DNA Extraction from Herbarium Specimens

2013 ◽  
pp. 69-84 ◽  
Author(s):  
Lenka Záveská Drábková
Keyword(s):  
Dna Extraction ◽  
Herbarium Specimens

DNA extraction from herbarium specimens of Rhodiola rosea

2016 ◽  
Author(s):  
Tagimanova D.S. ◽  
◽  
Khapilina O.N. ◽  
Amenov A.A. ◽  
Kalendar R.N.
Keyword(s):  
Dna Extraction ◽  
Rhodiola Rosea ◽  
Herbarium Specimens

scholarly journals Comparative Analysis of Different DNA Extraction Methods and Preliminary Analysis of Genetic Diversity of Hedera nepalensis K. Koch. in Vietnam Based on GBSSI Marker

2019 ◽  
Vol 35 (1) ◽  
Author(s):  
Dinh Doan Long ◽  
Nguyen Xuan Bach ◽  
Nguyen Thi Thu Thao ◽  
Pham Thi Hong Nhung ◽  
Do Thi Le Hang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Extraction ◽  
Genomic Dna ◽  
Preliminary Analysis ◽  
Herbarium Specimens ◽  
Arnold Arboretum ◽  
Sprague Dawley ◽  
National Academy Of Sciences ◽  
Manihot Esculenta Crantz ◽  
Spacer Length

Though the ivy (Hedera nepalensis K. Koch.) has long been utilized in traditional medicine, its genome information is very limited. For plants, an effective method of DNA extraction is a very important step which greatly affects subsequent genetic analyses. In this study, four different methods of DNA extraction from dry leaves were used. A comparison of different protocols resulted in the yield of extracted DNA that ranged from 10.5 to 437.4 ng/μl and with a purity ranged from 1.8 to 2.2. Based on the PCR results of GBSSI gene, Gene JET Plant Genomic DNA Purification Mini Kit is the most optimal extraction method for Vietnam ivy’s dry leaves. A preliminary analysis of the phylogenetic tree based on the GBSSI marker showed that ivy growing in a number of northern mountainous provinces of Vietnam belonged to the H. nepalensis K. Koch species. The high - quality total DNA will allow us to amplify different DNA markers, providing valuable genetic information to preserve and develop medicinal resources in Vietnam. Keywords GBSSI, Hedera nepalensis K. Koch, DNA extraction. References [1] J. Ackerfield, J. Wen, A morphometric analysis of Hedera L. (the ivy genus, Araliaceae) and its taxonomic implications, Adansonia Sér. 24 (2002) 187-212.[2] U.S. National Plant Germplasm System, Taxon: Hedera nepalensis K. Koch, https://npgsweb.ars -grin.gov/gringlobal/taxonomydetail.aspx?id= 18567, 2019 (accessed 21 March 2019). [3] L. Jafri, S. Saleem, T.P. Kondrytuk, I.Q. Haq, N. Ullah, J.M. Pezzuto, B. Mirza, Hedera nepalensis K. Koch: A Novel Source of Natural Cancer Chemopreventive and Anticancerous Compounds, Phytotherapy Reserch. 30 (2016) 447-453.[4] S. Saleem, L. Jafri, I. Haq, L.C. Chang, D. Calderwood, B.D. Green, B. Mirza, Plants Fagonia cretica L. and Hedera nepalensis K. Koch contain natural compounds with potent dipeptidyl peptidase-4 (DPP-4) inhibitory activity, Journal of Ethnopharmacology. 156 (2014) 26-32.[5] W.J. Hashmi, H. Ismail, F. Mehmood, B. Mirza, Neuroprotective, antidiabetic and antioxidant effect of Hedera nepalensis and lupeol against STZ+ AlCl3 induced rats model, DARU: Journal of faculty of Pharmacy, Tehran University of Medical Sciences. 26 (2018) 179-190.[6] H. Ismail, A. Rasheed, I.U. Haq, L. Jafri, N. Ullah, E. Dilshad, M. Sajd, B. Mirza, Five indigenous plants of Pakistan with Antinociceptive, anti-inflammatory, antidepressant, and anticoagulant properties in Sprague Dawley rats, Evidence-based Complementary and alternative medicine 2017 (2017) 1-10.[7] A. Mitchell, J. Wen. Phylogenetic utility and evidence for multiple copies of granule-bound starch synthase I (GBSSI) in Araliaceae, Taxon 53 (2004) 29-44.[8] M.A. Saghai-Maroof, K.M. Soliman, R.A. Jorgensen, R.W.L. Allard, Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics, Proceeding of the National Academy of Sciences of the USA. 81 (1984) 8014-8018.[9] M. Elias, G.S. Mühlen, D. McKey, A.C. Roa, J. Tohme, Genetic diversity of traditional South American landraces of cassava (Manihot esculenta Crantz): an analysis using microsatellites, Economic Botany. 58 (2004) 242-256.[10] B.D. Lade, A.S. Patil, H.M. Paikrao, Efficient genomic DNA extraction protocol from medicinal rich Passiflora foetida containing high level of polysaccharide and polyphenol, Springerplus. 3 (2014) 1-7.[11] J.H. Cota-Sánchez, K. Remarchuk, K. Ubayasena, Ready-to-use DNA extracted with a CTAB method adapted for herbarium specimens and mucilaginous plant tissue, Plant Molecular Biology Reporter. 24 (2006) 161.[12] J. Zhang, J.M. Stewart, Economical and rapid method for extracting cotton genomic DNA, Journal of Cotton Science. 4 (2000) 193-201.[13] T. Li, H. Pan, Y. Feng, H. Li, Y. Zhao, Bioactivity-guided isolation of anticancer constituents from Hedera nepalensis K. Koch, South African Journal of Botany. 100 (2015) 87-93.[14] L. Jafri, S. Saleem, N. Ullah, B. Mirza, In vitro assessment of antioxidant potential and determination of polyphenolic compounds of Hedera nepalensis K. Koch, Arabian Journal of Chemistry. 10 (2017) S3699-S3706.[15] B. Ahmad, N. Munir, S. Bashir, S. Azam, I. Khan, M. Ayub, Biological screening of Hedera nepalensis, Journal of Medicinal Plants Research. 6 (2012) 5250-5257.[16] K.H.E. Koch, Hortus Dendrologicus, F. Schneider & Co., Berlin, 1985, pp 250.[17] A. Rehder, New species, varieties and combinations from the herbarim and the collections of the Arnold arboretum, Journal of the Arnold Arboretum. 4 (1923) 250.  

Comparison of seven DNA extraction and amplification protocols in historical herbarium specimens of juncaceae

2002 ◽  
Vol 20 (2) ◽  
pp. 161-175 ◽  
Author(s):  
Lenka Drábková ◽  
Jan Kirschner ◽  
Ĉestmír Vlĉek
Keyword(s):  
Dna Extraction ◽  
Herbarium Specimens

scholarly journals At the crossroads of botanical collections and molecular genetics laboratory: a preliminary study of obtaining amplifiable DNA from moss herbarium material

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9109
Author(s):  
Marta Saługa
Keyword(s):  
Dna Extraction ◽  
Extreme Environments ◽  
Pcr Amplification ◽  
Extraction Methods ◽  
Herbarium Specimens ◽  
Polar Regions ◽  
Moss Species ◽  
Dna Yield ◽  
Herbarium Collections ◽  
Dna Extraction Methods

Background Research focused on extreme environments is often associated with difficulties in obtaining fresh plant material. Herbaria may provide great support as they house large collections of specimens from different parts of the world. Accordingly, there is also a growing interest in methods using herbarium specimens in molecular studies. Much of the literature on herbarium DNA is aimed to improve extraction and PCR amplification and is focused mostly on vascular plants. Here, I provide a brief study of DNA extraction efficiency from moss herbarium specimens, emphasizing the importance of herbaria as an invaluable source of material from hard-to-access geographical areas, such as the Antarctic region. Methods The presented study is based on herbarium collections of 25 moss species collected in the austral polar regions between 1979 and 2013. The majority of samples were obtained using the DNeasy Plant Mini Kit (Qiagen, Hilden, Germany). The remaining, smaller part was extracted using an adapted CTAB-based approach. The performance of DNA extraction methods in terms of PCR amplification success was measured by testing several DNA fragments of various size. Furthermore, in order to estimate of DNA fragmentation level, an automated on-chip electrophoresis system was used. Results Results reveal that DNA purity and the length of the target genetic region are the fundamental agents which drive the successful PCR reaction. Conversely, the DNA yield and specimen age seem to be less relevant. With this study, I present also an optimized CTAB-based approach which may effectively suppress inhibitors in the herbarium DNA. This method can be considered a cheaper alternative to column-based technology, particularly useful for dealing with a large number of samples. Results of this study confirmed previous reports and contribute to filling the existing gap in molecular analyses which involve the use of herbarium collections of mosses.

A rapid and cost-effective method for DNA extraction from archival herbarium specimens

2015 ◽  
Vol 80 (11) ◽  
pp. 1478-1484 ◽  
Author(s):  
A. A. Krinitsina ◽  
T. V. Sizova ◽  
M. A. Zaika ◽  
A. S. Speranskaya ◽  
A. P. Sukhorukov
Keyword(s):  
Dna Extraction ◽  
Cost Effective ◽  
Herbarium Specimens ◽  
Cost Effective Method

scholarly journals How to Open the Treasure Chest? Optimising DNA Extraction from Herbarium Specimens

PLoS ONE ◽  
2012 ◽  
Vol 7 (8) ◽  
pp. e43808 ◽  
Author(s):  
Tiina Särkinen ◽  
Martijn Staats ◽  
James E. Richardson ◽  
Robyn S. Cowan ◽  
Freek T. Bakker
Keyword(s):  
Dna Extraction ◽  
Herbarium Specimens ◽  
Treasure Chest

Historical herbarium specimens in plant molecular systematics — an example from the fern genus Lindsaea (Lindsaeaceae)

Biologia ◽  
2010 ◽  
Vol 65 (2) ◽  
Author(s):  
Samuli Lehtonen ◽  
Maarten Christenhusz
Keyword(s):  
Dna Extraction ◽  
Molecular Systematics ◽  
Type Locality ◽  
Herbarium Specimens ◽  
Dna Fragments ◽  
Type Specimens ◽  
High Quality ◽  
Herbarium Material ◽  
Typical Material

AbstractWe extracted, amplified and sequenced DNA from historical herbarium specimens and silica-dried samples of the fern genus Lindsaea in order to study the sequencing success between the two kinds of samples. High quality sequences were obtained from 57% of the herbarium samples. The specimens age was found to be of little importance for sequencing success when less than 75 years, but the colour of a specimen was found more indicative of sequencing success. Shorter DNA fragments were sequenced successfully twice as often as longer fragments from the herbarium material; in relatively recently collected silica-dried material longer sequences were obtained almost as frequently as short ones. No obvious differences in sequencing success between material originating from different herbaria was observed. We conclude that by using specifically designed DNA extraction protocols and by sequencing short DNA fragments from carefully selected specimens, herbarium material and type specimens can be successfully used in molecular systematics. Typical material or specimens from the type locality (topotypes) should be preferred, when placing a species in a phylogeny.

Non-destructive DNA extraction from herbarium specimens: a method particularly suitable for plants with small and fragile leaves

2019 ◽  
Vol 133 (1) ◽  
pp. 133-141 ◽  
Author(s):  
Norimasa Sugita ◽  
Atsushi Ebihara ◽  
Tsuyoshi Hosoya ◽  
Utsugi Jinbo ◽  
Shingo Kaneko ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Herbarium Specimens ◽  
Non Destructive

scholarly journals Modified method of DNA extraction from herbarium specimens

2011 ◽  
Vol 7 (4) ◽  
pp. 309-317 ◽  
Author(s):  
Andrii Tarieiev ◽  
Andrii Girin ◽  
Natalia Karpenko ◽  
Oxana Tyshchenko ◽  
Ihor Kostikov
Keyword(s):  
Dna Extraction ◽  
Herbarium Specimens ◽  
Modified Method
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