A modified SDS-based DNA extraction method from raw soybean

Xia, Yimiao; Chen, Fusheng; Du, Yan; Liu, Chen; Bu, Guanhao; Xin, Ying; Liu, Boye

doi:10.1042/bsr20182271

Cited by 74 publications

(44 citation statements)

References 24 publications

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“…It is suggested that SDS-based DNA extractions could be more appropriate for oily plant matrices like ground poppy seeds. The SDS-containing method modified for ground raw soybean seeds had the highest yield of DNA in comparison with the CTAB method and two commercial kits [ 39 ]. A lower amount of DNA yielded the CTAB method also from soybean flour [ 40 ].…”

Section: Resultsmentioning

confidence: 99%

Procedures for DNA Extraction from Opium Poppy (Papaver somniferum L.) and Poppy Seed-Containing Products

Kaňuková

Mrkvová

Mihálik

et al. 2020

Foods

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Several commonly used extraction procedures and commercial kits were compared for extraction of DNA from opium poppy (Papaver somniferum L.) seeds, ground seeds, pollen grains, poppy seed filling from a bakery product, and poppy oil. The newly developed extraction protocol was much simpler, reduced the cost and time required for DNA extraction from the native and ground seeds, and pollen grains. The quality of extracted DNA by newly developed protocol was better or comparable to the most efficient ones. After being extended by a simple purification step on a silica membrane column, the newly developed protocol was also very effective in extracting of poppy DNA from poppy seed filling. DNA extracted from this poppy matrix was amplifiable by PCR analysis. DNA extracted from cold-pressed poppy oil and suitable for amplifications was obtained only by methods developed previously for olive oil. Extracted poppy DNA from all tested matrices was analysed by PCR using primers flanking a microsatellite locus (156 bp) and two different fragments of the reference tubulin gene (553 bp and 96 bp). The long fragment of the reference gene was amplified in DNA extracted from native seeds, ground seeds, and pollen grains. Poppy DNA extracted from the filling of bakery product was confirmed only by amplification of short fragments (96 bp and 156 bp). DNA extracted from cold-pressed poppy oil was determined also only by amplification of these two short fragments.

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Section: Resultsmentioning

confidence: 99%

Procedures for DNA Extraction from Opium Poppy (Papaver somniferum L.) and Poppy Seed-Containing Products

Kaňuková

Mrkvová

Mihálik

et al. 2020

Foods

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“…Bal31 Sensitivity Assay HMW genomic DNA was extracted from 50 Anopheles albimanus following an SDS-based method as previously described [36]. The Bal31 Sensitivity Assay was performed based on the protocol of [20,21] with several modifications.…”

Section: Repeat Analysismentioning

confidence: 99%

The beginning of the end: a chromosomal assembly of the New World malaria mosquito ends with a novel telomere

Compton

Liang

Chen

et al. 2020

Preprint

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Chromosome level assemblies are accumulating in various taxonomic groups including mosquitoes. However, even in the few reference-quality mosquito assemblies, a significant portion of the heterochromatic regions including telomeres remain unresolved. Here we produce a de novo assembly of the New World malaria mosquito, Anopheles albimanus by integrating Oxford Nanopore sequencing, Illumina, Hi-C and optical mapping. This 172.6 Mbps female assembly, which we call AalbS3, is obtained by scaffolding polished large contigs (contig N50=13.7 Mbps) into three chromosomes. All chromosome arms end with telomeric repeats, which is the first in mosquito assemblies and represents a significant step towards the completion of a genome assembly. These telomeres consist of tandem repeats of a novel 30-32 bp telomeric repeat unit (TRU) and are confirmed by analysing the termini of long reads and through both chromosomal in situ hybridization and a Bal31 sensitivity assay. The AalbS3 assembly included previously uncharacterized centromeric and rDNA clusters and more than doubled the content of transposable elements and other repetitive sequences. This telomere-to-telomere assembly, although still containing gaps, represents a significant step towards resolving biologically important but previously hidden genomic components. The comparison of different scaffolding methods will also inform future efforts to obtain reference-quality genomes for other mosquito species. 100-word Article SummaryWe report AalbS3, a telomere-to-telomere assembly of the Anopheles albimanus genome produced by integrating advancing technologies including Oxford Nanopore and Bionano optical mapping. AalbS3 features much of the difficult-to-assemble genomic 'dark matters' including previously missed transposons, centromeres and rDNA clusters. We describe novel telomeric repeats that are confirmed by analysis of long reads and by telomere hybridization assays. This reference-quality assembly represents a significant step towards completing the genomic puzzle pieces and informs efforts to improve the assembly of other mosquito species. Future research into the relationship between telomere and mosquito life span may have significant implications to disease control.

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“…However, commercial kits are usually expensive, with reagent costs commonly ranging between 2 and 9 US$ per sample [8,28], and many times provide low yields, insufficient for some NGS applications [8,29].…”

Section: Introductionmentioning

confidence: 99%

SILEX: a fast and inexpensive high-quality DNA extraction method suitable for multiple sequencing platforms and recalcitrant plant species

et al. 2020

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Background: The use of sequencing and genotyping platforms has undergone dramatic improvements, enabling the generation of a wealth of genomic information. Despite this progress, the availability of high-quality genomic DNA (gDNA) in sufficient concentrations is often a main limitation, especially for third-generation sequencing platforms. A variety of DNA extraction methods and commercial kits are available. However, many of these are costly and frequently give either low yield or low-quality DNA, inappropriate for next generation sequencing (NGS) platforms. Here, we describe a fast and inexpensive DNA extraction method (SILEX) applicable to a wide range of plant species and tissues. Results: SILEX is a high-throughput DNA extraction protocol, based on the standard CTAB method with a DNA silica matrix recovery, which allows obtaining NGS-quality high molecular weight genomic plant DNA free of inhibitory compounds. SILEX was compared with a standard CTAB extraction protocol and a common commercial extraction kit in a variety of species, including recalcitrant ones, from different families. In comparison with the other methods, SILEX yielded DNA in higher concentrations and of higher quality. Manual extraction of 48 samples can be done in 96 min by one person at a cost of 0.12 €/sample of reagents and consumables. Hundreds of tomato gDNA samples obtained with either SILEX or the commercial kit were successfully genotyped with Single Primer Enrichment Technology (SPET) with the Illumina HiSeq 2500 platform. Furthermore, DNA extracted from Solanum elaeagnifolium using this protocol was assessed by Pulsed-field gel electrophoresis (PFGE), obtaining a suitable size ranges for most sequencing platforms that required high-molecular-weight DNA such as Nanopore or PacBio. Conclusions: A high-throughput, fast and inexpensive DNA extraction protocol was developed and validated for a wide variety of plants and tissues. SILEX offers an easy, scalable, efficient and inexpensive way to extract DNA for various next-generation sequencing applications including SPET and Nanopore among others.

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A modified SDS-based DNA extraction method from raw soybean

Cited by 74 publications

References 24 publications

Procedures for DNA Extraction from Opium Poppy (Papaver somniferum L.) and Poppy Seed-Containing Products

Procedures for DNA Extraction from Opium Poppy (Papaver somniferum L.) and Poppy Seed-Containing Products

The beginning of the end: a chromosomal assembly of the New World malaria mosquito ends with a novel telomere

SILEX: a fast and inexpensive high-quality DNA extraction method suitable for multiple sequencing platforms and recalcitrant plant species

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