Efficient genomic DNA extraction protocol from medicinal rich Passiflora foetida containing high level of polysaccharide and polyphenol

An innovative optimized protocol for high-quality genomic DNA extraction from recalcitrant Shea tree (Vitellaria paradoxa, C.F. Gaertn) plant and its suitability for downstream applications

BACKGROUND

It is not always easy to find a universal protocol for the extraction of genomic DNA (gDNA) from plants. Extraction of gDNA from plants such as shea with a lot of polysaccharides in their leaves is done in two steps: a first step to remove the polysaccharides and a second step for the extraction of the gDNA. In this work, we designed a protocol for extracting high-quality gDNA from shea tree and demonstrate its suitability for downstream molecular applications.

METHODS

Fifty milligrams of leaf and root tissues were used to test the efficiency of our protocol. The quantity of gDNA was measured with the NanoDrop spectrometer and the quality was checked on agarose gel. Its suitability for use in downstream applications was tested with restriction enzymes, SSRs and RAPD polymerase chain reactions and Sanger sequencing.

RESULTS

The average yield of gDNA was 5.17; 3.96; 2.71 and 2.41 µg for dry leaves, dry roots, fresh leaves and fresh roots respectively per 100 mg of tissue. Variance analysis of the yield showed significant difference between all tissue types. Leaf gDNA quality was better compared to root gDNA at the absorbance ratio A260/280 and A260/230. The minimum amplifiable concentration of leaf gDNA was 1 pg/µl while root gDNA remained amplifiable at 10 pg/µl. Genomic DNA obtained was also suitable for sequencing.

CONCLUSION

This protocol provides an efficient, convenient and cost effective DNA extraction method suitable for use in various vitellaria paradoxa genomic studies.

Taxonomic Identification and Molecular DNA Barcoding of Collected Wild-Growing Orchids Used Traditionally for Salep Production

Molecular DNA barcoding combined with botanical taxonomy can be used for the identification and conservation of collected Greek orchids used for salep production as well as in the regulation of fair salep trade. A modified CTAB protocol was used for DNA extraction, amplification of barcoding regions (ITS, matK, rbcL, trnH-psbA), and sequencing. Sequencing data were assembled using Bioedit software, and the BLAST algorithm was used on the NCBI database for species identification at the genus level. Molecular barcoding data based on genetic similarity identification was in full coherence with taxonomic classification based on morphological data. The combination of ITS and matK exhibited a greater capacity to identify a species among the Greek salep samples. Out of the 53 samples examined, 52.9% were classified as Dactylorhiza spp. and 33.3% as Anacamptis spp., whereas only 6 samples were identified as Orchis spp. (11.8%). Given that a superior-quality salep beverage comes from tubers of the latter, the number of samples classified as such in northwestern Greece is unexpectedly low. A database of 53 original reference sequences from wild-growing samples of Greek origin was generated, providing a valuable resource for the identification of other salep samples from different regions. The DNA barcoding results unveiled that salep samples from northwestern Greece are related to nine members of four different genera of Orchidaceae. All species are nationally protected and covered by the CITES convention, while many of these orchids are included in the EU Directive 92/43/EEC appendix as "Other Important Species". Thus, expedited coordinated management actions are needed to ensure their survival in the future.

Revealing the Introduction History and Phylogenetic Relationships of Passiflora foetida sensu lato in Australia

Genomic analysis can be a valuable tool to assistmanagement of non-native invasive species, through determining source and number of introductions as well as clarifying phylogenetic relationships. Here, we used whole chloroplast sequencing to investigate the introduction history of Passiflora foetida sensu lato in Australia and clarify its relationship with other Passiflora species present. Phylogenetic analysis of chloroplast genome data identified three separate genetic lineages of P. foetida s. l. present in Australia, indicating multiple introductions. These lineages had affinities to samples from three separate areas within the native range in Central and South America that represented phylogenetically distinct lineages. These results provide a basis for a targeted search of the native range of P. foetida s. l. for candidate biological control agents that have co-evolved with this species and are thus better adapted to the lineages that are present in Australia. Results also indicated that the Passiflora species native to Australia are in a separate clade to that of P. foetida s. l. and other introduced Passiflora species cultivated in Australia. This knowledge is important to assess the likelihood of finding biological control agents for P. foetida s. l. that will be sufficiently host-specific for introduction in Australia. As P. foetida s. l. is a widespread non-native invasive species across many regions of the world, outcomes from this work highlight the importance of first evaluating the specific entities present in a country before the initiation of a biological control program.

Isolation and Purification of DNA from Complicated Biological Samples

The isolation of nucleic acids from a biological sample is an important step for many molecular biology applications and medical diagnostic assays. This chapter describes an efficient protocol using established acidic CTAB (with a pH value of 5.0 to 6.8) based extraction method for isolation and/or purification of high molecular weight genomic DNA from a range of fresh and difficult sources from plant, animal, fungi, and soil material. This protocol is suitable for many sequencing and genotyping applications, including large-scale sample screening.

Fusarium virguliform e Transcriptional Plasticity Is Revealed by Host Colonization of Maize versus Soybean

We exploited the broad host range of Fusarium virguliforme to identify differential fungal responses leading to either an endophytic or a pathogenic lifestyle during colonization of maize (Zea mays) and soybean (Glycine max), respectively. To provide a foundation to survey the transcriptomic landscape, we produced an improved de novo genome assembly and annotation of F. virguliforme using PacBio sequencing. Next, we conducted a high-resolution time course of F. virguliforme colonization and infection of both soybean, a symptomatic host, and maize, an asymptomatic host. Comparative transcriptomic analyses uncovered a nearly complete network rewiring, with less than 8% average gene coexpression module overlap upon colonizing the different plant hosts. Divergence of transcriptomes originating from host specific temporal induction genes is central to infection and colonization, including carbohydrate-active enzymes (CAZymes) and necrosis inducing effectors. Upregulation of Zn(II)-Cys6 transcription factors were uniquely induced in soybean at 2 d postinoculation, suggestive of enhanced pathogen virulence on soybean. In total, the data described herein suggest that F. virguliforme modulates divergent infection profiles through transcriptional plasticity.

Allelic polymorphism of apple varieties of national selection by genes for scab resistance

The results of the analysis of allelic polymorphism of apple varieties of national selection for R genes of scab resistance are shown. The Rvi6 gene was not identified in the studied forms (putative rvi6rvi6 genotype). The Rvi4 gene was identified in the varieties Grushovka Moskovskaya and Titovka. Genes Rvi2 (Rvi8) - in varieties Pouring yellow, Antonovka kamenichka, Antonovka ordinary, Scarlet anis, Arkad red, Cinnamon striped, Grushovka Moskovskaya, Titovka, Mironchik, Suislepskoe.

Fast and inexpensive protocols for consistent extraction of high quality DNA and RNA from challenging plant and fungal samples for high-throughput SNP genotyping and sequencing applications

Modern genotyping techniques, such as SNP analysis and genotyping by sequencing (GBS), are hampered by poor DNA quality and purity, particularly in challenging plant species, rich in secondary metabolites. We therefore investigated the utility of a pre-wash step using a buffered sorbitol solution, prior to DNA extraction using a high salt CTAB extraction protocol, in a high throughput or miniprep setting. This pre-wash appears to remove interfering metabolites, such as polyphenols and polysaccharides, from tissue macerates. We also investigated the adaptability of the sorbitol pre-wash for RNA extraction using a lithium chloride-based protocol. The method was successfully applied to a variety of tissues, including leaf, cambium and fruit of diverse plant species including annual crops, forest and fruit trees, herbarium leaf material and lyophilized fungal mycelium. We consistently obtained good yields of high purity DNA or RNA in all species tested. The protocol has been validated for thousands of DNA samples by generating high data quality in dense SNP arrays. DNA extracted from Eucalyptus spp. leaf and cambium as well as mycelium from Trichoderma spp. was readily digested with restriction enzymes and performed consistently in AFLP assays. Scaled-up DNA extractions were also suitable for long read sequencing. Successful RNA quality control and good RNA-Seq data for Eucalyptus and cashew confirms the effectiveness of the sorbitol buffer pre-wash for high quality RNA extraction.

Reproducible genomic DNA preparation from diverse crop species for molecular genetic applications

BACKGROUND

Several high-throughput molecular genetic analyses rely on high-quality genomic DNA. Copurification of other molecules can negatively impact the functionality of plant DNA preparations employed in these procedures. Isolating DNA from agronomically important crops, such as sugarcane, rice, citrus, potato and tomato is a challenge due to the presence of high fiber, polysaccharides, or secondary metabolites. We present a simplified, rapid and reproducible SDS-based method that provides high-quality and -quantity of DNA from small amounts of leaf tissue, as required by the emerging biotechnology and molecular genetic applications.

RESULTS

We developed the TENS-CO method as a simplified SDS-based isolation procedure with sequential steps of purification to remove polysaccharides and polyphenols using 2-mercaptoethanol and potassium acetate, chloroform partitioning, and sodium acetate/ethanol precipitation to yield high-quantity and -quality DNA consistently from small amounts of tissue (0.15 g) for different plant species. The method is simplified and rapid in terms of requiring minimal manipulation, smaller extraction volume, reduced homogenization time (20 s) and DNA precipitation (one precipitation for 1 h). The method has been demonstrated to accelerate screening of large amounts of plant tissues from species that are rich in polysaccharides and secondary metabolites for Southern blot analysis of reporter gene overexpressing lines, pathogen detection by quantitative PCR, and genotyping of disease-resistant plants using marker-assisted selection.

CONCLUSION

To facilitate molecular genetic studies in major agronomical crops, we have developed the TENS-CO method as a simple, rapid, reproducible and scalable protocol enabling efficient and robust isolation of high-quality and -quantity DNA from small amounts of tissue from sugarcane, rice, citrus, potato, and tomato, thereby reducing significantly the time and resources used for DNA isolation.

Natural polyamines and synthetic analogs modify the growth and the morphology of Pyrus communis pollen tubes affecting ROS levels and causing cell death

Polyamines (PAs) are small molecules necessary for pollen maturation and tube growth. Their role is often controversial, since they may act as pro-survival factors as well as factors promoting Programmed Cell Death (PCD). The aim of the present work was to evaluate the effect of exogenous PAs on the apical growth of pear (Pyrus communis) pollen tube and to understand if PAs and reactive oxygen species (ROS) are interconnected in the process of tip-growth. In the present study besides natural PAs, also aryl-substituted spermine and methoctramine (Met 6-8-6) analogs were tested. Among the natural PAs, Spm showed strongest effects on tube growth. Spm entered through the pollen tube tip, then diffused in the sub-apical region that underwent drastic morphological changes, showing enlarged tip. Analogs were mostly less efficient than natural PAs but BD23, an asymmetric synthetic PAs bearing a pyridine ring, showed similar effects. These effects were related to the ability of PAs to cause the decrease of ROS level in the apical zone, leading to cell death, counteracted by the caspase-3 inhibitor Ac-DEVD-CHO (DEVD). In conclusions, ROS are essential for pollen germination and a strict correlation between ROS regulation and PA concentration is reported. Moreover, an imbalance between ROS and PAs can be detrimental thereby driving pollen toward cell death.

Development of an effective and efficient DNA isolation method for Cinnamomum species

Different species of Cinnamomum are rich in polysaccharide's and secondary metabolites, which hinder the process of DNA extraction. High quality DNA is the pre-requisite for any molecular biology study. In this paper we report a modified method for high quality and quantity of DNA extraction from both lyophilized and non-lyophilized leaf samples. Protocol reported differs from the CTAB procedure by addition of higher concentration of salt and activated charcoal to remove the polysaccharides and polyphenols. Wide utility of the modified protocol was proved by DNA extraction from different woody species and 4 Cinnamomum species. Therefore, this protocol has also been validated in different species of plants containing high levels of polyphenols and polysaccharides. The extracted DNA showed perfect amplification when subjected to RAPD, restriction digestion and amplification with DNA barcoding primers. The DNA extraction protocol is reproducible and can be applied for any plant molecular biology study.