Application of a simple and affordable protocol for isolating plant total nucleic acids for RNA and DNA virus detection

Biological and molecular characterization of a resistance-breaking isolate of citrus tristeza virus from Uruguay and its effects on Poncirus trifoliata growth performance

Resistance-breaking (RB) isolates of citrus tristeza virus (CTV) can replicate and move systemically in Poncirus trifoliata, a rootstock widely used for management of decline caused by CTV and other purposes. In Uruguay, severe CTV isolates are prevalent, and an RB isolate (designated as RB-UY1) was identified. In order to predict the implications of this genotype circulating in citrus crops grafted on trifoliate rootstocks, the aim of this work was to determine the biological and molecular characteristics of this isolate, the efficiency of its transmission by Toxoptera citricida, and its effects on plant growth performance of P. trifoliata. Our results show that RB-UY1 can be classified as a mild isolate, that it is phylogenetically associated with the RB1 group, and that it is efficiently transmitted by T. citrida. They also suggest that the RB-UY1 isolate should not affect the performance of citrus crops grafted on trifoliate rootstocks, although some growth parameters of P. trifoliata seedlings were affected four years after inoculation.

A multiplex RT-PCR assay combined with co-extraction of DNA and RNA for simultaneous detection of TYLCV and ToCV in whitefly

Tomato yellow leaf curl virus (TYLCV) and tomato chlorosis virus (ToCV) were transmitted by the sweet potato whitefly Bemisia tabaci (Gennadius) and cause serious yield losses on tomato around the world. To understand the actual situation of co-infection of TYLCV and ToCV of individual whiteflies, we developed multiplex RT-PCR combined with co-extraction of DNA and RNA from a single whitefly. First, a nucleic acid extraction method previously reported was modified and adopted to obtain the RNA-DNA mixture including TYLCV and ToCV in a simple form without manual homogenization. Second, primers were newly designed in actin gene of B. tabaci for the confirmation of extraction and PCR success, and multiplex RT-PCR method was developed using specific primer sets for TYLCV, ToCV and B. tabaci. This method enables the detection of TYLCV and ToCV from a single insect and efficient use of field samples obtained using sticky traps. The method will be useful to monitor infection status of TYLCV and ToCV in the field while reducing labor and cost.

Citrate-Citric Acid RNA Isolation (CiAR) for Fast, Low-Cost, and Reliable RNA Extraction from Multiple Plant Species and Tissues

RNA isolation is routinely carried out in many laboratories for different downstream applications. Although protocols for this can vary between labs depending on the specific plant species and tissues under study and the preferences of their researchers, these protocols usually include the use of volatile organic and toxic chemicals. As an alternative, several companies offer less hazardous RNA extraction kits, but these kits significantly increase the cost per sample and are thus not affordable for every lab, especially when a large number of samples is to be processed. We have previously described a fast and efficient method for RNA isolation from plant vegetative tissues that requires only two home-made, simple, inexpensive, and nontoxic buffers. Both buffers have low concentrations of citric acid and its sodium salt. The first buffer also contains a detergent to help with nucleic acid solubilization while keeping RNases inactive. The second buffer has sodium chloride at high molarity to separate protein from nucleic acids. RNA is precipitated, and contaminating DNA can then be optionally removed. Here, we describe and expand on this approach, which we call the citrate-citric acid RNA isolation, or CiAR, method. We provide a detailed description of the protocol, describe a modification to make it compatible with non-vegetative tissues, and compile and extend the number of species and tissues to which it can be applied. © 2021 Wiley Periodicals LLC.

Efficient method for isolation of high-quality RNA from Psidium guajava L. tissues

Acquiring high-quality RNA in sufficient amounts is crucial in plant molecular biology and genetic studies. Several methods for RNA extraction from plants are available in the literature, mainly due to the great biochemical diversity present in each species and tissue, which can complicate or prevent the extraction. Psidium guajava (Myrtaceae family) is a perennial fruit tree of medicinal and economic value; nevertheless, only a few molecular studies are available for the species. One reason is the difficulty in obtaining RNA due to the content of the samples, which are rich in polyphenols, polysaccharides, and secondary metabolites. Furthermore, there are few studies available for the isolation of RNA from guava or Psidium samples, which hampers advances in the study of the genus. Here, quality and yields of RNA isolates were compared using six extraction protocols: two protocols based on the application of cetyltrimethylammonium bromide (CTAB) lysis buffer, one protocol which uses the TRIzol reagent, one which applies guanidine thiocyanate lysis buffer followed by organic phase extraction, and two commercial kits (PureLink RNA Mini Kit and RNeasy Plant Mini Kit). The CTAB-based method provided the highest RNA yields and quality for five different tissues (flower bud, immature leaf, young leaf, mature leaf, and root), genotypes, and stress conditions. For the most efficient protocol, the average yield of RNA from guava leaves was 203.06 μg/g of tissue, and the A₂₆₀/A₂₈₀ and A₂₆₀/A₂₃₀ ratios were 2.1 and 2.2, respectively. RT-qPCR analysis demonstrated that the purity of the samples was sufficient for molecular biology experiments. CTAB-based methods for RNA isolation were found to be the most efficient, providing the highest RNA yields and quality for tissues from P. guajava. Additionally, they were compatible for downstream RNA-based applications, besides being simple and cost-effective.