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Buono D, Albach DC. Infrared spectroscopy for ploidy estimation: An example in two species of Veronica using fresh and herbarium specimens. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11516. [PMID: 37051581 PMCID: PMC10083463 DOI: 10.1002/aps3.11516] [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: 06/08/2022] [Accepted: 12/20/2022] [Indexed: 06/19/2023]
Abstract
PREMISE Polyploidy has become a central factor in plant evolutionary biological research in recent decades. Methods such as flow cytometry have revealed the widespread occurrence of polyploidy; however, its inference relies on expensive lab equipment and is largely restricted to fresh or recently dried material. METHODS Here, we assess the applicability of infrared spectroscopy to infer ploidy in two related species of Veronica (Plantaginaceae). Infrared spectroscopy relies on differences in the absorbance of tissues, which could be affected by primary and secondary metabolites related to polyploidy. We sampled 33 living plants from the greenhouse and 74 herbarium specimens with ploidy known through flow cytometrical measurements and analyzed the resulting spectra using discriminant analysis of principal components (DAPC) and neural network (NNET) classifiers. RESULTS Living material of both species combined was classified with 70% (DAPC) to 75% (NNET) accuracy, whereas herbarium material was classified with 84% (DAPC) to 85% (NNET) accuracy. Analyzing both species separately resulted in less clear results. DISCUSSION Infrared spectroscopy is quite reliable but is not a certain method for assessing intraspecific ploidy level differences in two species of Veronica. More accurate inferences rely on large training data sets and herbarium material. This study demonstrates an important way to expand the field of polyploid research to herbaria.
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Affiliation(s)
- Daniele Buono
- AG Plant Biodiversity and EvolutionCarl von Ossietzky UniversityAmmerlaender Heerstrasse 114‐11826129OldenburgGermany
- Institute of BotanyTechnical University of DresdenObergraben 601097DresdenGermany
- Present address:
Systematik, Biodiversität und Evolution der PflanzenLudwig‐Maximilians‐UniversityMenzinger Str. 6780638MunichGermany
| | - Dirk C. Albach
- AG Plant Biodiversity and EvolutionCarl von Ossietzky UniversityAmmerlaender Heerstrasse 114‐11826129OldenburgGermany
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Shipunov A, Fernández-Alonso JL, Hassemer G, Alp S, Lee HJ, Pay K. Molecular and Morphological Data Improve the Classification of Plantagineae (Lamiales). PLANTS (BASEL, SWITZERLAND) 2021; 10:2299. [PMID: 34834664 PMCID: PMC8625185 DOI: 10.3390/plants10112299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
The tribe Plantagineae (Lamiales) is a group of plants with worldwide distribution, notorious for its complicated taxonomy and still unresolved natural history. We describe the result of a broadly sampled phylogenetic study of tribe. The expanded sampling dataset is based on the trnL-F spacer, rbcL, and ITS2 markers across all three included genera (Aragoa, Littorella and Plantago) and makes this the most comprehensive study to date. The other dataset uses five markers and provides remarkably good resolution throughout the tree, including support for all of the major clades. In addition to the molecular phylogeny, a morphology database of 114 binary characters was assembled to provide comparison with the molecular phylogeny and to develop a means to assign species not sampled in the molecular analysis to their most closely related species that were sampled. Based on the molecular phylogeny and the assignment algorithm to place unsampled species, a key to sections is presented, and a revised classification of the tribe is provided. We also include the description of new species from North America.
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Affiliation(s)
- Alexey Shipunov
- Department of Biology, Minot State University, Minot, ND 58707, USA; (S.A.); (H.J.L.); (K.P.)
| | | | - Gustavo Hassemer
- Três Lagoas Campus, Federal University of Mato Grosso do Sul, Três Lagoas CEP 79610-100, Brazil;
| | - Sean Alp
- Department of Biology, Minot State University, Minot, ND 58707, USA; (S.A.); (H.J.L.); (K.P.)
| | - Hye Ji Lee
- Department of Biology, Minot State University, Minot, ND 58707, USA; (S.A.); (H.J.L.); (K.P.)
| | - Kyle Pay
- Department of Biology, Minot State University, Minot, ND 58707, USA; (S.A.); (H.J.L.); (K.P.)
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Smith RL, Sawbridge T, Mann R, Kaur J, May TW, Edwards J. Rediscovering an old foe: Optimised molecular methods for DNA extraction and sequencing applications for fungarium specimens of powdery mildew (Erysiphales). PLoS One 2020; 15:e0232535. [PMID: 32401807 PMCID: PMC7219758 DOI: 10.1371/journal.pone.0232535] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 04/16/2020] [Indexed: 11/18/2022] Open
Abstract
The purpose of this study was to identify a reliable DNA extraction protocol to use on 25-year-old powdery mildew specimens from the reference collection VPRI in order to produce high quality sequences suitable to address taxonomic phylogenetic questions. We tested 13 extraction protocols and two library preparation kits and found the combination of the E.Z.N.A.® Forensic DNA kit for DNA extraction and the NuGen Ovation® Ultralow System library preparation kit was the most suitable for this purpose.
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Affiliation(s)
- Reannon L. Smith
- Department of Jobs, Agriculture Victoria Research, Regions and Precincts, Bundoora, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Australia
- * E-mail:
| | - Tim Sawbridge
- Department of Jobs, Agriculture Victoria Research, Regions and Precincts, Bundoora, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Australia
| | - Ross Mann
- Department of Jobs, Agriculture Victoria Research, Regions and Precincts, Bundoora, Australia
| | - Jatinder Kaur
- Department of Jobs, Agriculture Victoria Research, Regions and Precincts, Bundoora, Australia
| | - Tom W. May
- Royal Botanic Gardens Victoria, Melbourne, Australia
| | - Jacqueline Edwards
- Department of Jobs, Agriculture Victoria Research, Regions and Precincts, Bundoora, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Australia
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Tuschhoff EJ, Hutter CR, Glor RE. Improving sustainable use of genetic resources in biodiversity archives. PeerJ 2020; 8:e8369. [PMID: 32095317 PMCID: PMC7024571 DOI: 10.7717/peerj.8369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/09/2019] [Indexed: 11/20/2022] Open
Abstract
Tissue sample databases housed in biodiversity archives represent a vast trove of genetic resources, and these tissues are often destructively subsampled and provided to researchers for DNA extractions and subsequent sequencing. While obtaining a sufficient quantity of DNA for downstream applications is vital for these researchers, it is also important to preserve tissue resources for future use given that the original material is destructively and consumptively sampled with each use. It is therefore necessary to develop standardized tissue subsampling and loaning procedures to ensure that tissues are being used efficiently. In this study, we specifically focus on the efficiency of DNA extraction methods by using anuran liver and muscle tissues maintained at a biodiversity archive. We conducted a series of experiments to test whether current practices involving coarse visual assessments of tissue size are effective, how tissue mass correlates with DNA yield and concentration, and whether the amount of DNA recovered is correlated with sample age. We found that tissue samples between 2 and 8 mg resulted in the most efficient extractions, with tissues at the lower end of this range providing more DNA per unit mass and tissues at the higher end of this range providing more total DNA. Additionally, we found no correlation between tissue age and DNA yield. Because we find that even very small tissue subsamples tend to yield far more DNA than is required by researchers for modern sequencing applications (including whole genome shotgun sequencing), we recommend that biodiversity archives consider dramatically improving sustainable use of their archived material by providing researchers with set quantities of extracted DNA rather than with the subsampled tissues themselves.
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Affiliation(s)
- E. J. Tuschhoff
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
- University of Kansas Biodiversity Institute, Lawrence, KS, USA
| | - Carl R. Hutter
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
- University of Kansas Biodiversity Institute, Lawrence, KS, USA
| | - Richard E. Glor
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
- University of Kansas Biodiversity Institute, Lawrence, KS, USA
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Höpke J, Brewer G, Dodsworth S, Ortiz E, Albach D. DNA extraction from old herbarium material of Veronica subgen. Pseudolysimachium (Plantaginaceae). UKRAINIAN BOTANICAL JOURNAL 2019. [DOI: 10.15407/ukrbotj75.06.564] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Koch MA, Michling F, Walther A, Huang XC, Tewes L, Müller C. Early-Mid Pleistocene genetic differentiation and range expansions as exemplified by invasive Eurasian Bunias orientalis (Brassicaceae) indicates the Caucasus as key region. Sci Rep 2017; 7:16764. [PMID: 29196646 PMCID: PMC5711908 DOI: 10.1038/s41598-017-17085-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/22/2017] [Indexed: 11/12/2022] Open
Abstract
Turkish Warty cabbage, Bunias orientalis L. (Brassicaceae) is a perennial herb known for its 250 years of invasion history into Europe and worldwide temperate regions. Putative centers of origin were debated to be located in Turkey, the Caucasus or Eastern Europe. Based on the genetic variation from the nuclear and plastid genomes, we identified two major gene pools in the Caucasian-Irano-Turanian region and close to the Northern Caucasus, respectively. These gene pools are old and started to diverge and expand approximately 930 kya in the Caucasus. Pleistocene glaciation and deglaciation cycles favoured later expansion of a European gene pool 230 kya, which was effectively separated from the Caucasian-Irano-Turanian gene pool. Although the European gene pool is genetically less diverse, it has largely served as source for colonization of Western and Northern Europe in modern times with rare observations of genetic contributions from the Caucasian-Irano-Turanian gene pool such as in North-East America. This study largely utilized herbarium material to take advantage of a biodiversity treasure trove providing biological material and also giving access to detailed collection information.
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Affiliation(s)
- Marcus A Koch
- Heidelberg University, Centre for Organismal Studies, Heidelberg, 69120, Germany.
| | - Florian Michling
- Heidelberg University, Centre for Organismal Studies, Heidelberg, 69120, Germany
| | - Andrea Walther
- Heidelberg University, Centre for Organismal Studies, Heidelberg, 69120, Germany
| | - Xiao-Chen Huang
- Heidelberg University, Centre for Organismal Studies, Heidelberg, 69120, Germany
| | - Lisa Tewes
- Bielefeld University, Chemical Ecology, Bielefeld, 33615, Germany
| | - Caroline Müller
- Bielefeld University, Chemical Ecology, Bielefeld, 33615, Germany
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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: 19] [Impact Index Per Article: 2.7] [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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