Analysis of the enhancer-blocking function of the TBS element from Petunia hybrida in transgenic Arabidopsis thaliana and Nicotiana tabacum

Transcriptional enhancers possess the ability to override the tissue-specificity and efficiency of nearby promoters, which is of concern when generating transgenic constructs bearing multiple cassettes. One means of preventing these inappropriate interactions is through the use of enhancer-blocking insulators. The 2-kb transformation booster sequence (TBS) from Petunia hybrida has been shown previously to exhibit this function when inserted between an enhancer and promoter in transgenic Arabidopsis thaliana. In this study, we attempted to further characterize the ability of this fragment to impede enhancer-promoter interference through an analysis of transgenic Arabidopsis and Nicotiana tabacum lines bearing various permutations of the TBS element between the cauliflower mosaic virus (CaMV) 35S enhancer and an assortment of tissue-specific promoters fused to the β-glucuronidase (GUS) reporter gene. The full-length TBS fragment was found to function in both orientations, although to a significantly lesser degree in the reverse orientation, and was operational in both plant species tested. While multiple deletion fragments were found to exhibit activity, it appeared that several regions of the TBS were required for maximal enhancer-blocking function. Furthermore, we found that this element exhibited promoter-like activity, which has implications in terms of possible mechanisms behind its ability to impede enhancer-promoter communication in plant

Comparison of Serological and Molecular Methods With High-Throughput Sequencing for the Detection and Quantification of Grapevine Fanleaf Virus in Vineyard Samples

Grapevine fanleaf virus (GFLV) is the main causal agent of fanleaf degeneration, the most damaging viral disease of grapevine. GFLV is included in most grapevine certification programs that rely on robust diagnostic tools such as biological indexing, serological methods, and molecular techniques, for the identification of clean stocks. The emergence of high throughput sequencing (HTS) offers new opportunities for detecting GFLV and other viruses in grapevine accessions of interest. Here, two HTS-based methods, i.e., RNAseq and smallRNAseq (focusing on the 21 to 27 nt) were explored for their potential to characterize the virome of grapevine samples from two 30-year-old GFLV-infected vineyards in the Champagne region of France. smallrnaseq was optimal for the detection of a wide range of viral species within a sample and RNAseq was the method of choice for full-length viral genome assembly. The implementation of a protocol to discriminate between low GFLV titer and in silico contamination (intra-lane contamination due to index misassignment) during data processing was critical for data analyses. Furthermore, we compared the performance of semi-quantitative DAS-ELISA (double antibody enzyme-linked immunosorbent assay), RT-qPCR (Reverse transcription-quantitative polymerase chain reaction), Immuno capture (IC)-RT-PCR, northern blot for viral small interfering RNA (vsiRNA) detection and RNAseq for the detection and quantification of GFLV. While detection limits were variable among methods, as expected, GFLV diagnosis was consistently achieved with all of these diagnostic methods. Together, this work highlights the robustness of DAS-ELISA, the current method routinely used in the French grapevine certification program, for the detection of GFLV and offers perspectives on the potential of HTS as an approach of high interest for certification

Detection of Multiple Variants of Grapevine Fanleaf Virus in Single Xiphinema index Nematodes

Grapevine fanleaf virus (GFLV) is responsible for a widespread disease in vineyards worldwide. Its genome is composed of two single-stranded positive-sense RNAs, which both show a high genetic diversity. The virus is transmitted from grapevine to grapevine by the ectoparasitic nematode Xiphinema index. Grapevines in diseased vineyards are often infected by multiple genetic variants of GFLV but no information is available on the molecular composition of virus variants retained in X. index following nematodes feeding on roots. In this work, aviruliferous X. index were fed on three naturally GFLV-infected grapevines for which the virome was characterized by RNAseq. Six RNA-1 and four RNA-2 molecules were assembled segregating into four and three distinct phylogenetic clades of RNA-1 and RNA-2, respectively. After 19 months of rearing, single and pools of 30 X. index tested positive for GFLV. Additionally, either pooled or single X. index carried multiple variants of the two GFLV genomic RNAs. However, the full viral genetic diversity found in the leaves of infected grapevines was not detected in viruliferous nematodes, indicating a genetic bottleneck. Our results provide new insights into the complexity of GFLV populations and the putative role of X. index as reservoirs of virus diversity

Mécanismes moléculaires impliqués dans la résistance virale d'une plante ligneuse transgénique

Le prunier transgénique C5 (Prunus domestica L.),contenant la séquence codant pour la protéine de capside PPV-CP, a été décrit comme hautement résistant au virus de la Sharka au travers du mécanisme d'extinction post-transcriptionnelle du transgène (PTGS). Nous avons confirmé ce phénotype de résistance après quztre années d'essai au champ. Cette immunité à l'inoculation naturelle du PPV par les pucerons, s'accompagne toujours des caractéristiques du PTGS : hyperméthylation du transgène PPV-CP et suppression des transcrits dans le cytoplasme. La détection des petits ARN interférants (siRNA) a confirmé l'implication du 'RNA silencing' dans cette résistance. Le prunier C5 produit de façon constitutive tout au lon du cycle végétatif (du stade embryonnaire à la plante mature), 2classes de siRNA (22 et 25-27 nt). Du fait de sa stabilité et son efficacité chez les ligneux, le 'RNA silencing' a été utilisé comme une approche pour produire de nouvelles générations d'OGM. Deux clones de P. domestica var. Stanley, transformés avec une construction ihpRNA, ont été obtenus. Les études préliminaires confirment l'état silencé de ces pruniers et renforcent un peu plus l'idée d'utiliser cette technologie pour améliorer les arbres fruitiers.The stability of resistance to Plum pox virus under field conditions has been demonstrated in the transgenic C5 plum (Prunus domestica L). This particular clone, transformed with the PPV-CP gene, is immune to aphid inoculation with PPV and still displays PTGS hallmarks with hypermethylation of the PPV-CP sequence and no detectable transgene expression. To better characterize RNA silencing in woody perennial crops, hallmarks of PTGS were investigated C5 clone constitutively produced both short (22 nt) and long (25-27 nt) siRNA species from embryo to mature plant. Following this concept of gene silencing-based virus resistance, constructions using RNA interference technology were engineered. This technology of dsRNA through expression of a self-complementary hairpin structure will interfere with the virus at the RNA level. Two transgenic clones containing an ihpRNA construct were obtained. Preliminary results of PPV infection under containment conditions indicated immunity to virus inoculation, confirming the potential use of RNA interference technology in tree breeding.BORDEAUX2-BU Santé (330632101) / SudocSudocFranceF

Silencing is an effective approach for knockdown of plum pox virus RNA

Silencing is an effective approach for knockdown of [i]plum pox virus[/i] RNA. 16. Rencontres de Virologie Végétale (RVV 2017

A genome-wide diversity study of grapevine rupestris stem pitting-associated virus.

Over the last decade, many scientific disciplines have been impacted by the dawn of new sequencing techniques (HTS: high throughput sequencing). Plant pathology and more specifically virology have been greatly transformed by this 'metagenomics' paradigm shift. Such tools significantly facilitate disease diagnostics with tremendous sensitivity, providing invaluable information such as an exhaustive list of viruses being present in a sample as well as their relative concentration. In addition, many new plant viruses have been discovered. Using RNAseq technology, in silico reconstruction of complete viral genome sequences is easily attainable. This step is of importance for taxonomy, population structure analyses, phylogeography and viral evolution studies. Here, after assembling 81 new near-complete genome sequences of grapevine rupestris stem pitting-associated virus (GRSPaV), we performed a genome-wide diversity study of this ubiquitous virus of grapevine worldwide