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Although many Agrobacterium radiobacter strains have already been identified, only a few genomes of strains belonging to genomovar G4 have been sequenced so far. In this study, we report the first virulent genome sequence of Agrobacterium radiobacter strain tun 183, which is highly virulent to almond specie. The genome size was estimated to be 5.53 Mb, with 57.9%GC content. In total, 6486 genes encoding proteins and 61 genes encoding RNAs were identified in this genome. Comparisons with the available sequenced genomes of genomovar G4 as well as with other A. sp. were conducted, revealing a hexapartite genome containing circular and linear chromosomes in addition to two accessory plasmids and a tumor inducing plasmid (pTi) in strain tun 183. The phylogenetic analysis of recA gene clearly showed the clustering of tun 183 strain within genomovar G4, supporting the monophyly within this genomovar.

This study was conducted to understand the high incidence of viruses previously reported in Tunisian olive groves. Forty three cultivars, native and introduced, under different cultivation regimes, were sampled in Tunisia, one of the countries with the highest levels of olive viruses. All olive-infecting viruses were tested. Total nucleic acids were extracted from 280 olive trees and their use as template for RT-PCR resulted in several non-specific products. Alternatively, dsRNAs were also extracted and 229 sampled trees showed dsRNAs molecules, suggesting the presence of viruses. However, RT-PCR tests using dsRNA as template, allowed to identify viruses in 209 samples. Olive mild mosaic virus (OMMV), Olive latent virus 1 (OLV-1), Olive leaf yellow associated virus (OLYaV) and Tobacco necrosis virus D (TNV-D) were detected. OLYaV was the most prevalent (63.0%), followed by OLV-1 (42.9%), TNV-D (21.80%) and OMMV (9.50%). The highest infection levels were observed in the northwest and centre east regions of Tunisia. Native cultivars presented higher virus incidences, mostly due to the most widespread cultivars in Tunisia: Chemlali (87%), Chetoui (94%), Meski (94%). Among the introduced cultivars, Picholine, Arbequina and Koroneiki presented the highest virus levels (88%, 79% and 64%, respectively). Considerable differences in virus presence were observed in samples from olive trees under different modes of management where levels were significantly (p > 0.05) higher in intensive orchards, regardless of the region and cultivar. To our knowledge, this was the first time that OMMV and TNV-D were detected in Tunisia and that such a complete analysis was performed.

The question asked in the present work was how to differentiate between contamination of field samples with and GM plants contained sequences provided from this bacterium in order to avoid false positives in the frame of the detection and the quantification of GMO. For this, new set of primers and corresponding TaqMan Minor Groove Binder (MGB) probes were designed to target Agrobacterium sp. using the tumor-morphology-shooty gene (TMS1). Final standard curves were calculated for each pathogen by plotting the threshold cycle value against the bacterial number (log (colony forming units) per milliliter) via linear regression. The method designed was highly specific and sensitive, with a detection limit of 10CFU/ml. No significant cross-reaction was observed. Results from this study showed that TaqMan real-time PCR, is potentially an effective method for the rapid and reliable quantification of Agrobacterium sp. in samples containing GMO or non GMO samples.

Tumor-inducing (Ti) and root-inducing (Ri) plasmids of Agrobacterium that display a large diversity are involved in crown gall and hairy root plant diseases. Their phylogenetic relationships were inferred from an exhaustive set of Ti and Ri plasmids (including 36 new complete Ti plasmids) by focusing on T-DNA and virulence regions. The opine synthase gene content of T-DNAs revealed 13 opine types corresponding to former classifications based on opines detected in diseased plants, while the T-DNA gene content more finely separate opine types in 18 T-DNA organizations. This classification was supported by the phylogeny of T-DNA oncogenes of Ti plasmids. The five gene organizations found in Ti/Ri vir regions was supported by the phylogeny of common vir genes. The vir organization was found to be likely an ancestral plasmid trait separating "classic" Ti plasmids (with one or two T-DNAs) and "Ri and vine-Ti" plasmids. A scenario generally supported by the repABC phylogeny. T-DNAs likely evolved later with the acquisition of opine characteristics as last steps in the Ti/Ri plasmid evolution. This novel evolutionary classification of Ti/Ri plasmids was found to be relevant for accurate crown gall and hairy root epidemiology.

Three hundred and eighteen symptomatic potato samples were collected from the main potato growing provinces of Tunisia, in main and late season crops (respectively spring and autumn 2013). Double antibody sandwich ELISA (DAS-ELISA) was used to assess the presence of the five most common potato viruses [Potato virus A (PVA), Potato virus X (PVX), Potato virus Y (PVY), Potato leafroll virus (PLRV) and Potato virus S (PVS)]. According to ELISA results, the highest overall percentage of infected samples was observed in the late season (84.5%), in comparison to the main season (30.7%). PVY was dominant in all infected plots with detection rates ranging from 20% in the North region (main season) to 100% in Cap Bon (late season). PLRV was the second most detected virus, with 4.3% distributed in the North West and Sahel during the main season, but was not detected in the late season. PVX was found with even lower detection rates of 0.6% and 1.3% in main and late seasons, respectively. No infection by PVA or PVS was detected in these two periods. Positive PVX detection results were confirmed by Reverse Transcription PCR using total RNA extracted from infected leaves. The near-complete nucleotide sequences of three PVX isolates were determined using an Illumina MiSeq sequencer. Phylogenetic analyses on full genome sequences or on coat protein (CP) gene sequences show that Tunisian PVX isolates belong to low diversity clade I.

Genetically modified organisms (GMO) invade more and more the agricultural production in the world. Although there are no legislations on GM labeling and cultivation of GM crops in Tunisia, the present study aims to check the status of GMO in Tunisian market using qualitative and quantitative real time-PCR (QRT-PCR). Three-hundred-sixty five samples were collected and different DNA extraction methods were adapted and optimized. Specific primers targeting 35S promoter from Cauliflower mosaic virus (CaMV) and nopaline synthase terminator from Agrobacterium tumefaciens (At) were used for the detection of the GMO insert and Taxon specific primers for the detection of plant species. Validated Taqman® probes (EU-RL) targeting event specific regions of the maize events MON810, Bt11, and the soybean event RRS were used for the quantification studies. Seven food and feed products showed different amounts of RRS (1.9%), MON810 (2.1%), and Bt11 (1.6%). The results demonstrate for the first time the presence of GMO in Tunisian markets reinforcing the need for the development of accurate quantitative methods in routine analyses.

In response to the increasing number of genetically modified (GM) events released on the market, control laboratories explore various strategies to simplify and reduce the number of tests needed to characterise the content in genetically modified organism (GMO) of a given sample. Lastly, multiplexing is considered as one of the possible ways to decrease the time and cost of analysis. Here, we report the development of four duplex polymerase chain reaction (PCR) tests for the identification and the quantification of four maize transformation events from which commercial lines have been authorised in Europe namely, Bt11 and Bt176 (Syngenta, DE, USA), Mon810 MaisGard™ (Monsanto, MO, USA) and T25 Liberty Link™ (Bayer CropScience, Monheim, Germany). The duplex PCR tests combine a maize-specific PCR test hybridising in the Adh1 locus with an event-specific detection system designed on a junction fragment for each of these four GM maize. Real-time PCR tests, suitable to comply with the European regulation, were designed by using Taqman® chemistry.

Genetic transformation of fish is mainly oriented towards the improvement of growth for the benefit of the aquaculture. Actually, Atlantic salmon (Salmo salar) is the species most transformed to achieve growth rates quite large compared to the wild. To anticipate the presence of contaminations with GM salmon in fish markets and the lack of labeling regulations with a mandatory threshold, the proper methods are needed to test the authenticity of the ingredients. A quantitative real-time polymerase chain reaction (QRT-PCR) method was used in this study. Ct values were obtained and validated using 15 processed food containing salmon. The relative and absolute limits of detection were 0.01% and 0.01 ng/μl of genomic DNA, respectively. Results demonstrate that the developed QRT-PCR method is suitable specifically for identification of S. salar in food ingredients based on the salmon growth hormone gene 1 (GH1). The processes used to develop the specific salmon reference gene case study are intended to serve as a model for performing quantification of Aquadvantage® GM salmon on future genetically modified (GM) fish to be commercialized.

To overcome the difficulties of obtaining the Certified Reference Material (CRM) and according to the key documents of the European Union Reference Laboratory (EU-RL), a new standard reference molecule containing the construct specific of the canola event Oxy-235 (3′-junction Nitrilase/Tnos) and the canola endogenous reference gene (acety-CoA-carboxylase) was constructed and used for duplex real-time quantitative analysis. The limits of detection (LOD) were less than 5 Haploid Genome Copy (HGC) and the limits of quantification (LOQ) were about 10 HGC. Furthermore, mixed GM and non-GM canola samples were analysed with duplex QRT-PCR to evaluate the performance criteria as required for validation procedures in the EU-RL, namely, the precision and the accuracy. The accuracy expressed as bias ranged from 2% to 10% and the precision (repeatability and reproducibility) expressed as the RSD r and RSD R was from 2.2 to 5.12 and 2.15 to 5.46 respectively. All these indicated that the developed construct specific method and the reference molecule are suitable for the identification and the quantification of the canola event Oxy-235.

KEY MESSAGE : Here, we describe a new developed quantitative real-time PCR method for the detection and quantification of a new specific endogenous reference gene used in GMO analysis. The key requirement of this study was the identification of a new reference gene used for the differentiation of the four genomic sections of the sugar beet (Beta vulgaris L.) (Beta, Corrollinae, Nanae and Procumbentes) suitable for quantification of genetically modified sugar beet. A specific qualitative polymerase chain reaction (PCR) assay was designed to detect the sugar beet amplifying a region of the adenylate transporter (ant) gene only from the species of the genomic section I of the genus Beta (cultivated and wild relatives) and showing negative PCR results for 7 species of the 3 other sections, 8 related species and 20 non-sugar beet plants. The sensitivity of the assay was 15 haploid genome copies (HGC). A quantitative real-time polymerase chain reaction (QRT-PCR) assay was also performed, having high linearity (R (2) 0.994) over sugar beet standard concentrations ranging from 20,000 to 10 HGC of the sugar beet DNA per PCR. The QRT-PCR assay described in this study was specific and more sensitive for sugar beet quantification compared to the validated test previously reported in the European Reference Laboratory. This assay is suitable for GMO quantification in routine analysis from a wide variety of matrices.