High quality RNA extraction from Maqui berry for its application in next-generation sequencing

DNA-free high-quality RNA extraction from 39 difficult-to-extract plant species (representing seasonal tissues and tissue types) of 32 families, and its validation for downstream molecular applications

BACKGROUND

High-purity RNA serves as the basic requirement for downstream molecular analysis of plant species, especially the differential expression of genes to various biotic and abiotic stimuli. But, the extraction of high-quality RNA is usually difficult from plants rich in polysaccharides and polyphenols, and their presence usually interferes with the downstream applications. The aim of the study is to optimize the extraction of high-quality RNA from diverse plant species/tissues useful for downstream molecular applications.

RESULTS

Extraction of RNA using commercially available RNA extraction kits and routine hexadecyltrimethylammonium bromide (CTAB) methods did not yield good quality DNA-free RNA from Prosopis cineraria, Conocarpus erectus, and Phoenix dactylifera. A reliable protocol for the extraction of high-quality RNA from mature leaves of these difficult-to-extract trees was optimized after screening nine different methods. The DNase I-, and proteinase K treatment-free modified method, consisting of extraction with CTAB method followed by TRIzol, yielded high-quality DNA-free RNA with an A260/A280 and A260/A230 ratios > 2.0. Extraction of RNA from Conocarpus, the most difficult one, was successful by avoiding the heat incubation of ground tissue in a buffer at 65 oC. Pre-warming of the buffer for 5-10 min was sufficient to extract good-quality RNA. RNA integrity number of the extracted RNA samples ranged between 7 and 9.1, and the gel electrophoresis displayed intact bands of 28S and 18S RNA. A cDNA library constructed from the RNA of P. cineraria was used for the downstream applications. Real-time qPCR analysis using the cDNA from P. cineraria RNA confirmed the quality. The extraction of good quality RNA from samples of the desert-growing P. cineraria (> 20-years-old) collected in alternate months of the year 2021 (January to December covering winter, spring, autumn, and the very dry and hot summer) proved the efficacy of the protocol. The protocol's broad applicability was further validated by extracting good-quality RNA from 36 difficult-to-extract plant species, including tissues such as roots, flowers, floral organs, fruits, and seeds.

CONCLUSIONS

The modified DNase I and Proteinase K treatment-free protocol enables to extract DNA-free, high-quality, intact RNA from a total of 39 difficult-to-extract plant species belonging to 32 angiosperm families is useful to extract good-quality RNA from dicots and monocots irrespective of tissue types and growing seasons.

An optimized method for RNA extraction from the polyurethane oligomer degrading strain Pseudomonas capeferrum TDA1 growing on aromatic substrates such as phenol and 2,4-diaminotoluene

Bacterial degradation of xenobiotic compounds is an intense field of research already for decades. Lately, this research is complemented by downstream applications including Next Generation Sequencing (NGS), RT-PCR, qPCR, and RNA-seq. For most of these molecular applications, high-quality RNA is a fundamental necessity. However, during the degradation of aromatic substrates, phenolic or polyphenolic compounds such as polycatechols are formed and interact irreversibly with nucleic acids, making RNA extraction from these sources a major challenge. Therefore, we established a method for total RNA extraction from the aromatic degrading Pseudomonas capeferrum TDA1 based on RNAzol® RT, glycogen and a final cleaning step. It yields a high-quality RNA from cells grown on TDA1 and on phenol compared to standard assays conducted in the study. To our knowledge, this is the first report tackling the problem of polyphenolic compound interference with total RNA isolation in bacteria. It might be considered as a guideline to improve total RNA extraction from other bacterial species.

Genome-wide screening of novel RT-qPCR reference genes for study of GLRaV-3 infection in wine grapes and refinement of an RNA isolation protocol for grape berries

BACKGROUND

Grapevine, as an essential fruit crop with high economic values, has been the focus of molecular studies in diverse areas. Two challenges exist in the grapevine research field: (i) the lack of a rapid, user-friendly and effective RNA isolation protocol for mature dark-skinned berries and, (ii) the lack of validated reference genes that are stable for quantification of gene expression across desired experimental conditions. Successful isolation of RNA with sufficient yield and quality is essential for downstream analyses involving nucleic acids. However, ripe berries of dark-skinned grape cultivars are notoriously challenging in RNA isolation due to high contents of polyphenolics, polysaccharides, RNase and water.

RESULTS

We have optimized an RNA isolation protocol through modulating two factors at the lysis step that could impact results of RNA isolation - 2-ME concentration and berry mass. By finding the optimal combination among the two factors, our refined protocol was highly effective in isolating total RNA with high yield and quality from whole mature berries of an array of dark-skinned wine grape cultivars. Our protocol takes a much shorter time to complete, is highly effective, and eliminates the requirement for hazardous organic solvents. We have also shown that the resulting RNA preps were suitable for multiple downstream analyses, including the detection of viruses and amplification of grapevine genes using reverse transcription-polymerase chain reaction (RT-PCR), gene expression analysis via quantitative reverse transcription PCR (RT-qPCR), and RNA Sequencing (RNA-Seq). By using RNA-Seq data derived from Cabernet Franc, we have identified seven novel reference gene candidates (CYSP, NDUFS8, YLS8, EIF5A2, Gluc, GDT1, and EF-Hand) with stable expression across two tissue types, three developmental stages and status of infection with grapevine leafroll-associated virus 3 (GLRaV-3). We evaluated the stability of these candidate genes together with two conventional reference genes (actin and NAD5) using geNorm, NormFinder and BestKeeper. We found that the novel reference gene candidates outperformed both actin and NAD5. The three most stable reference genes were CYSP, NDUFS8 and YSL8, whereas actin and NAD5 were among the least stable. We further tested if there would be a difference in RT-qPCR quantification results when the most stable (CYSP) and the least stable (actin and NAD5) genes were used for normalization. We concluded that both actin and NAD5 led to erroneous RT-qPCR results in determining the statistical significance and fold-change values of gene expressional change.

CONCLUSIONS

We have formulated a rapid, safe and highly effective protocol for isolating RNA from recalcitrant berry tissue of wine grapes. The resulting RNA is of high quality and suitable for RT-qPCR and RNA-Seq. We have identified and validated a set of novel reference genes based on RNA-Seq dataset. We have shown that these new reference genes are superior over actin and NAD5, two of the conventional reference genes commonly used in early studies.

Towards Biological Control of Aspergillus carbonarius and Botrytis cinerea in Grapevine Berries and Transcriptomic Changes of Genes Encoding Pathogenesis-Related (PR) Proteins

Grapevine bunch rot, caused by Botrytis cinerea and Aspergillus carbonarius, causes important economic losses every year in grape production. In the present study, we examined the plant protective activity of the biological control agents, Paenibacillus alvei K165, Blastobotrys sp. FP12 and Arthrobacter sp. FP15 against B. cinerea and A. carbonarius on grapes. The in vitro experiments showed that strain K165 significantly reduced the growth of both fungi, while FP15 restricted the growth of A. carbonarius and FP12 was ineffective. Following the in vitro experiments, we conducted in planta experiments on grape berries. It was shown that K165, FP12 and FP15 reduced A. carbonarius rot severity by 81%, 57% and 37%, respectively, compared to the control, whereas, in the case of B. cinerea, the only protective treatment was that with K165, which reduced rot by 75%. The transcriptomic analysis of the genes encoding the pathogenesis-related proteins PR2, PR3, PR4 and PR5 indicates the activation of multiple defense responses involved in the biocontrol activity of the examined biocontrol agents.

A CTAB protocol for obtaining high-quality total RNA from cinnamon (Cinnamomum zeylanicum Blume)

Cinnamomum zeylanicum Blume is an endemic Sri Lankan species commonly known as Ceylon cinnamon or true cinnamon. It is considered the king of spices in addition to its medicinal benefits. Despite recent scientific evidence on its medicinal properties and the industrial demand, cinnamon breeding and crop improvement are not been improved to the expectation. It is mainly due to the limited availability of the genomic information of cinnamon, linked with technical challenges caused by abundant secondary metabolites in all plant parts. Therefore, obtaining high-quality RNA is the fundamental step of transcriptomic analysis and the gene discovery process of cinnamon. We have optimized a CTAB based protocol for high-quality RNA extraction from different cinnamon tissues at various maturity stages collected from the field. Regular pH around 8 and the presence of Polyvinylpyrrolidone (PVP) in CTAB buffer increased the viscosity of the cinnamon lysate. Adjusting the pH of the lysis buffer to 6-6.5 reduced the viscosity of lysate while chloroform precipitates protein efficiently at the adjusted pH with no phenol. Therefore, this protocol excludes PVP and phenol extraction steps. Nanodrop spectrophotometer, gel electrophoresis, and bioanalyzer readings confirmed the quality of extracted RNA. RNA-seq libraries prepared were sequenced with Illumina Sequencing by synthesis technology and obtained good quality data to be used for transcriptomic analysis.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02756-1.

Comparative assessment of three RNA extraction methods for obtaining high-quality RNA from Candida viswanathii biomass

Isolating high quality RNA is a limiting factor in molecular analysis, since it is the base for transcriptional studies. The RNA extraction method can directly affect the RNA quality and quantity, as well as, its overall cost. The industrial importance of the yeast genus Candida in several sectors comes from their capacity to produce Lipases. These enzymes are one of the main metabolites produced by some Candida species, and it has been shown that Candida yeast can biodegrade petroleum hydrocarbons and diesel oil from biosurfactants that they can produce, a feature that turns these organisms into potential combatants for bioremediation techniques. Thus, this study aimed to determine an efficient method for isolating high quality RNA from Candida viswanathii biomass. To achieve this aim, three different RNA extraction methods, TRIzol, Hot Acid Phenol, and CTAB (Cetyltrimethylammonium Bromide), were tested. The three tested methods allowed the isolation of high-quality RNA from C. viswanathii biomass and yielded suitable RNA quantity for carrying out RT-qPCR studies. In addition, all methods displayed high sensitivity for the expression analysis of the CvGPH1 gene through RT-qPCR, with TRIzol and CTAB showing the best results and the CTAB method displaying the best cost-benefit ratio (US$0.35/sample).

A potential endogenous gibberellin-mediated signaling cascade regulated floral transition in Magnolia × soulangeana 'Changchun'

The floral transition is a critical developmental switch in plants, and has profound effects on the flower production and yield. Magnolia × soulangeana 'Changchun' is known as a woody ornamental plant, which can bloom in spring and summer, respectively. In this study, anatomical observation, physiological measurement, transcriptome, and small RNA sequencing were performed to investigate potential endogenous regulatory mechanisms underlying floral transition in 'Changchun'. Transition of the shoot apical meristem from vegetative to reproductive growth occurred between late April and early May. During this specific developmental process, a total of 161,645 unigenes were identified, of which 73,257 were significantly differentially expressed, while a number of these two categories of miRNAs were 299 and 148, respectively. Further analysis of differentially expressed genes (DEGs) revealed that gibberellin signaling could regulate floral transition in 'Changchun' in a DELLA-dependent manner. In addition, prediction and analysis of miRNA targeted genes suggested that another potential molecular regulatory module was mediated by the miR172 family and other several novel miRNAs (Ms-novel_miR139, Ms-novel_miR229, and Ms-novel_miR232), with the participation of up- or down-regulating genes, including MsSVP, MsAP2, MsTOE3, MsAP1, MsGATA6, MsE2FA, and MsMDS6. Through the integrated analysis of mRNA and miRNA, our research results will facilitate the understanding of the potential molecular mechanism underlying floral transition in 'Changchun', and also provide basic experimental data for the plant germplasm resources innovation in Magnolia.

An efficient method for total RNA extraction from leaves of arboreal species from the Brazilian Cerrado

Abstract Considering the lack of information on RNA extraction from arboreal species, specially from the Brazilian Cerrado, the aim of this study was to test RNA extraction methods for a wide variety of native plant species from this biome. The methods tested consisted of: (i) TRIzol® reagent, (ii) TRIzol® reagent with modifications, (iii) CTAB buffer, and (iv) Modified CTAB buffer, initially for leaf samples of Xylopia aromatica and Piper arboreum. Later the procedure with the best results was used to obtain purified RNA from 17 other native species. Based on A260/A280 absorbance ratio the Modified CTAB method was the best for total RNA extraction for those woody species. Ten out of eleven species tested through RT-PCR generated fragments of the expected size from the total RNA extracted by the selected method, confirming it as the best option to obtain high-quality RNA for molecular analyses and for use in the detection of viruses infecting these tree species.

A New Insight into Flowering Regulation: Molecular Basis of Flowering Initiation in Magnolia × soulangeana 'Changchun'

Magnolia × soulangeana ‘Changchun’ are trees that bloom in spring and summer respectively after flower bud differentiation. Here, we use phenological and morphological observation and RNA-seq technology to study the molecular basis of flowering initiation in ‘Changchun’. During the process of flowering initiation in spring and summer, the growth of expanded flower buds increased significantly, and their shape was obviously enlarged, which indicated that flowering was initiated. A total of 168,120 expressed genes were identified in spring and summer dormant and expanded flower buds, of which 11,687 genes showed significantly differential expression between spring and summer dormant and expanded flower buds. These differentially expressed genes (DEGs) were mainly involved in plant hormone signal transduction, metabolic processes, cellular components, binding, and catalytic activity. Analysis of differential gene expression patterns revealed that gibberellin signaling, and some transcription factors were closely involved in the regulation of spring and summer flowering initiation in ‘Changchun’. A qRT-PCR (quantitative Real Time Polymerase Chain Reaction) analysis showed that BGISEQ-500 sequencing platform could truly reflect gene expression patterns. It also verified that GID1B (GIBBERELLIN INSENSITIVE DWARF1 B), GID1C, SPL8 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 8), and GASA (GIBBERELLIC ACID-STIMULATED ARABIDOPSIS) family genes were expressed at high levels, while the expression of SPY (SPINDLY) was low during spring and summer flowering initiation. Meanwhile, the up- and down-regulated expression of, respectively, AGL6 (AGAMOUS-LIKE 6) and DREB3 (DEHYDRATION-RESPONSIVE ELEMENT-BINDING PROTEIN 3), AG15, and CDF1 (CYCLIC DOF FACTOR 1) might also be involved in the specific regulation of spring and summer flowering initiation. Obviously, flowering initiation is an important stage of the flowering process in woody plants, involving the specific regulation of relevant genes and transcription factors. This study provides a new perspective for the regulation of the flowering process in perennial woody plants.

Efficient and High-Quality RNA Isolation from Metabolite-Rich Tissues of Stevia rebaudiana, an Important Commercial Crop

Stevia rebaudiana, a perennial herb native to northeastern Paraguay, has gained immense attention globally over the recent decades due to the natural sweetness of its leaves. Like in most plants, this particular species contains high amount of secondary metabolites, thus rendering the isolation of high quality and quantity RNA extract for molecular applications rather challenging. An effective, high-yield and high-quality RNA isolation protocol for this economically important plant species was devised here based on the cetyltrimethylammonium bromide (CTAB) extraction method, with an additional genomic DNA (gDNA) removal step. DNA and other contaminants that may affect downstream applications were effectively removed. Our results exhibited that RNA samples isolated from the leaves and stems of Stevia rebaudiana using this improvised method are high in integrity and quality with RNA integrity number (RIN) of more than 8 and low in contaminants.

An optimized isolation protocol yields high-quality RNA from cassava tissues (Manihot esculenta Crantz)

We developed and modified a precise, rapid, and reproducible protocol isolating high-quality RNA from tissues of multiple varieties of cassava plants (Manihot esculenta Crantz). The resulting method is suitable for use in mini, midi, and maxi preparations and rapidly achieves high total RNA yields (170-600 μg·g^-1) using low-cost chemicals and consumables and with minimal contamination from polysaccharides, polyphenols, proteins, and other secondary metabolites. In particular, A ₂₆₀ : A ₂₈₀ ratios were > 2.0 for RNA from various tissues, and all of the present RNA samples yielded ribosomal integrity number values of greater than six. The resulting high purity and quality of isolated RNA will facilitate downstream applications (quantitative reverse transcriptase-polymerase chain reaction or RNA sequencing) in cassava molecular breeding.