products are increasingly used in Europe, but prevalent authentication methods have significant gaps in detection. In this study, three authentication methods were tested in a tiered approach to improve accuracy on a collection of 51 TCM plant ingredients obtained on the European market. We show the relative performance of conventional barcoding, metabarcoding and standardized chromatographic profiling for TCM ingredients used in one of the most diagnosed disease patterns in women, endometriosis. DNA barcoding using marker ITS2 and chromatographic profiling are methods of choice reported by regulatory authorities and relevant national pharmacopeias. HPTLC was shown to be a valuable authentication tool, combined with metabarcoding, which gives an increased resolution on species diversity, despite dealing with highly processed herbal ingredients. Conventional DNA barcoding as a recommended method was shown to be an insufficient tool for authentication of these samples, while DNA metabarcoding yields an insight into biological contaminants. We conclude that a tiered identification strategy can provide progressive qualitative and quantitative insight in an integrative approach for quality control of processed herbal ingredients.
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Affiliation(s)
- Felicitas Mück
- Section for Pharmaceutical Chemistry, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Francesca Scotti
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, London, United Kingdom
| | | | | | - Helle Wangensteen
- Section for Pharmaceutical Chemistry, Department of Pharmacy, University of Oslo, Oslo, Norway
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3
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McLay TGB, Fowler RM, Fahey PS, Murphy DJ, Udovicic F, Cantrill DJ, Bayly MJ. Phylogenomics reveals extreme gene tree discordance in a lineage of dominant trees: hybridization, introgression, and incomplete lineage sorting blur deep evolutionary relationships despite clear species groupings in Eucalyptus subgenus Eudesmia. Mol Phylogenet Evol 2023; 187:107869. [PMID: 37423562 DOI: 10.1016/j.ympev.2023.107869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/11/2023]
Abstract
Eucalypts are a large and ecologically important group of plants on the Australian continent, and understanding their evolution is important in understanding evolution of the unique Australian flora. Previous phylogenies using plastome DNA, nuclear-ribosomal DNA, or random genome-wide SNPs, have been confounded by limited genetic sampling or by idiosyncratic biological features of the eucalypts, including widespread plastome introgression. Here we present phylogenetic analyses of Eucalyptus subgenus Eudesmia (22 species from western, northern, central and eastern Australia), in the first study to apply a target-capture sequencing approach using custom, eucalypt-specific baits (of 568 genes) to a lineage of Eucalyptus. Multiple accessions of all species were included, and target-capture data were supplemented by separate analyses of plastome genes (average of 63 genes per sample). Analyses revealed a complex evolutionary history likely shaped by incomplete lineage sorting and hybridization. Gene tree discordance generally increased with phylogenetic depth. Species, or groups of species, toward the tips of the tree are mostly supported, and three major clades are identified, but the branching order of these clades cannot be confirmed with confidence. Multiple approaches to filtering the nuclear dataset, by removing genes or samples, could not reduce gene tree conflict or resolve these relationships. Despite inherent complexities in eucalypt evolution, the custom bait kit devised for this research will be a powerful tool for investigating the evolutionary history of eucalypts more broadly.
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Affiliation(s)
- Todd G B McLay
- Royal Botanic Gardens Victoria, Melbourne 3004, Vic, Australia; School of BioSciences, The University of Melbourne, Parkville 3010, Vic, Australia.
| | - Rachael M Fowler
- School of BioSciences, The University of Melbourne, Parkville 3010, Vic, Australia
| | - Patrick S Fahey
- Research Centre for Ecosystem Resilience, The Royal Botanic Garden Sydney, Sydney 2000, NSW, Australia; Qld Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia 4072, Qld, Australia
| | - Daniel J Murphy
- Royal Botanic Gardens Victoria, Melbourne 3004, Vic, Australia; School of BioSciences, The University of Melbourne, Parkville 3010, Vic, Australia
| | - Frank Udovicic
- Royal Botanic Gardens Victoria, Melbourne 3004, Vic, Australia
| | - David J Cantrill
- Royal Botanic Gardens Victoria, Melbourne 3004, Vic, Australia; School of BioSciences, The University of Melbourne, Parkville 3010, Vic, Australia
| | - Michael J Bayly
- School of BioSciences, The University of Melbourne, Parkville 3010, Vic, Australia
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Montanari S, Deng C, Koot E, Bassil NV, Zurn JD, Morrison-Whittle P, Worthington ML, Aryal R, Ashrafi H, Pradelles J, Wellenreuther M, Chagné D. A multiplexed plant-animal SNP array for selective breeding and species conservation applications. G3 (BETHESDA, MD.) 2023; 13:jkad170. [PMID: 37565490 PMCID: PMC10542201 DOI: 10.1093/g3journal/jkad170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/15/2023] [Accepted: 06/30/2023] [Indexed: 08/12/2023]
Abstract
Reliable and high-throughput genotyping platforms are of immense importance for identifying and dissecting genomic regions controlling important phenotypes, supporting selection processes in breeding programs, and managing wild populations and germplasm collections. Amongst available genotyping tools, single nucleotide polymorphism arrays have been shown to be comparatively easy to use and generate highly accurate genotypic data. Single-species arrays are the most commonly used type so far; however, some multi-species arrays have been developed for closely related species that share single nucleotide polymorphism markers, exploiting inter-species cross-amplification. In this study, the suitability of a multiplexed plant-animal single nucleotide polymorphism array, including both closely and distantly related species, was explored. The performance of the single nucleotide polymorphism array across species for diverse applications, ranging from intra-species diversity assessments to parentage analysis, was assessed. Moreover, the value of genotyping pooled DNA of distantly related species on the single nucleotide polymorphism array as a technique to further reduce costs was evaluated. Single nucleotide polymorphism performance was generally high, and species-specific single nucleotide polymorphisms proved suitable for diverse applications. The multi-species single nucleotide polymorphism array approach reported here could be transferred to other species to achieve cost savings resulting from the increased throughput when several projects use the same array, and the pooling technique adds another highly promising advancement to additionally decrease genotyping costs by half.
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Affiliation(s)
- Sara Montanari
- The New Zealand Institute for Plant and Food Research Ltd, Motueka 7198, New Zealand
| | - Cecilia Deng
- The New Zealand Institute for Plant and Food Research Ltd, Auckland 1025, New Zealand
| | - Emily Koot
- The New Zealand Institute for Plant and Food Research Ltd, Palmerston North 4410, New Zealand
| | - Nahla V Bassil
- USDA-ARS National Clonal Germplasm Repository, Corvallis, OR 97333, USA
| | - Jason D Zurn
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | | | | | - Rishi Aryal
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Hamid Ashrafi
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
| | | | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research Ltd, Nelson 7010, New Zealand
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Ltd, Palmerston North 4410, New Zealand
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Kang M, Chanderbali A, Lee S, Soltis DE, Soltis PS, Kim S. High-molecular-weight DNA extraction for long-read sequencing of plant genomes: An optimization of standard methods. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11528. [PMID: 37342161 PMCID: PMC10278927 DOI: 10.1002/aps3.11528] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 04/30/2023] [Accepted: 05/04/2023] [Indexed: 06/22/2023]
Abstract
Premise Developing an effective and easy-to-use high-molecular-weight (HMW) DNA extraction method is essential for genomic research, especially in the era of third-generation sequencing. To efficiently use technologies capable of generating long-read sequences, it is important to maximize both the length and purity of the extracted DNA; however, this is frequently difficult to achieve with plant samples. Methods and Results We present a HMW DNA extraction method that combines (1) a nuclei extraction method followed by (2) a traditional cetyltrimethylammonium bromide (CTAB) DNA extraction method for plants with optimized extraction conditions that influence HMW DNA recovery. Our protocol produced DNA fragments (percentage of fragments >20 kbp) that were, on average, ca. five times longer than those obtained using a commercial kit, and contaminants were removed more effectively. Conclusions This effective HMW DNA extraction protocol can be used as a standard protocol for a diverse array of taxa, which will enhance plant genomic research.
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Affiliation(s)
- Myoungbo Kang
- Department of BiotechnologySungshin Women's UniversitySeoul01133Republic of Korea
| | - Andre Chanderbali
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611USA
| | - Seungyeon Lee
- Department of BiotechnologySungshin Women's UniversitySeoul01133Republic of Korea
| | - Douglas E. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611USA
- Department of BiologyUniversity of FloridaGainesvilleFlorida32611USA
| | - Pamela S. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611USA
| | - Sangtae Kim
- Department of BiotechnologySungshin Women's UniversitySeoul01133Republic of Korea
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6
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Johnson G, Canty SWJ, Lichter‐Marck IH, Wagner W, Wen J. Ethanol preservation and pretreatments facilitate quality DNA extractions in recalcitrant plant species. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11519. [PMID: 37342166 PMCID: PMC10278939 DOI: 10.1002/aps3.11519] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 06/22/2023]
Abstract
PREMISE The preservation of plant tissues in ethanol is conventionally viewed as problematic. Here, we show that leaf preservation in ethanol combined with proteinase digestion can provide high-quality DNA extracts. Additionally, as a pretreatment, ethanol can facilitate DNA extraction for recalcitrant samples. METHODS DNA was isolated from leaves preserved with 96% ethanol or from silica-desiccated leaf samples and herbarium fragments that were pretreated with ethanol. DNA was extracted from herbarium tissues using a special ethanol pretreatment protocol, and these extracts were compared with those obtained using the standard cetyltrimethylammonium bromide (CTAB) method. RESULTS DNA extracted from tissue preserved in, or pretreated with, ethanol was less fragmented than DNA from tissues without pretreatment. Adding proteinase digestion to the lysis step increased the amount of DNA obtained from the ethanol-pretreated tissues. The combination of the ethanol pretreatment with liquid nitrogen freezing and a sorbitol wash prior to cell lysis greatly improved the quality and yield of DNA from the herbarium tissue samples. DISCUSSION This study critically reevaluates the consequences of ethanol for plant tissue preservation and expands the utility of pretreatment methods for molecular and phylogenomic studies.
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Affiliation(s)
- Gabriel Johnson
- Department of Botany/MRC 166National Museum of Natural History, Smithsonian InstitutionWashingtonD.C.20560USA
| | - Steven W. J. Canty
- Smithsonian Marine StationFort PierceFlorida34949USA
- Working Land and Seascapes, Smithsonian InstitutionWashingtonD.C.20013USA
| | - Isaac H. Lichter‐Marck
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaLos Angeles, 612 Charles E. Young Dr. SouthLos AngelesCalifornia90095USA
- Department of Integrative Biology and Jepson herbariumUniversity of California, Berkeley1001 Valley Life Sciences Bldg.BerkeleyCalifornia94720USA
| | - Warren Wagner
- Department of Botany/MRC 166National Museum of Natural History, Smithsonian InstitutionWashingtonD.C.20560USA
| | - Jun Wen
- Department of Botany/MRC 166National Museum of Natural History, Smithsonian InstitutionWashingtonD.C.20560USA
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Lu QX, Chang X, Gao J, Wu X, Wu J, Qi ZC, Wang RH, Yan XL, Li P. Evolutionary Comparison of the Complete Chloroplast Genomes in Convallaria Species and Phylogenetic Study of Asparagaceae. Genes (Basel) 2022; 13:genes13101724. [PMID: 36292609 PMCID: PMC9601677 DOI: 10.3390/genes13101724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/18/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
The genus Convallaria (Asparagaceae) comprises three herbaceous perennial species that are widely distributed in the understory of temperate deciduous forests in the Northern Hemisphere. Although Convallaria species have high medicinal and horticultural values, studies related to the phylogenetic analysis of this genus are few. In the present study, we assembled and reported five complete chloroplast (cp) sequences of three Convallaria species (two of C. keiskei Miq., two of C. majalis L., and one of C. montana Raf.) using Illumina paired-end sequencing data. The cp genomes were highly similar in overall size (161,365–162,972 bp), and all consisted of a pair of inverted repeats (IR) regions (29,140–29,486 bp) separated by a large single-copy (LSC) (85,183–85,521 bp) and a small single-copy (SSC) region (17,877–18,502 bp). Each cp genome contained the same 113 unique genes, including 78 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. Gene content, gene order, AT content and IR/SC boundary structure were nearly identical among all of the Convallaria cp genomes. However, their lengths varied due to contraction/expansion at the IR/LSC borders. Simple sequence repeat (SSR) analyses indicated that the richest SSRs are A/T mononucleotides. Three highly variable regions (petA-psbJ, psbI-trnS and ccsA-ndhD) were identified as valuable molecular markers. Phylogenetic analysis of the family Asparagaceae using 48 cp genome sequences supported the monophyly of Convallaria, which formed a sister clade to the genus Rohdea. Our study provides a robust phylogeny of the Asparagaceae family. The complete cp genome sequences will contribute to further studies in the molecular identification, genetic diversity, and phylogeny of Convallaria.
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Affiliation(s)
- Qi-Xiang Lu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xiao Chang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Jing Gao
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xue Wu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Jing Wu
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhe-Chen Qi
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
- Shaoxing Academy of Biomedicine, Zhejiang Sci-Tech University, Shaoxing 312366, China
- Correspondence: (Z.-C.Q.); (R.-H.W.)
| | - Rui-Hong Wang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
- Correspondence: (Z.-C.Q.); (R.-H.W.)
| | - Xiao-Ling Yan
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Pan Li
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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Delvento C, Pavan S, Miazzi MM, Marcotrigiano AR, Ricciardi F, Ricciardi L, Lotti C. Genotyping-by-Sequencing Defines Genetic Structure within the “Acquaviva” Red Onion Landrace. PLANTS 2022; 11:plants11182388. [PMID: 36145789 PMCID: PMC9502971 DOI: 10.3390/plants11182388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/05/2022] [Accepted: 09/11/2022] [Indexed: 11/26/2022]
Abstract
Genetic structure and distinctive features of landraces, such as adaptability to local agro-ecosystems and specific qualitative profiles, can be substantially altered by the massive introduction of allochthonous germplasm. The landrace known as “Cipolla rossa di Acquaviva” (Acquaviva red onion, further referred to as ARO) is traditionally cultivated and propagated in a small area of the Apulia region (southern Italy). However, the recent rise of its market value and cultivation area is possibly causing genetic contamination with foreign propagating material. In this work, genotyping-by-sequencing (GBS) was used to characterize genetic variation of seven onion populations commercialized as ARO, as well as one population of the landrace “Montoro” (M), which is phenotypically similar, but originates from another cultivation area and displays different qualitative features. A panel of 5011 SNP markers was used to perform parametric and non-parametric genetic structure analyses, which supported the hypothesis of genetic contamination of germplasm commercialized as ARO with a gene pool including the M landrace. Four ARO populations formed a core genetic group, homogeneous and clearly distinct from the other ARO and M populations. Conversely, the remaining three ARO populations did not display significant differences with the M population. A set of private alleles for the ARO core genetic group was identified, indicating the possibility to trace the ARO landrace by means of a SNP-based molecular barcode. Overall, the results of this study provide a framework for further breeding activities and the traceability of the ARO landrace.
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Affiliation(s)
- Chiara Delvento
- Department of Soil, Plant and Food Sciences, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
| | - Stefano Pavan
- Department of Soil, Plant and Food Sciences, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
- Correspondence: (S.P.); (C.L.)
| | - Monica Marilena Miazzi
- Department of Soil, Plant and Food Sciences, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
| | - Angelo Raffaele Marcotrigiano
- Department of Soil, Plant and Food Sciences, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
| | - Francesca Ricciardi
- Department of Agriculture, Food, Natural Resources and Engineering, University of Foggia, Via Napoli 25, 71122 Foggia, Italy
| | - Luigi Ricciardi
- Department of Soil, Plant and Food Sciences, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
| | - Concetta Lotti
- Department of Agriculture, Food, Natural Resources and Engineering, University of Foggia, Via Napoli 25, 71122 Foggia, Italy
- Correspondence: (S.P.); (C.L.)
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Brown GK, Aju J, Bayly MJ, Murphy DJ, McLay TGB. Phylogeny and classification of the Australasian and Indomalayan mimosoid legumes Archidendron and Archidendropsis (Leguminosae, subfamily Caesalpinioideae, mimosoid clade). PHYTOKEYS 2022; 205:299-333. [PMID: 36762019 PMCID: PMC9848999 DOI: 10.3897/phytokeys.205.79381] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/29/2022] [Indexed: 05/05/2023]
Abstract
The morphologically variable genus Archidendron is the second largest mimosoid legume genus from the Indomalayan-Australasian region, yet it has not been well represented in phylogenetic studies. Phylogenies that have included multiple representatives of Archidendron suggest it may not be monophyletic, and the same applies to Archidendropsis, another understudied genus of the Archidendron clade. The most comprehensive phylogeny of Archidendron and Archidendropsis to date is presented, based on four nuclear markers (ITS, ETS, SHMT and RBPCO). Exemplars from all genera of the wider Archidendron clade are sampled, including representatives of all series within Archidendron and the two subgenera of Archidendropsis. Our results confirm that Archidendron and Archidendropsis are not monophyletic. Within Archidendron, only one series (ser. Ptenopae) is resolved as monophyletic and species of Archidendron are divided into two primarily geographic lineages. One clade is distributed in western Malesia and mainland Asia and includes most representatives of series Clypeariae, while the other is mostly restricted to eastern Malesia and Australia and includes representatives of the seven other series plus two samples of series Clypeariae. No taxonomic changes are made for Archidendron due to the high level of topological uncertainty and the lack of discrete macromorphological characters separating these two lineages. Each of the two subgenera of Archidendropsis is monophyletic but they are not closely related. A new genus endemic to Queensland (Australia), Heliodendron Gill.K. Br. & Bayly, gen. nov., is described for the former Archidendropsissubg.Basaltica, and combinations for its three species are proposed: Heliodendronbasalticum (F. Muell.) Gill.K. Br. & Bayly, comb. nov., Heliodendronthozetianum (F. Muell.) Gill.K. Br. & Bayly, comb. nov., and Heliodendronxanthoxylon (C.T. White & W.D. Francis) Gill.K. Br. & Bayly, comb. nov.
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Affiliation(s)
- Gillian K. Brown
- School of Biosciences, University of Melbourne, Parkville, Victoria, 3010, AustraliaUniversity of MelbourneParkvilleAustralia
- Queensland Herbarium, Department of Environment and Science, Toowong, Queensland, 4066, AustraliaQueensland Herbarium, Department of Environment and ScienceToowongAustralia
| | - Javier Aju
- School of Biosciences, University of Melbourne, Parkville, Victoria, 3010, AustraliaUniversity of MelbourneParkvilleAustralia
- Departmento de Biología, Universidad del Valle de Guatemala, Guatemala, GuatemalaUniversidad del Valle de GuatemalaGuatemalaGuatemala
| | - Michael J. Bayly
- School of Biosciences, University of Melbourne, Parkville, Victoria, 3010, AustraliaUniversity of MelbourneParkvilleAustralia
| | - Daniel J. Murphy
- National Herbarium of Victoria, Royal Botanic Gardens Victoria, South Yarra, Victoria, 3141, AustraliaNational Herbarium of Victoria, Royal Botanic Gardens VictoriaSouth YarraAustralia
| | - Todd G. B. McLay
- School of Biosciences, University of Melbourne, Parkville, Victoria, 3010, AustraliaUniversity of MelbourneParkvilleAustralia
- National Herbarium of Victoria, Royal Botanic Gardens Victoria, South Yarra, Victoria, 3141, AustraliaNational Herbarium of Victoria, Royal Botanic Gardens VictoriaSouth YarraAustralia
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10
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Otero A, Vargas P, Fernández-Mazuecos M, Jiménez-Mejías P, Valcárcel V, Villa-Machío I, Hipp AL. A snapshot of progenitor-derivative speciation in Iberodes (Boraginaceae). Mol Ecol 2022; 31:3192-3209. [PMID: 35390211 DOI: 10.1111/mec.16459] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 03/27/2022] [Accepted: 04/01/2022] [Indexed: 11/28/2022]
Abstract
Traditional classification of speciation modes has focused on physical barriers to gene flow. Allopatric speciation with complete reproductive isolation is viewed as the most common mechanism of speciation. Parapatry and sympatry, by contrast, entail speciation in the face of ongoing gene flow, making them more difficult to detect. The genus Iberodes (Boraginaceae, NW Europe) comprises five species with contrasting morphological traits, habitats, and species distributions. Based on the predominance of narrow and geographically distant endemic species, we hypothesized that geographic barriers were responsible for most speciation events in Iberodes. We undertook an integrative study including: (i) phylogenomics through restriction-site associated DNA sequencing, (ii) genetic structure analyses, (iii) demographic modeling, (iv) morphometrics, and (v) climatic niche modeling and niche overlap analysis. Results revealed a history of recurrent progenitor-derivative speciation manifested by a paraphyletic pattern of nested species differentiation. Budding speciation mediated by ecological differentiation is suggested for the coastal lineage, deriving from the inland widespread I. linifolia during Late Pliocene. Meanwhile, geographic isolation followed by niche shifts are suggested for the more recent differentiation of the coastland taxa. Our work provides a model for distinguishing speciation via ecological differentiation of peripheral, narrowly endemic I. kuzinskyanae and I. littoralis from a widespread extant ancestor, I. linifolia. Ultimately, our results illustrate a case of Pliocene speciation in the probable absence of geographic barriers and get away from the traditional cladistic perspective of speciation as producing two species from an extinct ancestor, thus reminding us that phylogenetic trees tell only part of the story.
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Affiliation(s)
- Ana Otero
- Grainger Bioinformatics Center, Department of Science and Education, The Field Museum, 1400 S. DuSable Lake Shore Dr, 60605, Chicago, Illinois, USA.,Departamento de Biodiversidad y Conservación, Real Jardín Botánico (RJB-CSIC). Pza. de Murillo, 28014, Madrid, Spain
| | - Pablo Vargas
- Departamento de Biodiversidad y Conservación, Real Jardín Botánico (RJB-CSIC). Pza. de Murillo, 28014, Madrid, Spain
| | - Mario Fernández-Mazuecos
- Departamento de Biodiversidad y Conservación, Real Jardín Botánico (RJB-CSIC). Pza. de Murillo, 28014, Madrid, Spain.,Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, 28049, Madrid, Spain.,Departamento de Biología (Botánica), Universidad Autónoma de Madrid, C/ Darwin, 2, 28049, Madrid, Spain
| | - Pedro Jiménez-Mejías
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, 28049, Madrid, Spain.,Departamento de Biología (Botánica), Universidad Autónoma de Madrid, C/ Darwin, 2, 28049, Madrid, Spain
| | - Virginia Valcárcel
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, 28049, Madrid, Spain.,Departamento de Biología (Botánica), Universidad Autónoma de Madrid, C/ Darwin, 2, 28049, Madrid, Spain
| | - Irene Villa-Machío
- Departamento de Biodiversidad y Conservación, Real Jardín Botánico (RJB-CSIC). Pza. de Murillo, 28014, Madrid, Spain
| | - Andrew L Hipp
- Grainger Bioinformatics Center, Department of Science and Education, The Field Museum, 1400 S. DuSable Lake Shore Dr, 60605, Chicago, Illinois, USA.,The Morton Arboretum, 4100 Illinois Route 53, 60532, Lisle, Illinois, USA
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11
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Abstract
Growing popularity of herbal medicine has increased the demand of medicinal orchids in the global markets leading to their overharvesting from natural habitats for illegal trade. To stop such illegal trade, the correct identification of orchid species from their traded products is a foremost requirement. Different species of medicinal orchids are traded as their dried or fresh parts (tubers, pseudobulbs, stems), which look similar to each other making it almost impossible to identify them merely based on morphological observation. To overcome this problem, DNA barcoding could be an important method for accurate identification of medicinal orchids. Therefore, this research evaluated DNA barcoding of medicinal orchids in Asia where illegal trade of medicinal orchids has long existed. Based on genetic distance, similarity-based and tree-based methods with sampling nearly 7,000 sequences from five single barcodes (ITS, ITS2, matK, rbcL, trnH-psbA and their seven combinations), this study revealed that DNA barcoding is effective for identifying medicinal orchids. Among single locus, ITS performed the best barcode, whereas ITS + matK exhibited the most efficient barcode among multi-loci. A barcode library as a resource for identifying medicinal orchids has been established which contains about 7,000 sequences of 380 species (i.e. 90%) of medicinal orchids in Asia.
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12
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Lal A, Kim YH, Vo TTB, Wira Sanjaya IGNP, Ho PT, Byun HS, Choi HS, Kil EJ, Lee S. Identification of a Novel Geminivirus in Fraxinus rhynchophylla in Korea. Viruses 2021; 13:2385. [PMID: 34960653 PMCID: PMC8705360 DOI: 10.3390/v13122385] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/20/2021] [Accepted: 11/22/2021] [Indexed: 02/07/2023] Open
Abstract
Fraxinus rhynchophylla, common name ash, belongs to the family Oleaceae and is found in China, Korea, North America, the Indian subcontinent, and eastern Russia. It has been used as a traditional herbal medicine in Korea and various parts of the world due to its chemical constituents. During a field survey in March 2019, mild vein thickening (almost negligible) was observed in a few ash trees. High-throughput sequencing of libraries of total DNA from ash trees, rolling-circle amplification (RCA), and polymerase chain reaction (PCR) allowed the identification of a Fraxinus symptomless virus. This virus has five confirmed open reading frames along with a possible sixth open reading frame that encodes the movement protein and is almost 2.7 kb in size, with a nonanucleotide and stem loop structure identical to begomoviruses. In terms of its size and structure, this virus strongly resembles begomoviruses, but does not show any significant sequence identity with them. To confirm movement of the virus within the trees, different parts of infected trees were examined, and viral movement was successfully observed. No satellite molecules or DNA B were identified. Two-step PCR confirmed the virion and complementary strands during replication in both freshly collected infected samples of ash tree and Nicotiana benthamiana samples agro-inoculated with infectious clones. This taxon is so distantly grouped from other known geminiviruses that it likely represents a new geminivirus genus.
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Affiliation(s)
- Aamir Lal
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea; (A.L.); (T.T.B.V.); (I.G.N.P.W.S.); (P.T.H.)
| | - Yong-Ho Kim
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 55365, Korea; (Y.-H.K.); (H.-S.B.)
| | - Thuy Thi Bich Vo
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea; (A.L.); (T.T.B.V.); (I.G.N.P.W.S.); (P.T.H.)
| | | | - Phuong Thi Ho
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea; (A.L.); (T.T.B.V.); (I.G.N.P.W.S.); (P.T.H.)
| | - Hee-Seong Byun
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 55365, Korea; (Y.-H.K.); (H.-S.B.)
| | - Hong-Soo Choi
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 55365, Korea; (Y.-H.K.); (H.-S.B.)
| | - Eui-Joon Kil
- Department of Plant Medicals, Andong National University, Andong 36729, Korea
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea; (A.L.); (T.T.B.V.); (I.G.N.P.W.S.); (P.T.H.)
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13
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Shepherd LD, Ann Smith C, Lowe BJ, Campbell D, Ngarimu R. The identification of plants used to make tapa artefacts: development of a reference DNA database and trial of non-destructive DNA extraction methods. J R Soc N Z 2021. [DOI: 10.1080/03036758.2021.1981402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Lare D. Shepherd
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Catherine Ann Smith
- Archaeology, School of Social Science, University of Otago/Te Whare Wānanga o Otāgo, Dunedin, New Zealand
| | | | - Donna Campbell
- Faculty of Māori and Indigenous Studies, University of Waikato, Hamilton, New Zealand
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14
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Gericke O, Fowler RM, Heskes AM, Bayly MJ, Semple SJ, Ndi CP, Stærk D, Løland CJ, Murphy DJ, Buirchell BJ, Møller BL. Navigating through chemical space and evolutionary time across the Australian continent in plant genus Eremophila. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:555-578. [PMID: 34324744 PMCID: PMC9292440 DOI: 10.1111/tpj.15448] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/07/2021] [Accepted: 07/22/2021] [Indexed: 05/13/2023]
Abstract
Eremophila is the largest genus in the plant tribe Myoporeae (Scrophulariaceae) and exhibits incredible morphological diversity across the Australian continent. The Australian Aboriginal Peoples recognize many Eremophila species as important sources of traditional medicine, the most frequently used plant parts being the leaves. Recent phylogenetic studies have revealed complex evolutionary relationships between Eremophila and related genera in the tribe. Unique and structurally diverse metabolites, particularly diterpenoids, are also a feature of plants in this group. To assess the full dimension of the chemical space of the tribe Myoporeae, we investigated the metabolite diversity in a chemo-evolutionary framework applying a combination of molecular phylogenetic and state-of-the-art computational metabolomics tools to build a dataset involving leaf samples from a total of 291 specimens of Eremophila and allied genera. The chemo-evolutionary relationships are expounded into a systematic context by integration of information about leaf morphology (resin and hairiness), environmental factors (pollination and geographical distribution), and medicinal properties (traditional medicinal uses and antibacterial studies), augmenting our understanding of complex interactions in biological systems.
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Affiliation(s)
- Oliver Gericke
- Plant Biochemistry LaboratoryDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDK‐1871Denmark
| | - Rachael M. Fowler
- School of BioSciencesThe University of MelbourneParkvilleVic.3010Australia
| | - Allison M. Heskes
- Plant Biochemistry LaboratoryDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDK‐1871Denmark
| | - Michael J. Bayly
- School of BioSciencesThe University of MelbourneParkvilleVic.3010Australia
| | - Susan J. Semple
- Quality Use of Medicines and Pharmacy Research CentreSchool of Pharmacy and Medical SciencesUniversity of South AustraliaAdelaideSA5000Australia
| | - Chi P. Ndi
- Quality Use of Medicines and Pharmacy Research CentreSchool of Pharmacy and Medical SciencesUniversity of South AustraliaAdelaideSA5000Australia
| | - Dan Stærk
- Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDK‐2100Denmark
| | - Claus J. Løland
- Department of NeuroscienceFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDK‐2100Denmark
| | | | | | - Birger Lindberg Møller
- Plant Biochemistry LaboratoryDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDK‐1871Denmark
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15
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Burns KC, Hutton I, Shepherd L. Primitive eusociality in a land plant? Ecology 2021; 102:e03373. [PMID: 33988245 DOI: 10.1002/ecy.3373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 02/03/2021] [Accepted: 02/22/2021] [Indexed: 11/08/2022]
Affiliation(s)
- K C Burns
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington, 6012, New Zealand
| | - Ian Hutton
- Lord Howe Island Museum, Lord Howe Island, New South Wales, Australia
| | - Lara Shepherd
- Museum of New Zealand Te Papa Tongarewa, Wellington, 6011, New Zealand
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16
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Rucińska A, Olszak M, Świerszcz S, Nobis M, Zubek S, Kusza G, Boczkowska M, Nowak A. Looking for Hidden Enemies of Metabarcoding: Species Composition, Habitat and Management Can Strongly Influence DNA Extraction while Examining Grassland Communities. Biomolecules 2021; 11:318. [PMID: 33669773 PMCID: PMC7921978 DOI: 10.3390/biom11020318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 12/02/2022] Open
Abstract
Despite the raising preoccupation, the critical question of how the plant community is composed belowground still remains unresolved, particularly for the conservation priority types of vegetation. The usefulness of metabarcoding analysis of the belowground parts of the plant community is subjected to a considerable bias, that often impedes detection of all species in a sample due to insufficient DNA quality or quantity. In the presented study we have attempted to find environmental factors that determine the amount and quality of DNA extracted from total plant tissue from above- and belowground samples (1000 and 10,000 cm2). We analyzed the influence of land use intensity, soil properties, species composition, and season on DNA extraction. The most important factors for DNA quality were vegetation type, soil conductometry (EC), and soil pH for the belowground samples. The species that significantly decreased the DNA quality were Calamagrostis epigejos, Coronilla varia, and Holcus lanatus. For the aboveground part of the vegetation, the season, management intensity, and certain species-with the most prominent being Centaurea rhenana and Cirsium canum-have the highest influence. Additionally, we found that sample size, soil granulation, MgO, organic C, K2O, and total soil N content are important for DNA extraction effectiveness. Both low EC and pH reduce significantly the yield and quality of DNA. Identifying the potential inhibitors of DNA isolation and predicting difficulties of sampling the vegetation plots for metabarcoding analysis will help to optimize the universal, low-cost multi-stage DNA extraction procedure in molecular ecology studies.
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Affiliation(s)
- Anna Rucińska
- Polish Academy of Sciences Botanical Garden, Center for Biological Diversity Conservation in Powsin, Prawdziwka 2, 02-976 Warszawa, Poland; (A.R.); (M.O.); (M.B.); (A.N.)
| | - Marcin Olszak
- Polish Academy of Sciences Botanical Garden, Center for Biological Diversity Conservation in Powsin, Prawdziwka 2, 02-976 Warszawa, Poland; (A.R.); (M.O.); (M.B.); (A.N.)
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warszawa, Poland
| | - Sebastian Świerszcz
- Polish Academy of Sciences Botanical Garden, Center for Biological Diversity Conservation in Powsin, Prawdziwka 2, 02-976 Warszawa, Poland; (A.R.); (M.O.); (M.B.); (A.N.)
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239 Kraków, Poland
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland; (M.N.); (S.Z.)
- Research Laboratory ‘Herbarium’, National Research Tomsk State University, 634050 Tomsk, Russia
| | - Szymon Zubek
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland; (M.N.); (S.Z.)
| | - Grzegorz Kusza
- Institute of Biology, University of Opole, Oleska 22, 45-052 Opole, Poland;
| | - Maja Boczkowska
- Polish Academy of Sciences Botanical Garden, Center for Biological Diversity Conservation in Powsin, Prawdziwka 2, 02-976 Warszawa, Poland; (A.R.); (M.O.); (M.B.); (A.N.)
- National Centre for Plant Genetic Resources, Plant Breeding and Acclimatization Institute (IHAR)–National Research Institute, Radzików, 05-870 Błonie, Poland
| | - Arkadiusz Nowak
- Polish Academy of Sciences Botanical Garden, Center for Biological Diversity Conservation in Powsin, Prawdziwka 2, 02-976 Warszawa, Poland; (A.R.); (M.O.); (M.B.); (A.N.)
- Institute of Biology, University of Opole, Oleska 22, 45-052 Opole, Poland;
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17
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Imai R, Tsuda Y, Ebihara A, Matsumoto S, Tezuka A, Nagano AJ, Ootsuki R, Watano Y. Mating system evolution and genetic structure of diploid sexual populations of Cyrtomium falcatum in Japan. Sci Rep 2021; 11:3124. [PMID: 33542454 PMCID: PMC7862634 DOI: 10.1038/s41598-021-82731-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 01/12/2021] [Indexed: 11/09/2022] Open
Abstract
Evolution of mating systems has become one of the most important research areas in evolutionary biology. Cyrtomium falcatum is a homosporous fern species native to eastern Asia. Two subspecies belonging to a sexual diploid race of C. falcatum are recognized: subsp. littorale and subsp. australe. Subspecies littorale shows intermediate selfing rates, while subsp. australe is an obligate outcrosser. We aimed to evaluate the process of mating system evolution and divergence for the two subspecies using restriction site associated DNA sequencing (RAD-seq). The results showed that subsp. littorale had lower genetic diversity and stronger genetic drift than subsp. australe. Fluctuations in the effective population size over time were evaluated by extended Bayesian skyline plot and Stairway plot analyses, both of which revealed a severe population bottleneck about 20,000 years ago in subsp. littorale. This bottleneck and the subsequent range expansion after the LGM appear to have played an important role in the divergence of the two subspecies and the evolution of selfing in subsp. littorale. These results shed new light on the relationship between mating system evolution and past demographic change in fern species.
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Affiliation(s)
- Ryosuke Imai
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira, Ueda , Nagano, 386-2204, Japan.
| | - Yoshiaki Tsuda
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira, Ueda , Nagano, 386-2204, Japan
| | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, 305-0005, Japan
| | - Sadamu Matsumoto
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, 305-0005, Japan
| | - Ayumi Tezuka
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194, Japan
| | - Ryo Ootsuki
- Department of Natural Sciences, Faculty of Arts and Sciences, Komazawa University, 1-23-1 Komazawa, Setagaya-ku, Tokyo, 154-8525, Japan
| | - Yasuyuki Watano
- Department of Biology, Graduate School of Science, Chiba University, Inage, Chiba, Chiba, 263-8522, Japan
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18
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Kates HR, Doby JR, Siniscalchi CM, LaFrance R, Soltis DE, Soltis PS, Guralnick RP, Folk RA. The Effects of Herbarium Specimen Characteristics on Short-Read NGS Sequencing Success in Nearly 8000 Specimens: Old, Degraded Samples Have Lower DNA Yields but Consistent Sequencing Success. FRONTIERS IN PLANT SCIENCE 2021; 12:669064. [PMID: 34249041 PMCID: PMC8262526 DOI: 10.3389/fpls.2021.669064] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/12/2021] [Indexed: 05/22/2023]
Abstract
Phylogenetic datasets are now commonly generated using short-read sequencing technologies unhampered by degraded DNA, such as that often extracted from herbarium specimens. The compatibility of these methods with herbarium specimens has precipitated an increase in broad sampling of herbarium specimens for inclusion in phylogenetic studies. Understanding which sample characteristics are predictive of sequencing success can guide researchers in the selection of tissues and specimens most likely to yield good results. Multiple recent studies have considered the relationship between sample characteristics and DNA yield and sequence capture success. Here we report an analysis of the relationship between sample characteristics and sequencing success for nearly 8,000 herbarium specimens. This study, the largest of its kind, is also the first to include a measure of specimen quality ("greenness") as a predictor of DNA sequencing success. We found that taxonomic group and source herbarium are strong predictors of both DNA yield and sequencing success and that the most important specimen characteristics for predicting success differ for DNA yield and sequencing: greenness was the strongest predictor of DNA yield, and age was the strongest predictor of proportion-on-target reads recovered. Surprisingly, the relationship between age and proportion-on-target reads is the inverse of expectations; older specimens performed slightly better in our capture-based protocols. We also found that DNA yield itself is not a strong predictor of sequencing success. Most literature on DNA sequencing from herbarium specimens considers specimen selection for optimal DNA extraction success, which we find to be an inappropriate metric for predicting success using next-generation sequencing technologies.
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Affiliation(s)
- Heather R. Kates
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
- *Correspondence: Heather R. Kates,
| | - Joshua R. Doby
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
| | - Carol M. Siniscalchi
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States
| | - Raphael LaFrance
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
| | - Douglas E. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
- Department of Biology, University of Florida, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
- Biodiversity Institute, University of Florida, Gainesville, FL, United States
| | - Pamela S. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
- Biodiversity Institute, University of Florida, Gainesville, FL, United States
| | - Robert P. Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
- Biodiversity Institute, University of Florida, Gainesville, FL, United States
- Robert P. Guralnick,
| | - Ryan A. Folk
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States
- Ryan A. Folk,
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19
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Herbarium Specimens: A Treasure for DNA Extraction, an Update. Methods Mol Biol 2020; 2222:69-88. [PMID: 33301088 DOI: 10.1007/978-1-0716-0997-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
With the expansion of molecular techniques, the historical collections have become widely used. The last boom started with using next- and second-generation sequencing in which massive parallel sequencing replaced targeted sequencing and third-generation technology involves single molecule technology. Studying plant DNA using these modern molecular techniques plays an important role in understanding evolutionary relationships, identification through DNA barcoding, conservation status, and many other aspects of plant biology. Enormous herbarium collections are an important source of material especially for taxonomic long-standing issues, specimens from areas difficult to access or from taxa that are now extinct. The ability to utilize these specimens greatly enhances the research. However, the process of extracting DNA from herbarium specimens is often fraught with difficulty related to such variables as plant chemistry, drying method of the specimen, and chemical treatment of the specimen. The result of these applications is often fragmented DNA. The reason new sequencing approaches have been so successful is that the template DNA needs to be fragmented for proper library building, and herbarium DNA is exactly that. Although many methods have been developed for extraction of DNA from herbarium specimens, the most frequently used are modified CTAB and DNeasy Plant Mini Kit protocols. Nine selected protocols in this chapter have been successfully used for high-quality DNA extraction from different kinds of plant herbarium tissues. These methods differ primarily with respect to their requirements for input material (from algae to vascular plants), type of the plant tissue (leaves with incrustations, sclerenchyma strands, mucilaginous tissues, needles, seeds), and further possible applications (PCR-based methods, microsatellites, AFLP or next-generation sequencing).
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20
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Ricciardi L, Mazzeo R, Marcotrigiano AR, Rainaldi G, Iovieno P, Zonno V, Pavan S, Lotti C. Assessment of Genetic Diversity of the "Acquaviva Red Onion" ( Allium cepa L.) Apulian Landrace. PLANTS 2020; 9:plants9020260. [PMID: 32085407 PMCID: PMC7076509 DOI: 10.3390/plants9020260] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 11/18/2022]
Abstract
Onion (Allium cepa L.) is the second most important vegetable crop worldwide and is widely appreciated for its health benefits. Despite its significant economic importance and its value as functional food, onion has been poorly investigated with respect to its genetic diversity. Herein, we surveyed the genetic variation in the “Acquaviva red onion” (ARO), a landrace with a century-old history of cultivation in a small town in the province of Bari (Apulia, Southern of Italy). A set of 11 microsatellite markers were used to explore the genetic variation in a germplasm collection consisting of 13 ARO populations and three common commercial types. Analyses of genetic structure with parametric and non-parametric methods highlighted that the ARO represents a well-defined gene pool, clearly distinct from the Tropea and Montoro landraces with which it is often mistaken. In order to provide a description of bulbs, usually used for fresh consumption, soluble solid content and pungency were evaluated, showing higher sweetness in the ARO with respect to the two above mentioned landraces. Overall, the present study is useful for the future valorization of the ARO, which could be promoted through quality labels which could contribute to limit commercial frauds and improve the income of smallholders.
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Affiliation(s)
- Luigi Ricciardi
- Department of Soil, Plant and Food Sciences, Plant Genetics and Breeding Unit University of Bari, Via Amendola 165/A, 70125 Bari, Italy; (L.R.); (A.R.M.); (V.Z.); (S.P.)
| | - Rosa Mazzeo
- Department of the Sciences of Agriculture, Food and Environment, University of Foggia, Via Napoli 25, 71122 Foggia, Italy
- Correspondence: (R.M.); (C.L.)
| | - Angelo Raffaele Marcotrigiano
- Department of Soil, Plant and Food Sciences, Plant Genetics and Breeding Unit University of Bari, Via Amendola 165/A, 70125 Bari, Italy; (L.R.); (A.R.M.); (V.Z.); (S.P.)
| | - Guglielmo Rainaldi
- Department of Biosciences, Biotechnologies and Biopharmaceuticals, University of Bari, Via Orabona 4, 70125 Bari, Italy;
| | - Paolo Iovieno
- Department of Energy Technologies, Bioenergy, Biorefinery and Green Chemistry Division, ENEA Trisaia Research Center, S.S. 106 Ionica, km 419+500, 75026 Rotondella (MT), Italy;
| | - Vito Zonno
- Department of Soil, Plant and Food Sciences, Plant Genetics and Breeding Unit University of Bari, Via Amendola 165/A, 70125 Bari, Italy; (L.R.); (A.R.M.); (V.Z.); (S.P.)
| | - Stefano Pavan
- Department of Soil, Plant and Food Sciences, Plant Genetics and Breeding Unit University of Bari, Via Amendola 165/A, 70125 Bari, Italy; (L.R.); (A.R.M.); (V.Z.); (S.P.)
| | - Concetta Lotti
- Department of the Sciences of Agriculture, Food and Environment, University of Foggia, Via Napoli 25, 71122 Foggia, Italy
- Correspondence: (R.M.); (C.L.)
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21
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Orel HK, Fahey PS, Fowler RM, Bayly MJ. The complete chloroplast genome sequence of the Australian Mirbelioid pea Platylobium obtusangulum Hook. (Leguminosae: subf. Papilionoideae, tribe Bossiaeeae). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:3618-3620. [PMID: 33366111 PMCID: PMC7707395 DOI: 10.1080/23802359.2019.1677187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We sequenced and assembled the whole chloroplast genome of the Australian-endemic shrub Platylobium obtusangulum. The total size of the genome is 150,090 base pairs (bp), including two inverted repeat regions of 25,511 bp each, one large single copy region of 80,567 bp and a small single copy region of 18,501 bp. The genome has a GC content of 36.7% and includes 127 annotated genes (83 protein coding, 36 tRNA genes and eight rRNA genes). Phylogenetic analysis of chloroplast genomes placed the Platylobium obtusangulum genome in the expected position of the Mirbelioid clade in the legume family (Leguminosae: Papilionoideae).
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Affiliation(s)
- Harvey K Orel
- School of Biosciences, The University of Melbourne, Parkville, Australia
| | - Patrick S Fahey
- School of Biosciences, The University of Melbourne, Parkville, Australia
| | - Rachael M Fowler
- School of Biosciences, The University of Melbourne, Parkville, Australia
| | - Michael J Bayly
- School of Biosciences, The University of Melbourne, Parkville, Australia
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22
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Muscat KM, Ladiges PY, Bayly MJ. Molecular phylogenetic relationships reveal taxonomic and biogeographic clades inDianella(flax lilies; Asphodelaceae, Hemerocallidoideae). SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2019.1607617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Karen M. Muscat
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010 Australia
| | - Pauline Y. Ladiges
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010 Australia
| | - Michael J. Bayly
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010 Australia
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23
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Shepherd LD, Brownsey PJ, Stowe C, Newell C, Perrie LR. Genetic and morphological identification of a recurrent Dicksonia tree fern hybrid in New Zealand. PLoS One 2019; 14:e0216903. [PMID: 31107899 PMCID: PMC6527230 DOI: 10.1371/journal.pone.0216903] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/30/2019] [Indexed: 11/18/2022] Open
Abstract
Hybridization is common in many ferns and has been a significant factor in fern evolution and speciation. However, hybrids are rare between the approximately 30 species of Dicksonia tree ferns world-wide, and none are well documented. In this study we examine the relationship of a newly-discovered Dicksonia tree fern from Whirinaki, New Zealand, which does not fit the current taxonomy of the three species currently recognized in New Zealand. Our microsatellite genotyping and ddRAD-seq data indicate these plants are F1 hybrids that have formed multiple times between D. fibrosa and D. lanata subsp. lanata. The Whirinaki plants have intermediate morphology between D. fibrosa and D. lanata subsp. lanata and their malformed spores are consistent with a hybrid origin. The Whirinaki plants–Dicksonia fibrosa × D. lanata subsp. lanata–are an example of hybridization between distantly related fern lineages, with the two parent species estimated to have diverged 55–25 mya. Our chloroplast sequencing indicates asymmetric chloroplast inheritance in the Whirinaki morphology with D. lanata subsp. lanata always contributing the chloroplast genome.
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Affiliation(s)
- Lara D. Shepherd
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
- * E-mail:
| | | | | | | | - Leon R. Perrie
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
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24
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Veldman S, Kim SJ, van Andel TR, Bello Font M, Bone RE, Bytebier B, Chuba D, Gravendeel B, Martos F, Mpatwa G, Ngugi G, Vinya R, Wightman N, Yokoya K, de Boer HJ. Trade in Zambian Edible Orchids-DNA Barcoding Reveals the Use of Unexpected Orchid Taxa for Chikanda. Genes (Basel) 2018; 9:E595. [PMID: 30513666 PMCID: PMC6315803 DOI: 10.3390/genes9120595] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/17/2018] [Accepted: 11/22/2018] [Indexed: 02/01/2023] Open
Abstract
In Zambia, wild edible terrestrial orchids are used to produce a local delicacy called chikanda, which has become increasingly popular throughout the country. Commercialization puts orchid populations in Zambia and neighbouring countries at risk of overharvesting. Hitherto, no study has documented which orchid species are traded on local markets, as orchid tubers are difficult to identify morphologically. In this study, the core land-plant DNA barcoding markers rbcL and matK were used in combination with nrITS to determine which species were sold in Zambian markets. Eighty-two interviews were conducted to determine harvesting areas, as well as possible sustainability concerns. By using nrITS DNA barcoding, a total of 16 orchid species in six different genera could be identified. Both rbcL and matK proved suitable to identify the tubers up to the genus or family level. Disa robusta, Platycoryne crocea and Satyrium buchananii were identified most frequently and three previously undocumented species were encountered on the market. Few orchid species are currently listed on the global International Union for the Conservation of Nature (IUCN) Red List. Local orchid populations and endemic species could be at risk of overharvesting due to the intensive and indiscriminate harvesting of chikanda orchids, and we therefore encourage increased conservation assessment of terrestrial African orchids.
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Affiliation(s)
- Sarina Veldman
- Department of Organismal Biology, Systematic Biology, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden.
| | - Seol-Jong Kim
- Department of Organismal Biology, Systematic Biology, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden.
| | - Tinde R van Andel
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands.
| | - Maria Bello Font
- Natural History Museum, University of Oslo, Postboks 1172, Blindern, 0318 Oslo, Norway.
| | - Ruth E Bone
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK.
| | - Benny Bytebier
- Bews Herbarium, School of Life Sciences, University of KwaZulu-Natal, Pr. Bag X01, Scottsville 3209, South Africa.
| | - David Chuba
- Department of Biological Sciences, University of Zambia, Box 32379 Lusaka, Zambia.
| | - Barbara Gravendeel
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands.
- Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands.
- University of Applied Sciences Leiden, Zernikedreef 11, 2333 CK Leiden, The Netherlands.
| | - Florent Martos
- Bews Herbarium, School of Life Sciences, University of KwaZulu-Natal, Pr. Bag X01, Scottsville 3209, South Africa.
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'histoire naturelle, CNRS, Sorbonne Université, EPHE, CP50, 45 rue Buffon 75005 Paris, France.
| | - Geophat Mpatwa
- School of Natural Resources, The Copperbelt University, PO Box 21692 Kitwe, Zambia.
| | - Grace Ngugi
- Bews Herbarium, School of Life Sciences, University of KwaZulu-Natal, Pr. Bag X01, Scottsville 3209, South Africa.
- East African Herbarium, National Museums of Kenya, P.O. Box 40658-00100 Nairobi, Kenya.
| | - Royd Vinya
- School of Natural Resources, The Copperbelt University, PO Box 21692 Kitwe, Zambia.
| | - Nicholas Wightman
- Homegarden Landscape Consultants Ltd., P/Bag 30C, Chilanga, Lusaka, Zambia.
| | | | - Hugo J de Boer
- Department of Organismal Biology, Systematic Biology, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden.
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands.
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25
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Shepherd LD, Bulgarella M, de Lange PJ. Genetic structuring of the coastal herb Arthropodium cirratum (Asparagaceae) is shaped by low gene flow, hybridization and prehistoric translocation. PLoS One 2018; 13:e0204943. [PMID: 30332433 PMCID: PMC6192600 DOI: 10.1371/journal.pone.0204943] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/16/2018] [Indexed: 11/19/2022] Open
Abstract
We examined the genetic structuring of rengarenga (Arthropodium cirratum; Asparagaceae), an endemic New Zealand coastal herb, using nuclear microsatellite markers. This species was brought into cultivation by Māori within the last 700–800 years for its edible roots and was transplanted beyond its natural distribution as part of its cultivation. We found very high levels of genetic structuring in the natural populations (FST = 0.84), indicating low levels of gene flow. Reduced genetic diversity was found in the translocated populations, suggesting a large loss of genetic diversity early in the domestication process. The data indicates that rengarenga was brought into cultivation independently at least three times, with the sources of these introductions located within a narrow area encompassing about 250km of coastline. Hybridization was inferred between A. cirratum and the closely related A. bifurcatum, despite A. birfucatum not occurring in the vicinity.
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Affiliation(s)
- Lara D. Shepherd
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
- * E-mail:
| | | | - Peter J. de Lange
- Environment and Animal Sciences, Unitec Institute of Technology, Auckland, New Zealand
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26
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Clowes C, Fowler RM, Brown GK, Bayly MJ. The complete chloroplast genome sequence of Spyridium parvifolium var. parvifolium (family Rhamnaceae; tribe Pomaderreae). Mitochondrial DNA B Resour 2018; 3:807-809. [PMID: 33474330 PMCID: PMC7800025 DOI: 10.1080/23802359.2018.1483776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 05/29/2018] [Indexed: 11/24/2022] Open
Abstract
We assembled the complete chloroplast genome of the Australian shrub Spyridium parvifolium var. parvifolium. The genome was 161,012 bp in length, with a pair of inverted repeats (IRs) of 26,515 bp, separated by a large single copy (LSC) region of 88,814 bp and a small single copy region (SCC) of 19,168 bp. The GC content was 36.9%. In total, 130 genes were annotated, including 86 protein coding genes, 36 tRNA genes and 8 rRNA genes. Phylogenetic analysis of 56 chloroplast genes placed this genome of S. parvifolium var. parvifolium within the family Rhamnaceae.
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Affiliation(s)
- Catherine Clowes
- School of Biosciences, The University of Melbourne, Parkville, Australia
| | - Rachael M. Fowler
- School of Biosciences, The University of Melbourne, Parkville, Australia
| | - Gillian K. Brown
- Department of Environment and Science, Queensland Herbarium, Toowong, Australia
| | - Michael J. Bayly
- School of Biosciences, The University of Melbourne, Parkville, Australia
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27
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Schuster TM, Setaro SD, Tibbits JFG, Batty EL, Fowler RM, McLay TGB, Wilcox S, Ades PK, Bayly MJ. Chloroplast variation is incongruent with classification of the Australian bloodwood eucalypts (genus Corymbia, family Myrtaceae). PLoS One 2018; 13:e0195034. [PMID: 29668710 PMCID: PMC5905893 DOI: 10.1371/journal.pone.0195034] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 03/15/2018] [Indexed: 11/19/2022] Open
Abstract
Previous molecular phylogenetic analyses have resolved the Australian bloodwood eucalypt genus Corymbia (~100 species) as either monophyletic or paraphyletic with respect to Angophora (9-10 species). Here we assess relationships of Corymbia and Angophora using a large dataset of chloroplast DNA sequences (121,016 base pairs; from 90 accessions representing 55 Corymbia and 8 Angophora species, plus 33 accessions of related genera), skimmed from high throughput sequencing of genomic DNA, and compare results with new analyses of nuclear ITS sequences (119 accessions) from previous studies. Maximum likelihood and maximum parsimony analyses of cpDNA resolve well supported trees with most nodes having >95% bootstrap support. These trees strongly reject monophyly of Corymbia, its two subgenera (Corymbia and Blakella), most taxonomic sections (Abbreviatae, Maculatae, Naviculares, Septentrionales), and several species. ITS trees weakly indicate paraphyly of Corymbia (bootstrap support <50% for maximum likelihood, and 71% for parsimony), but are highly incongruent with the cpDNA analyses, in that they support monophyly of both subgenera and some taxonomic sections of Corymbia. The striking incongruence between cpDNA trees and both morphological taxonomy and ITS trees is attributed largely to chloroplast introgression between taxa, because of geographic sharing of chloroplast clades across taxonomic groups. Such introgression has been widely inferred in studies of the related genus Eucalyptus. This is the first report of its likely prevalence in Corymbia and Angophora, but this is consistent with previous morphological inferences of hybridisation between species. Our findings (based on continent-wide sampling) highlight a need for more focussed studies to assess the extent of hybridisation and introgression in the evolutionary history of these genera, and that critical testing of the classification of Corymbia and Angophora requires additional sequence data from nuclear genomes.
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Affiliation(s)
- Tanja M. Schuster
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
- National Herbarium of Victoria, Royal Botanic Gardens Victoria, Birdwood Avenue, South Yarra, VIC, Australia
- * E-mail:
| | - Sabrina D. Setaro
- Department of Biology, Wake Forest University, Winston-Salem, NC,United States of America
| | - Josquin F. G. Tibbits
- Department of Economic Development, Jobs, Transport and Resources, AgriBiosciences Centre, La Trobe University, Bundoora, VIC, Australia
| | - Erin L. Batty
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Rachael M. Fowler
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Todd G. B. McLay
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Stephen Wilcox
- Genomics Hub, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, Australia
| | - Peter K. Ades
- School of Ecosystem and Forest Sciences, The University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Michael J. Bayly
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
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28
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Shepherd LD. A non-destructive DNA sampling technique for herbarium specimens. PLoS One 2017; 12:e0183555. [PMID: 28859137 PMCID: PMC5578499 DOI: 10.1371/journal.pone.0183555] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/07/2017] [Indexed: 11/18/2022] Open
Abstract
Herbarium specimens are an important source of DNA for plant research but current sampling methods require the removal of material for DNA extraction. This is undesirable for irreplaceable specimens such as rare species or type material. Here I present the first non-destructive sampling method for extracting DNA from herbarium specimens. DNA was successfully retrieved from robust leaves and/or stems of herbarium specimens up to 73 years old.
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Affiliation(s)
- Lara D Shepherd
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
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29
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Bulgarella M, Biggs PJ, de Lange PJ, Shepherd LD. Isolation and characterization of microsatellite loci from Arthropodium cirratum (Asparagaceae). APPLICATIONS IN PLANT SCIENCES 2017; 5:apps1700041. [PMID: 28924514 PMCID: PMC5584818 DOI: 10.3732/apps.1700041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 05/22/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY Microsatellite markers were developed for Arthropodium cirratum (Asparagaceae) to study population genetic structure and translocation of this species. These markers were tested for cross-amplification in two other Arthropodium species. METHODS AND RESULTS Sixteen microsatellite markers were developed from a genomic library and tested in three populations of A. cirratum. The loci exhibited one to five alleles per locus, with private alleles present in each of the populations. Cross-amplification tests in the two other New Zealand Arthropodium species revealed that many of the loci amplify and demonstrate polymorphism in A. bifurcatum. CONCLUSIONS These markers will be useful for determining genetic structure in A. cirratum and for determining the origins of translocated populations of this species.
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Affiliation(s)
- Mariana Bulgarella
- Museum of New Zealand Te Papa Tongarewa, P.O. Box 467, Wellington, New Zealand
| | - Patrick J. Biggs
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Peter J. de Lange
- Science and Capability Group, Terrestrial Ecosystems, Department of Conservation, Newton, Auckland, New Zealand
| | - Lara D. Shepherd
- Museum of New Zealand Te Papa Tongarewa, P.O. Box 467, Wellington, New Zealand
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30
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Ghorbani A, Gravendeel B, Selliah S, Zarré S, de Boer H. DNA barcoding of tuberous Orchidoideae: a resource for identification of orchids used in Salep. Mol Ecol Resour 2016; 17:342-352. [DOI: 10.1111/1755-0998.12615] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 08/26/2016] [Accepted: 09/06/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Abdolbaset Ghorbani
- Department of Organismal Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-75236 Uppsala Sweden
- Traditional Medicine and Materia Medica Research Center; Shahid Beheshti University of Medical Sciences; No 19, Tavanir Street, Hemmat Highway P.O. Box 14155-6153 Tehran Iran
| | - Barbara Gravendeel
- Naturalis Biodiversity Center; Darwinweg 2 2333 CR Leiden The Netherlands
- University of Applied Sciences Leiden; Zernikedreef 11 2333 CK Leiden The Netherlands
| | - Sugirthini Selliah
- The Natural History Museum; University of Oslo; P.O. Box 1172 Blindern 0318 Oslo Norway
| | - Shahin Zarré
- Department of Plant Sciences; School of Biology; College of Science; University of Tehran; 14155-6455 Tehran Iran
| | - Hugo de Boer
- Department of Organismal Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-75236 Uppsala Sweden
- Naturalis Biodiversity Center; Darwinweg 2 2333 CR Leiden The Netherlands
- The Natural History Museum; University of Oslo; P.O. Box 1172 Blindern 0318 Oslo Norway
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31
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The Relationship between Mating System and Genetic Diversity in Diploid Sexual Populations of Cyrtomium falcatum in Japan. PLoS One 2016; 11:e0163683. [PMID: 27706257 PMCID: PMC5051678 DOI: 10.1371/journal.pone.0163683] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 09/11/2016] [Indexed: 11/24/2022] Open
Abstract
The impact of variation in mating system on genetic diversity is a well-debated topic in evolutionary biology. The diploid sexual race of Cyrtomium falcatum (Japanese holly fern) shows mating system variation, i.e., it displays two different types of sexual expression (gametangia formation) in gametophytes: mixed (M) type and separate (S) type. We examined whether there is variation in the selfing rate among populations of this species, and evaluated the relationship between mating system, genetic diversity and effective population size using microsatellites. In this study, we developed eight new microsatellite markers and evaluated genetic diversity and structure of seven populations (four M-type and three S-type). Past effective population sizes (Ne) were inferred using Approximate Bayesian computation (ABC). The values of fixation index (FIS), allelic richness (AR) and gene diversity (h) differed significantly between the M-type (FIS: 0.626, AR: 1.999, h: 0.152) and the S-type (FIS: 0.208, AR: 2.718, h: 0.367) populations (when admixed individuals were removed from two populations). Although evidence of past bottleneck events was detected in all populations by ABC, the current Ne of the M-type populations was about a third of that of the S-type populations. These results suggest that the M-type populations have experienced more frequent bottlenecks, which could be related to their higher colonization ability via gametophytic selfing. Although high population differentiation among populations was detected (FST = 0.581, F’ST = 0.739), there was no clear genetic differentiation between the M- and S-types. Instead, significant isolation by distance was detected among all populations. These results suggest that mating system variation in this species is generated by the selection for single spore colonization during local extinction and recolonization events and there is no genetic structure due to mating system.
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Pilkington KM, Symonds VV. Isolation and characterization of polymorphic microsatellite loci in Selliera radicans (Goodeniaceae). APPLICATIONS IN PLANT SCIENCES 2016; 4:apps1600012. [PMID: 27347454 PMCID: PMC4915921 DOI: 10.3732/apps.1600012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 03/03/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY Microsatellite markers were developed for species in the genus Selliera (Goodeniaceae) for future investigations of population genetic structure and interspecific hybridization within the genus. METHODS AND RESULTS Using 454 pyrosequencing, 15 new markers were developed from microsatellite loci isolated from S. radicans. Primers for the new markers amplify di- and trinucleotide repeat loci from the three Selliera species screened. Ten of the new markers are polymorphic in S. radicans and six of those 10 loci were found to be polymorphic within each congener. For the focal species, S. radicans, the average number of alleles per locus is 3.7 (SE = 0.60) and the average observed and expected heterozygosities are 0.23 (SE = 0.07) and 0.47 (SE = 0.08), respectively. CONCLUSIONS The new markers provide an important resource for future investigations in the genus Selliera for both population genetics and research into hybridization between species.
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Affiliation(s)
- Kay M. Pilkington
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North, New Zealand
| | - V. Vaughan Symonds
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North, New Zealand
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33
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Shepherd LD, de Lange PJ, Cox S, McLenachan PA, Roskruge NR, Lockhart PJ. Evidence of a Strong Domestication Bottleneck in the Recently Cultivated New Zealand Endemic Root Crop, Arthropodium cirratum (Asparagaceae). PLoS One 2016; 11:e0152455. [PMID: 27011209 PMCID: PMC4806853 DOI: 10.1371/journal.pone.0152455] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/15/2016] [Indexed: 11/18/2022] Open
Abstract
We use chloroplast DNA sequencing to examine aspects of the pre-European Māori cultivation of an endemic New Zealand root crop, Arthropodium cirratum (rengarenga). Researching the early stages of domestication is not possible for the majority of crops, because their cultivation began many thousands of years ago and/or they have been substantially altered by modern breeding methods. We found high levels of genetic variation and structuring characterised the natural distribution of A. cirratum, while the translocated populations only retained low levels of this diversity, indicating a strong bottleneck even at the early stages of this species’ cultivation. The high structuring detected at four chloroplast loci within the natural A. cirratum range enabled the putative source(s) of the translocated populations to be identified as most likely located in the eastern Bay of Plenty/East Cape region. The high structuring within A. cirratum also has implications for the conservation of genetic diversity within this species, which has undergone recent declines in both its natural and translocated ranges.
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Affiliation(s)
- Lara D. Shepherd
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- * E-mail:
| | - Peter J. de Lange
- Science and Capability Group, Terrestrial Ecosystems, Department of Conservation, Newton, Auckland, New Zealand
| | - Simon Cox
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | | | - Nick R. Roskruge
- Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Peter J. Lockhart
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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34
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Atherton RA, Lockhart PJ, McLenachan PA, de Lange PJ, Wagstaff SJ, Shepherd LD. A molecular investigation into the origin and relationships of karaka/kōpi (Corynocarpus laevigatus) in New Zealand. J R Soc N Z 2015. [DOI: 10.1080/03036758.2015.1093006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Prebble JM, Tate JA, Meudt HM, Symonds VV. Microsatellite markers for the New Zealand endemic Myosotis pygmaea species group (Boraginaceae) amplify across species. APPLICATIONS IN PLANT SCIENCES 2015; 3:apps1500027. [PMID: 26082880 PMCID: PMC4467761 DOI: 10.3732/apps.1500027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 04/27/2015] [Indexed: 06/04/2023]
Abstract
PREMISE OF THE STUDY Microsatellite loci were developed as polymorphic markers for the New Zealand endemic Myosotis pygmaea species group (Boraginaceae) for use in species delimitation and population and conservation genetic studies. METHODS AND RESULTS Illumina MiSeq sequencing was performed on genomic DNA from seedlings of M. drucei. From trimmed paired-end sequences >400 bp, 484 microsatellite loci were identified. Twelve of 48 microsatellite loci tested were found to be polymorphic and consistently scorable when screened on 53 individuals from four populations representing the geographic range of M. drucei. They also amplify in all other species in the M. pygmaea species group, i.e., M. antarctica, M. brevis, M. glauca, and M. pygmaea, as well as 18 other Myosotis species. CONCLUSIONS These 12 polymorphic microsatellite markers establish an important resource for research and conservation of the M. pygmaea species group and potentially other Southern Hemisphere Myosotis.
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Affiliation(s)
- Jessica M. Prebble
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
- Museum of New Zealand Te Papa Tongarewa, P.O. Box 467, Cable Street, Wellington 6140, New Zealand
| | - Jennifer A. Tate
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Heidi M. Meudt
- Museum of New Zealand Te Papa Tongarewa, P.O. Box 467, Cable Street, Wellington 6140, New Zealand
| | - V. Vaughan Symonds
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
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37
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DNA extraction protocol for biological ingredient analysis of Liuwei Dihuang Wan. GENOMICS PROTEOMICS & BIOINFORMATICS 2014; 12:137-43. [PMID: 24838067 PMCID: PMC4411345 DOI: 10.1016/j.gpb.2014.03.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 03/29/2014] [Accepted: 03/31/2014] [Indexed: 11/23/2022]
Abstract
Traditional Chinese medicine (TCM) preparations are widely used for healthcare and clinical practice. So far, the methods commonly used for quality evaluation of TCM preparations mainly focused on chemical ingredients. The biological ingredient analysis of TCM preparations is also important because TCM preparations usually contain both plant and animal ingredients, which often include some mis-identified herbal materials, adulterants or even some biological contaminants. For biological ingredient analysis, the efficiency of DNA extraction is an important factor which might affect the accuracy and reliability of identification. The component complexity in TCM preparations is high, and DNA might be destroyed or degraded in different degrees after a series of processing procedures. Therefore, it is necessary to establish an effective protocol for DNA extraction from TCM preparations. In this study, we chose a classical TCM preparation, Liuwei Dihuang Wan (LDW), as an example to develop a TCM-specific DNA extraction method. An optimized cetyl trimethyl ammonium bromide (CTAB) method (TCM-CTAB) and three commonly-used extraction kits were tested for extraction of DNA from LDW samples. Experimental results indicated that DNA with the highest purity and concentration was obtained by using TCM-CTAB. To further evaluate the different extraction methods, amplification of the second internal transcribed spacer (ITS2) and the chloroplast genome trnL intron was carried out. The results have shown that PCR amplification was successful only with template of DNA extracted by using TCM-CTAB. Moreover, we performed high-throughput 454 sequencing using DNA extracted by TCM-CTAB. Data analysis showed that 3–4 out of 6 prescribed species were detected from LDW samples, while up to 5 contaminating species were detected, suggesting TCM-CTAB method could facilitate follow-up DNA-based examination of TCM preparations.
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Nagori R, Sharma P, Habibi N, Purohit SD. An Efficient Genomic DNA Extraction Protocol for Molecular Analysis in Annona reticulata. NATIONAL ACADEMY SCIENCE LETTERS-INDIA 2014. [DOI: 10.1007/s40009-013-0213-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Van Etten ML, Houliston GJ, Mitchell CM, Heenan PB, Robertson AW, Tate JA. Sophora microphylla (Fabaceae) microsatellite markers and their utility across the genus. APPLICATIONS IN PLANT SCIENCES 2014; 2:apps1300081. [PMID: 25202609 PMCID: PMC4103103 DOI: 10.3732/apps.1300081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 11/08/2013] [Indexed: 06/03/2023]
Abstract
PREMISE OF THE STUDY Genus-specific microsatellite markers were developed for Sophora for population genetic and systematic studies of the group in New Zealand, and potentially elsewhere in the geographic range. • METHODS AND RESULTS From sequencing a total genomic DNA library (using Roche 454), we identified and developed 29 polymorphic microsatellite markers for S. microphylla and S. chathamica. We tested 12 of these markers on 14 S. chathamica individuals and four S. microphylla populations. All loci amplified in both species and species-specific alleles occurred at seven loci. In S. microphylla populations, the observed and expected heterozygosities ranged from 0.000-0.960 and 0.000-0.908, respectively, with alleles per locus ranging from seven to 23. • CONCLUSIONS The developed markers will be valuable in studies of phylogenetics, population structure, mating system, and selection of provenances for restoration projects.
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Affiliation(s)
- Megan L. Van Etten
- Institute of Agriculture and Environment, Massey University, Palmerston North 4442, New Zealand
| | | | | | | | - Alastair W. Robertson
- Institute of Agriculture and Environment, Massey University, Palmerston North 4442, New Zealand
| | - Jennifer A. Tate
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
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Abstract
With the expansion of molecular techniques, the historical collections have become widely used. Studying plant DNA using modern molecular techniques such as DNA sequencing plays an important role in understanding evolutionary relationships, identification through DNA barcoding, conservation status, and many other aspects of plant biology. Enormous herbarium collections are an important source of material especially for specimens from areas difficult to access or from taxa that are now extinct. The ability to utilize these specimens greatly enhances the research. However, the process of extracting DNA from herbarium specimens is often fraught with difficulty related to such variables as plant chemistry, drying method of the specimen, and chemical treatment of the specimen. Although many methods have been developed for extraction of DNA from herbarium specimens, the most frequently used are modified CTAB and DNeasy Plant Mini Kit protocols. Nine selected protocols in this chapter have been successfully used for high-quality DNA extraction from different kinds of plant herbarium tissues. These methods differ primarily with respect to their requirements for input material (from algae to vascular plants), type of the plant tissue (leaves with incrustations, sclerenchyma strands, mucilaginous tissues, needles, seeds), and further possible applications (PCR-based methods or microsatellites, AFLP).
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Affiliation(s)
- Lenka Záveská Drábková
- Department of Taxonomy, Institute of Botany, Academy of Sciences of the Czech Republic, Pruhonice, Czech Republic
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Bai J, Baldwin E, Liao HL, Zhao W, Kostenyuk I, Burns J, Irey M. Extraction of DNA from orange juice, and detection of bacterium Candidatus Liberibacter asiaticus by real-time PCR. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:9339-9346. [PMID: 24047134 DOI: 10.1021/jf402364y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Orange juice processed from Huanglongbing (HLB) affected fruit is often associated with bitter taste and/or off-flavor. HLB disease in Florida is associated with Candidatus Liberibacter asiaticus (CLas), a phloem-limited bacterium. The current standard to confirm CLas for citrus trees is to take samples from midribs of leaves, which are rich in phloem tissues, and use a quantitative real-time polymerase chain reaction (qPCR) test to detect the 16S rDNA gene of CLas. It is extremely difficult to detect CLas in orange juice because of the low CLas population, high sugar and pectin concentration, low pH, and possible existence of an inhibitor to DNA amplification. The objective of this research was to improve extraction of DNA from orange juice and detection of CLas by qPCR. Homogenization using a sonicator increased DNA yield by 86% in comparison to mortar and pestle extraction. It is difficult to separate DNA from pectin; however, DNA was successfully extracted by treating the juice with pectinase. Application of an elution column successfully removed the unidentified inhibitor to DNA amplification. This work provided a protocol to extract DNA from whole orange juice and detect CLas in HLB-affected fruit.
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Affiliation(s)
- Jinhe Bai
- USDA , ARS, USHRL, 2001 South Rock Road, Ft. Pierce, Florida 34945, United States
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Van Etten ML, Robertson AW, Tate JA. Microsatellite markers for the New Zealand endemic tree Fuchsia excorticata (Onagraceae). APPLICATIONS IN PLANT SCIENCES 2013; 1:apps1300045. [PMID: 25202492 PMCID: PMC4103472 DOI: 10.3732/apps.1300045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 06/26/2013] [Indexed: 06/03/2023]
Abstract
PREMISE OF THE STUDY Microsatellite markers were developed from a New Zealand endemic understory tree, Fuchsia excorticata, to investigate factors affecting the mating system. • METHODS AND RESULTS Using 454 pyrosequencing, 48 microsatellite markers were developed and tested for polymorphism within populations. Twelve of these microsatellite loci were identified as being polymorphic within at least three populations and consistently amplified in the four populations tested. These primers amplified di-, tri-, and tetranucleotide repeats with 1-10 alleles per population. • CONCLUSIONS These results indicate the utility of microsatellite loci for future mating system and population genetic studies in F. excorticata.
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Affiliation(s)
- Megan L. Van Etten
- Institute of Agriculture and Environment, Massey University, Palmerston North 4442, New Zealand
| | - Alastair W. Robertson
- Institute of Agriculture and Environment, Massey University, Palmerston North 4442, New Zealand
| | - Jennifer A. Tate
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
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Takakura KI, Nishio T. Safer DNA extraction from plant tissues using sucrose buffer and glass fiber filter. JOURNAL OF PLANT RESEARCH 2012; 125:805-807. [PMID: 22695723 DOI: 10.1007/s10265-012-0502-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 05/15/2012] [Indexed: 06/01/2023]
Abstract
For some plant species, DNA extraction and downstream experiments are inhibited by various chemicals such as polysaccharides and polyphenols. This short communication proposed an organic-solvent free (except for ethanol) extraction method. This method consists of an initial washing step with STE buffer (0.25 M sucrose, 0.03 M Tris, 0.05 M EDTA), followed by DNA extraction using a piece of glass fiber filter. The advantages of this method are its safety and low cost. The purity of the DNA solution obtained using this method is not necessarily as high as that obtained using the STE/CTAB method, but it is sufficient for PCR experiments. These points were demonstrated empirically with two species, Japanese speedwell and common dandelion, for which DNA has proven difficult to amplify via PCR in past studies.
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Affiliation(s)
- Koh-Ichi Takakura
- Osaka City Institute of Public Health and Environmental Sciences, Osaka, Japan.
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Franck AR, Cochrane BJ, Garey JR. Low-copy nuclear primers and ycf1 primers in Cactaceae. AMERICAN JOURNAL OF BOTANY 2012; 99:e405-e407. [PMID: 23002162 DOI: 10.3732/ajb.1200128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
PREMISE OF THE STUDY To increase the number of variable regions available for phylogenetic study in the Cactaceae, primers were developed for a portion of the plastid ycf1 gene and intron-spanning regions of two low-copy nuclear genes (isi1, nhx1). • METHODS AND RESULTS Primers were tested on several families within Caryophyllales, focusing on the Cactaceae. Gel electrophoresis indicated positive amplification in most samples. Sequences of these three regions (isi1, nhx1, ycf1) from Harrisia exhibited variation similar to or greater than two plastid regions (atpB-rbcL intergenic spacer and rpl16 intron). • CONCLUSIONS The isi, nhx, and ycf1 primers amplify phylogenetically useful information applicable to the Cactaceae and other families in the Caryophyllales.
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Affiliation(s)
- Alan R Franck
- Department of Cell Biology, Microbiology, and Molecular Biology, ISA 2015, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, USA.
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McLay TGB, Tate JA, Symonds VV. Microsatellite markers for the endangered root holoparasite Dactylanthus taylorii (Balanophoraceae) from 454 pyrosequencing. AMERICAN JOURNAL OF BOTANY 2012; 99:e323-e325. [PMID: 22837411 DOI: 10.3732/ajb.1200013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
PREMISE OF THE STUDY Microsatellite loci were isolated and developed as polymorphic markers for the New Zealand endemic root holoparasite Dactylanthus taylorii for use in population and conservation genetics studies. METHODS AND RESULTS Shotgun 454 pyrosequencing was performed on genomic DNA pooled from three individuals of D. taylorii. From 61709 individual sequence reads, primers for 753 microsatellite loci were developed in silico and 72 of these were tested for consistent amplification and variability. Ten microsatellite loci were found to be polymorphic and consistently scorable when screened in 44 individuals from five geographically distant populations. The number of alleles per locus ranged from four to 16 with an average of 9.7, and average observed heterozygosity per locus was between 0.182 and 0.634. CONCLUSIONS These polymorphic microsatellite markers establish an important resource for ongoing conservation initiatives and planned population genetic studies of D. taylorii.
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Affiliation(s)
- Todd G B McLay
- Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand
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Gupta AK, Harish, Rai MK, Phulwaria M, Shekhawat NS. Isolation of genomic DNA suitable for community analysis from mature trees adapted to arid environment. Gene 2011; 487:156-9. [PMID: 21827837 DOI: 10.1016/j.gene.2011.06.029] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Revised: 06/20/2011] [Accepted: 06/24/2011] [Indexed: 10/18/2022]
Abstract
Isolation of intact and pure genomic DNA (gDNA) is essential for many molecular biology applications. It is difficult to isolate pure DNA from mature trees of hot and dry desert regions because of the accumulation of high level of polysaccharides, phenolic compounds, tannins etc. We hereby report the standardized protocol for the isolation and purification of gDNA from seven ecologically and medically important tree species of Combretaceae viz. Anogeissus (Anogeissus sericea var. nummularia, Anogeissus pendula, and Anogeissus latifolia) and Terminalia (Terminalia arjuna, Terminalia bellirica, Terminalia catappa and Terminalia chebula). This method involves (i) washing the sample twice with Triton buffer (2%) then (ii) isolation of gDNA by modified-CTAB (cetyl trimethyl ammonium bromide) method employing a high concentration (4%) of PVP (Polyvinylpyrrolidone) and 50mM ascorbic acid, and (iii) purification of this CTAB-isolated gDNA by spin-column. gDNA isolated by modified CTAB or spin-column alone were not found suitable for PCR amplification. The Triton washing step is also critical. The quality of DNA was determined by the A(260)/A(280) absorbance ratio. gDNA was also observed for its intactness by running on 0.8% agarose gel. The suitability of extracted DNA for PCR was tested by amplification with RAPD primers, which was successful. Further, rbcLa (barcoding gene) was amplified and sequenced to check the quality of extracted gDNA for its downstream applications.
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Affiliation(s)
- Amit Kumar Gupta
- Biotechnology Unit, Department of Botany, Jai Narain Vyas University, Jodhpur, India
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