scholarly journals Comparison of Methods for Genomic Deoxyribonucleic Acid (DNA) Extraction Suitable for Whole-Genome Genotyping in Traditional Varieties of Rice

2019 ◽  
Vol 39 (03) ◽  
Author(s):  
B Priyadharshini ◽  
M Vignesh ◽  
M Prakash ◽  
R Anandan
Keyword(s):  
Genomic Dna ◽  
Large Scale ◽  
Dna Isolation ◽  
High Throughput Analysis ◽  
Ctab Method ◽  
Maximum Quantity ◽  
Rice Genotypes ◽  
Step Over ◽  
Generation Sequencing

The utilization and conservation traditional rice genotypes have attracted global attention. Optimization of DNA isolation protocol for genetic characterization of plants is a necessary and primary step. Over the recent years, next generation sequencing and microarray technologies have revolutionized scientific research, with their applications to high-throughput analysis of biological systems. Isolation of high quantities of pure, intact, double stranded, highly concentrated DNA is prerequisite for successful and reliable large-scale genotyping analysis. Therefore, standardization of DNA isolation is a basic requirement. Here we employed three methods of DNA isolation namely, Dellaporta, Hi-purA and modified CTAB techniques for isolation of genomic DNA from 25 indigenous rice genotypes. From the results, it was found that genomic DNA isolated by modified CTAB method to be the most appropriate for extracting high quality and maximum quantity DNA suitable for genotyping. The quality and quantity of the differentially extracted DNA was subsequently assessed by spectrophotometric measurements and gel electrophoresis.

An Optimized Method for the Preparation of Monascus purpureus DNA for Genome Sequencing

2014 ◽  
Vol 563 ◽  
pp. 379-383 ◽  
Author(s):  
Yue Yang ◽  
Xin Jun Du ◽  
Ping Li ◽  
Bin Liang ◽  
Shuo Wang
Keyword(s):  
Genome Sequencing ◽  
Genomic Dna ◽  
Benzyl Chloride ◽  
Monascus Purpureus ◽  
Sequencing Technologies ◽  
Fungal Evolution ◽  
Ctab Method ◽  
Fungal Dna ◽  
Gene Functional Analysis ◽  
Generation Sequencing

More and more attention has been paid to filamentous fungal evolution, metabolic pathway and gene functional analysis via genome sequencing. However, the published methods for the extraction of fungal genomic DNA were usually costly or inefficient. In the present study, we compared five different DNA extraction protocols: CTAB protocol with some modifications, benzyl chloride protocol with some modifications, snailase protocol, SDS protocol and extraction with the E.Z.N.A. Fungal DNA Maxi Kit (Omega Bio-Tek, USA). The CTAB method which we established with some modification in several steps is not only economical and convenient, but also can be reliably used to obtain large amounts of highly pure genomic DNA fromMonascus purpureusfor sequencing with next-generation sequencing technologies (Illumina and 454) successfully.

scholarly journals A Simple Technique for the Identification of Environmental DNA (eDNA ) in the Water Samples

2021 ◽  
pp. 77-80
Author(s):  
Chitra K. Y.
Keyword(s):  
Water Samples ◽  
Large Scale ◽  
Dna Isolation ◽  
Simple Technique ◽  
Environmental Dna ◽  
Water Bodies ◽  
Easy Method ◽  
Selective Staining ◽  
Generation Sequencing ◽  
Dark Pink

The environmental DNA(eDNA) is the DNA that is shed by the organisms in their environment by different ways viz. , mucous, faeces, skin, eggs, sperms and also when these organisms die due to natural death or disease. The eDNA will persist for several days. Identification of eDNA is a useful method of determining the organisms present in an aquatic environment like amphibians, reptiles, fishes , insects and larval forms of some of these organisms. By analysing the e-DNA it is possible to monitor the species distribution in water bodies like lakes and ponds simply by collecting a sample of water. The technique can be applied for the survey of the water bodies on a large scale for the genomic, taxonomic as well as pollutional studies. The DNA isolation procedures that are available are laborious and time consuming. Therefore, during the present study, a simplified method was devised i. e. , isolation of eDNA with ethanol after which Feulgen stain was applied to identify and confirm it, as it is an easy method before proceeding to work with the isolated eDNA using other techniqnies for further studies. The Feulgen method is used for the selective staining and the localisation of the DNA in the tissues but is adopted during the present study for the water samples for quick identification of eDNA. The smear of eDNA stained with Feulgen showed dark pink or magenta colour under the microscope where it was concentrated but stained lightly when dispersed and fragmented as observed in the present study. Further studies of the isolated eDNA are in progress in our laboratory for quantifying and sequencing eDNA using latest techniques like next generation sequencing for the identification of fish species in the lakes.

scholarly journals Genomic DNA Isolation and Purification of Two Endemic Medicinal Plants (Pterocarpus Santalinus Linn.F & Pimpinella Tirupatiensis Bal&Subr) of Seshachalam Hills, Tirumala.

2012 ◽  
Vol 4 (1) ◽  
Author(s):  
S. Vipranarayana ◽  
T.N.V.K. V.Prasad ◽  
A. Rajinikanth ◽  
T. Damodharam
Keyword(s):  
Gel Electrophoresis ◽  
Genomic Dna ◽  
Dna Isolation ◽  
Low Cost ◽  
Isolation And Purification ◽  
Genomic Dna Isolation ◽  
Pterocarpus Santalinus ◽  
Ctab Method ◽  
Endemic Medicinal Plant ◽  
High Level

Ptercarpus santalinus is an important endemic medicinal plant with high medicinal values that interfere with DNA extraction procedures and qualitative, quantitative agaros gel electrophoresis. An effective and low-cost protocol for isolating genomic DNA from the roots of Pterocarpus santilinus and Pimpinella tirupatiensis was described in this paper. It involved a modified CTAB method with distilled water pretreating samples.  The A260/A280 absorbance ratio of extracted DNA was found to be free from polysaccharide, poly-phenols and tannins contaminants ranged from 2.2 to 2.8 within the high level of purity.

scholarly journals A protocol for large scale genomic DNA isolation for cacao genetics analysis

2014 ◽  
Vol 13 (7) ◽  
pp. 814-820 ◽  
Author(s):  
Mercs Ferreira Santos Rogrio ◽  
Vanderlei Lopes Uilson ◽  
Clement Didier ◽  
Luis Pires Jose ◽  
Matos Lima Eline ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Large Scale ◽  
Dna Isolation ◽  
Genomic Dna Isolation

Enhanced characterization of 109 genomic dna reference material for 6 HLA loci by next-generation sequencing (NGS)

2015 ◽  
Vol 76 ◽  
pp. 70
Author(s):  
Deborah Ferriola ◽  
Jamie Duke ◽  
Anh Huynh ◽  
Alison Gasiewski ◽  
Marianne Rogers ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Reference Material ◽  
Genomic Dna ◽  
Next Generation ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

scholarly journals Uji Efektivitas Metode Isolasi DNA Genom Kopi Arabika (Coffea arabica L.) Asal Kabupaten Jayawijaya

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Arsyam Mawardi ◽  
Maria L. Simonapendi
Keyword(s):  
Genomic Dna ◽  
Dna Isolation ◽  
Dna Amplification ◽  
Initial Information ◽  
Arabica Coffee ◽  
Modified Method ◽  
Ctab Method ◽  
Young Leaves ◽  
Amplification Technique ◽  
The Difference

Genetic substance of DNA has many functions as a basic component of the organism. DNA can be obtained directly through the isolation of DNA. Isolation of genomic DNA Wamena arabica coffee is done by treating the young leaves to get DNA extract. This reasearch is intended to provide scientific contributions in an effort to screen the best methods of DNA isolation, including a modified extraction of Zheng et al method (2005), a modified method of Doyle and Doyle (1990), and method of George and Khan modificaation (2008) or CTAB method. All of methods were tested on Arabica coffee Jayawijaya Wamena. Testing was done by looking at the difference in quality and quantity of products in the form of genomic DNA concentration and DNA thickness, comparing with the marker DNA then electrophoresis on agarose gel. From the results of testing the effectiveness of three types of isolation methods, it was found that the method of George and Khan (2008) or CTAB genomic DNA  produce the best quality than other methods. In terms of quantity, the criteria in the form of DNA concentrations ranging from 100 ng λ-DNA/ml, λ-DNA 50 ng/ml, λ-DNA 10 ng/ml. Concentration of genomic DNA bands visible when the profile is visualized in gel electrophoresis with UV luminescence. This study will be a step and initial information about the genetic composition of a population of arabica coffee which still exists, and will be developed through DNA amplification technique. Key words: coffee, isolation of genomic DNA, CTAB method, profile band pattern

scholarly journals Comparative investigation of DNA extraction methods in black gram (Vigna mungo (L.)

2019 ◽  
Author(s):  
M. . Prakash ◽  
B. . Priyadharshini ◽  
M. . Vignesh ◽  
R. . Anandan
Keyword(s):  
Dna Extraction ◽  
Extraction Method ◽  
Large Scale ◽  
Dna Isolation ◽  
Extraction Methods ◽  
Comparative Investigation ◽  
Black Gram ◽  
Dna Extraction Method ◽  
Ctab Method ◽  
Dna Extraction Methods

Isolation of intact, double stranded, pure and non- contaminated genomic DNA is prerequisite for large scale genotyping analysis including DNA-banks. Three methods of DNA isolation (Dellaporta, CTAB and Hi-PurAg DNA isolation kits) from 25 black gram genotypes were compared in terms of the yield, purity, integrity, and stability of extracted DNA. Purity and quantification of isolated DNA samples was confirmed by using the UV nano-spectrophotometer at OD260/280 and the same is confirmed based by agarose gel electrophoresis. The CTAB method showed the best results followed by Hi-PurAg and Dellaporta method. The CTAB DNA extraction method was found to be the most efficient DNA extraction method, capable of providing high quality, pure and stable DNA and could be used for various molecular related works. All the 25 black gram genotypes for this research gave good yield of DNA from the established modified CTAB protocol.

scholarly journals An improved method for genomic DNA extraction from strawberry leaves

2011 ◽  
Vol 41 (8) ◽  
pp. 1383-1389 ◽  
Author(s):  
Claudinéia Ferreira Nunes ◽  
Juliano Lino Ferreira ◽  
Mônique Carolina Nunes Fernandes ◽  
Sâmera de Souza Breves ◽  
Andressa Leal Generoso ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Genomic Dna ◽  
Extraction Methods ◽  
Isolation And Purification ◽  
Modified Method ◽  
Freeze Dried ◽  
Ctab Method ◽  
Young Leaves ◽  
Tissue Maceration

Several extraction methods of genomic DNA for identification and characterization of genetic diversity in different plant species are routinely applied during molecular analysis. However, the presence of undesirable compounds such as polyphenols and polysaccharides is one of the biggest problems faced during the isolation and purification of high quality DNA in plants. Therefore, achievement of fast and accurate methods for DNA extraction is crucial in order to produce pure samples. Leaves of strawberry genotypes (Fragaria ananassa) have high contents of polysaccharides and polyphenols which increase the sample viscosity and decrease the DNA quality, interfering with the PCR performance. Thereby, in this study we evaluated the quality and amount of genomic DNA extracted from young leaves of strawberry after tissue lyophilization and maceration in presence of polivinilpirrolidone (PVP). The CTAB method was used as reference procedure and it was modified to improve the DNA extraction. The modifications consisted of tissue lyophilization overnight until it was completely freeze-dried and addition of PVP during the tissue maceration in liquid nitrogen. The results showed the efficiency and reliability of the modified method compared to the unmodified method, indicating that combination of lyophilization and PVP improve the quality and amount of the DNA extracted from strawberry leaves.

scholarly journals Utilities for High-Throughput Analysis of B-Cell Clonal Lineages

2015 ◽  
Vol 2015 ◽  
pp. 1-9 ◽  
Author(s):  
William D. Lees ◽  
Adrian J. Shepherd
Keyword(s):  
B Cell ◽  
Large Scale ◽  
Cell Lineage ◽  
Next Generation Sequencing Data ◽  
Sequencing Data ◽  
High Throughput Analysis ◽  
Large Scale Analysis ◽  
Automated Pipeline ◽  
Lineage Trees ◽  
Generation Sequencing

There are at present few tools available to assist with the determination and analysis of B-cell lineage trees from next-generation sequencing data. Here we present two utilities that support automated large-scale analysis and the creation of publication-quality results. The tools are available on the web and are also available for download so that they can be integrated into an automated pipeline. Critically, and in contrast to previously published tools, these utilities can be used with any suitable phylogenetic inference method and with any antibody germline library and hence are species-independent.

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