High-throughput sequencing (HTS) technologies have brought tremendous improvements in the ability to detect plant viruses and have a great potential for application in virus routine diagnostics. The performance criteria of an HTS test need therefore to be estimated and compared to traditional virus indexing tests before it can be used in routine diagnostic. In this study, 78 Musa accessions previously indexed for viruses by molecular tests and/or electron microscopy were tested individually or in pools using an HTS protocol based on total RNA sequencing. The analytical sensitivity of HTS and RT-PCR was also compared by independent testing on serial dilutions of RNA extracts. In total, 136 libraries were sequenced in five batches, and the sequences analyzed for virus detection. The external alien control, a wheat sample infected by BYDV, monitored the contamination burden and determined an adaptative detection threshold. Overall, HTS test displayed a better analytical sensitivity compared to RT-PCR and a better inclusivity than the classical indexing protocol, as distant isolates and new viral species were only detected by the HTS test. Repeatability and reproducibility of virus detection were both of 100% although differences in number of sequencing reads per virus were observed between replicates. The diagnostic sensitivity was very high but false positive results were observed. Finally, the results also underlined the need of expert judgement in the interpretation of the results. In conclusion, the HTS test with an alien control and completed by expert evaluation has fulfilled the criteria of virus indexing protocol for Musa germplasm.

The need to reduce the use of chemical pesticides currently fosters great interest in eco-friendly biological control agents. In addition, the isolation of plant allelopathic substances and the evaluation of their phytotoxic effects can lead to the discovery of new natural herbicides. In this context, our study aimed to assess the herbicidal activity of ten crude extracts obtained from aerial parts of Tunisian spontaneous plants against Trifolium incarnatum, Silybum marianum and Phalaris minor. It confirmed that the Cynara cardunculus methanolic extract best inhibited weed germination and seedling growth, and caused necrosis or chlorosis. Following a bioassay-guided fractionation, five main phenolic compounds, (1) syringic acid, (2) p-coumaric acid, (3) myricitrin, (4) quercetin and (5) naringenin were identified in the most active crude methanolic extract. Then, only 3 of the flavonoids contained in the most active fraction were tested on Trifolium incarnatum. The 3 compounds had a significant phytotoxic effect and therefore could be employed in a new composition of botanical herbicides to control crop weeds. Besides, a novel herbicide composition was designed to improve the post-emergence activity of the methanolic extract. The formulation containing the C. cardunculus crude methanolic extract showed the same herbicidal activity as the standard industrial bioherbicide containing pelargonic acid. These results make C. cardunculus a suitable source of natural compounds potentially usable as natural herbicides.

The use of chemical herbicides could not only potentially induce negative impacts on the environment, animals, and human health, but also increase the weed resistance to herbicides. In this context, the use of plant extracts could be an interesting and natural alternative to chemical products. It is important to understand the mode of action of their bioactive compounds. This is why we have studied the herbicidal effect of Cynara cardunculus crude extract in terms of inhibition of weeds’ seedling growth and its impact on physiological parameters of treated plantlets, like conductivity, dry weight, and fluorescence, and biochemical parameters linked to oxidative stress. We have observed that C. cardunculus crude extract induces oxidative stress in the treated plants and consequently disturbs the physiological and biochemical functions of the plant cells. We have investigated the herbicidal activity of three bioactive compounds, naringenin, myricitrin, and quercetin, from the C. cardunculus crude extract. In both pre- and post-emergence trials, naringenin and myricitrin were significantly more phytotoxic than quercetin. We suggest that their differential initial interaction with the plant’s plasma membrane could be one of the main signals for electrolyte leakage and production of high levels of phenoxyl radicals.