Comparison of DNA extraction methods for non-marine molluscs: is modified CTAB DNA extraction method more efficient than DNA extraction kits?

Chakraborty, Sudeshna; Saha, Anwesha; Aravind, N. A.

doi:10.1007/s13205-020-2051-7

Cited by 30 publications

(24 citation statements)

References 31 publications

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“…Despite many DNA extraction methods available, the efficiency of methods depends on specimen and preservation (Abdel-Latif & Osman, 2017;Psifidi et al, 2015). DNA extraction methods in marine organisms have been evaluated for PCR application (Chakraborty, Saha & Ananthram, 2020;Jasrotia & Langer, 2019;Nadia & Sadok, 2017;Pereira et al, 2011) but not for long-read sequencing.…”

Section: Introductionmentioning

confidence: 99%

Optimization of high molecular weight DNA extraction methods in shrimp for a long-read sequencing platform

Angthong

Uengwetwanit

Pootakham

et al. 2020

PeerJ

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Marine organisms are important to global food security as they are the largest source of animal proteins feeding mankind. Genomics-assisted aquaculture can increase yield while preserving the environment to ensure sufficient and sustainable production for global food security. However, only few high-quality genome sequences of marine organisms, especially shellfish, are available to the public partly because of the difficulty in the sequence assembly due to the complex nature of their genomes. A key step for a successful genome sequencing is the preparation of high-quality high molecular weight (HMW) genomic DNA. This study evaluated the effectiveness of five DNA extraction protocols (CTAB, Genomic-tip, Mollusc DNA, TIANamp Marine Animals DNA, and Sbeadex livestock kits) in obtaining shrimp HMW DNA for a long-read sequencing platform. DNA samples were assessed for quality and quantity using a Qubit fluorometer, NanoDrop spectrophotometer and pulsed-field gel electrophoresis. Among the five extraction methods examined without further optimization, the Genomic-tip kit yielded genomic DNA with the highest quality. However, further modifications of these established protocols might yield even better DNA quality and quantity. To further investigate whether the obtained genomic DNA could be used in a long-read sequencing application, DNA samples from the top three extraction methods (CTAB method, Genomic-tip and Mollusc DNA kits) were used for Pacific Biosciences (PacBio) library construction and sequencing. Genomic DNA obtained from Genomic-tip and Mollusc DNA kits allowed successful library construction, while the DNA obtained from the CTAB method did not. Genomic DNA isolated using the Genomic-tip kit yielded a higher number of long reads (N50 of 14.57 Kb) than those obtained from Mollusc DNA kits (N50 of 9.74 Kb). Thus, this study identified an effective extraction method for high-quality HMW genomic DNA of shrimp that can be applied to other marine organisms for a long-read sequencing platform.

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Section: Introductionmentioning

confidence: 99%

Optimization of high molecular weight DNA extraction methods in shrimp for a long-read sequencing platform

Angthong

Uengwetwanit

Pootakham

et al. 2020

PeerJ

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“…Investigating the marine organism's genomes can bring interesting insights into clarifying phylogenetic relationships among and within different genera and species, thus shedding light on some plasticity and adaptability characteristics of the species. However, a lack of genomic data from marine fauna is noted, which may be limited by the fastidious high‐quality DNA extraction in sufficient amounts (Chakraborty et al, 2020 ). Marine organisms naturally retain composites that interfere not only with the extraction of high molecular weight DNA but also with downstream molecular analysis.…”

Section: Discussionmentioning

confidence: 99%

Whole genome sequencing of marine organisms by Oxford Nanopore Technologies: Assessment and optimization of HMW‐DNA extraction protocols

Boughattas

Albatesh

Al‐Khater³

et al. 2021

Ecology and Evolution

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Previous biogeographic studies revealed exclusive divergence of animal species composition in Gulf region, particularly in Qatar, as its marine ecosystems are driven mainly by high temperature and salinity with a semi-closed basin, depending thus on water input from the Indian Ocean, supplied on the Gulf's southeast coast, and creating a marine barrier for different species as, for example, Decapods (Al-Khayat & Giraldes, 2020). Due to these peculiar conditions, the fauna and flora have adapted to survive under extreme conditions (Al-Khayat, 2010), contributing to the evolution of the marine species in this area and consequently enriching the environment with endemic species (Fotedar et al., 2019;Giraldes et al., 2020;Kardousha et al., 2016). The identification of some of these species has so far been based on conventional taxonomic parameters, although this type of analysis can be notoriously difficult (Bork, 2015).

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“…These organic compounds represent no environmental or health hazard according to their safety data sheets. Other commonly used components of extraction buffers are β-mercaptoethanol, a reducing agent that irreversibly denatures proteins, including degrading enzymes, by reducing disulphide bonds and destroying the native conformation required for enzyme functionality and Cetyltrimethylammonium bromide (CTAB), a cationic detergent of low cost that is generally the method of choice in DNA extractions without kits for a diverse kind of sample, but especially for plant tissues with high polysaccharides and other inhibitory substances [97][98][99]. Although very useful, these two chemicals have been reported as toxic by ecotoxicity tests [100][101][102] and are established as hazardous chemicals by their safety data sheet.…”

Section: Biologicalmentioning

confidence: 99%

Extracellular DNA: Insight of a Signal Molecule in Crop Protection

Carbajal-Valenzuela

Medina-Ramos

Caicedo-López

et al. 2021

Biology

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Agricultural systems face several challenges in terms of meeting everyday-growing quantities and qualities of food requirements. However, the ecological and social trade-offs for increasing agricultural production are high, therefore, more sustainable agricultural practices are desired. Researchers are currently working on diverse sustainable techniques based mostly on natural mechanisms that plants have developed along with their evolution. Here, we discuss the potential agricultural application of extracellular DNA (eDNA), its multiple functioning mechanisms in plant metabolism, the importance of hormetic curves establishment, and as a challenge: the technical limitations of the industrial scale for this technology. We highlight the more viable natural mechanisms in which eDNA affects plant metabolism, acting as a damage/microbe-associated molecular pattern (DAMP, MAMP) or as a general plant biostimulant. Finally, we suggest a whole sustainable system, where DNA is extracted from organic sources by a simple methodology to fulfill the molecular characteristics needed to be applied in crop production systems, allowing the reduction in, or perhaps the total removal of, chemical pesticides, fertilizers, and insecticides application.

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Comparison of DNA extraction methods for non-marine molluscs: is modified CTAB DNA extraction method more efficient than DNA extraction kits?

Cited by 30 publications

References 31 publications

Optimization of high molecular weight DNA extraction methods in shrimp for a long-read sequencing platform

Optimization of high molecular weight DNA extraction methods in shrimp for a long-read sequencing platform

Whole genome sequencing of marine organisms by Oxford Nanopore Technologies: Assessment and optimization of HMW‐DNA extraction protocols

Extracellular DNA: Insight of a Signal Molecule in Crop Protection

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