An optimal genomic DNA extraction method for shoots of four Dendrocalamus species based on membership function analysis

High-quality genomic DNA extraction is fundamental for the study of gene cloning and expression in plants. Therefore, this study evaluated several methods for extracting genomic DNA from shoots of four Dendrocalamus species to determine the optimal technique. Genomic DNA was extracted using three different methods: a commercial DNA extraction kit method, a modified cetyltrimethylammonium bromide method and a sodium dodecyl sulfate method. A membership function analysis was employed to compare these methods. The results demonstrated that the commercial DNA extraction kit method was the most effective and comprehensive approach for extracting genomic DNA from shoots of four Dendrocalamus species. Furthermore, this study provided valuable insights into optimizing techniques for extracting genomic DNA in other bamboo species.

What is the "modified" CTAB protocol? Characterizing modifications to the CTAB DNA extraction protocol

Cetyltrimethylammonium bromide (CTAB)-based methods are widely used to isolate DNA from plant tissues, but the unique chemical composition of secondary metabolites among plant species has necessitated optimization. Research articles often cite a "modified" CTAB protocol without explicitly stating how the protocol had been altered, creating non-reproducible studies. Furthermore, the various modifications that have been applied to the CTAB protocol have not been rigorously reviewed and doing so could reveal optimization strategies across study systems. We surveyed the literature for modified CTAB protocols used for the isolation of plant DNA. We found that every stage of the CTAB protocol has been modified, and we summarized those modifications to provide recommendations for extraction optimization. Future genomic studies will rely on optimized CTAB protocols. Our review of the modifications that have been used, as well as the protocols we provide here, could better standardize DNA extractions, allowing for repeatable and transparent studies.

Quality analysis of genomic DNA and authentication of fisheries products based on distinct methods of DNA extraction

Molecular genetic techniques are an effective monitoring tool, but high-quality DNA samples are usually required. In this study, we compared three different protocols of DNA extraction: NaCl (saline); phenol-chloroform and commercial kit (Promega)-from three biological tissues of five individuals of Lutjanus purpureus under two methods of storage. The evaluated items included DNA concentration and purity, processing time and cost, as well as the obtaining of functional sequences. The highest average values of DNA concentration were obtained using the saline procedure and the commercial kit. Pure DNA was only obtained using the saline protocol, evaluated by the ratio of 260/280. The saline and phenol-chloroform protocols were the least expensive methods. The commercial kit costs are counterbalanced by the short time required. The procedure based on phenol-chloroform presented the worst results regarding DNA yield and the time required to perform all steps. The saline and commercial kit protocols showed similar results concerning the amount and quality of extracted DNA. Therefore, the final choice should be based on the available financial resources and the available time for carrying out each procedure of DNA extraction.

Establishing MinION Sequencing and Genome Assembly Procedures for the Analysis of the Rooibos (Aspalathus linearis) Genome

While plant genome analysis is gaining speed worldwide, few plant genomes have been sequenced and analyzed on the African continent. Yet, this information holds the potential to transform diverse industries as it unlocks medicinally and industrially relevant biosynthesis pathways for bioprospecting. Considering that South Africa is home to the highly diverse Cape Floristic Region, local establishment of methods for plant genome analysis is essential. Long-read sequencing is becoming standard procedure for plant genome research, as these reads can span repetitive regions of the DNA, substantially facilitating reassembly of a contiguous genome. With the MinION, Oxford Nanopore offers a cost-efficient sequencing method to generate long reads; however, DNA purification protocols must be adapted for each plant species to generate ultra-pure DNA, essential for these analyses. Here, we describe a cost-effective procedure for the extraction and purification of plant DNA and evaluate diverse genome assembly approaches for the reconstruction of the genome of rooibos (Aspalathus linearis), an endemic South African medicinal plant widely used for tea production. We discuss the pros and cons of nine tested assembly programs, specifically Redbean and NextDenovo, which generated the most contiguous assemblies, and Flye, which produced an assembly closest to the predicted genome size.

RAPD-based evaluation of genetic diversity among populations of the Iranian endemic species Rhabdosciadium aucheri Boiss. (Apiaceae)

Rhabosciadium aucheri is an Iranian endemic herbaceous species that grows in the west, center, and south regions of Iran. In the present study, genetic variation of 70 individuals belonging to seven natural populations of four provinces was investigated using Random Amplified Polymorphic DNA (RAPD) markers. Ten out of twenty-two RAPD primers employed in this study, generated 110 highly amplified and reproducible loci and a mean of 11.1 bands per primer and 48.13% of polymorphism was obtained. According to our results, the primer OPA10 presented the highest effective number of alleles, Shannon's index, and genetic diversity. The highest value of genetic identity (0.916) was determined between Hamadan, Nahavand and Hamadan, Alvand Mts. populations and the highest genetic distance (0.277) was observed between Hamadan, Asadabad and Kurdistan, Qorveh populations. Therefore, there is an obvious correlation between genetic diversity and geographical distribution. PCA was obtained based on RAPD molecular data and Neighbor Joining (NJ) dendrogram was provided successively. Similar results were attained employing UPGMA and Neighbor Joining dendrograms, supported by PCA ordination plot. Overall, almost moderate level of polymorphism was obtained by RAPD molecular markers at the population level that shows a reasonable amount of intraspecific variability. The reason might be due to the low level of gene flow between populations that could give rise to high genetic differentiation.