Contribution of metagenomics to the diagnosis of tomato RNA viruses (Solanum lycopersicum L.) in BURKINA FASO
Background In recent decades, RNA viruses have caused enormous damage to vegetable plants due to the invasive nature of their insect vectors in many tropical, subtropical and temperate regions. These viruses induce symptoms of yellowing and/or leaf deformation associated or not with dwarfing of the plants. Previous studies have shown the existence of a wide diversity of RNA viruses with a range of hosts, but efforts must be made for a better knowledge of the virus. Consequently, in 2023–24, 9 leaf samples were collected from tomato plants in farmer fields in Guiriko region, Burkina Faso, showing symptoms such as leaf curling, vein banding, mosaic, mottling, filiform, leathery, dull-colored, and bunchy leaves. Total RNA was extracted, pooled at equimolar concentrations, and subjected to virome profiling. Total RNA was used to prepare library, which were sequenced on the Illumina NovaSeq 6000 platform. Bioinformatics tools were used to analyze the sequencing data and identify plant viruses.  Results The results showed that Illumina sequencing respectively. They showed the presence, in Burkina Faso, of a complex of at least six species of RNA viruses, all the six are new species in Burkina Faso. It also allowed the detection of Epicoccum nigrum ourmia-like virus 2, Plasmopara viticola lesion associated ourmia-like virus 34, and Epicoccum nigrum ourmia-like virus 2 on tomato for the first time in the world.  Conclusion Overall, this study highlights the fact that our knowledge of the structure and function of RNA viruses' populations is still incomplete and the need to continue efforts towards establishing the host range for more effective control of these viruses.
Background In recent decades, RNA viruses have caused enormous damage to vegetable plants due to the invasive nature of their insect vectors in many tropical, subtropical and temperate regions. These viruses induce symptoms of yellowing and/or leaf deformation associated or not with dwarfing of the plants. Previous studies have shown the existence of a wide diversity of RNA viruses with a range of hosts, but efforts must be made for a better knowledge of the virus. Consequently, in 2023–24, 9 leaf samples were collected from tomato plants in farmer fields in Guiriko region, Burkina Faso, showing symptoms such as leaf curling, vein banding, mosaic, mottling, filiform, leathery, dull-colored, and bunchy leaves. Total RNA was extracted, pooled at equimolar concentrations, and subjected to virome profiling. Total RNA was used to prepare library, which were sequenced on the Illumina NovaSeq 6000 platform. Bioinformatics tools were used to analyze the sequencing data and identify plant viruses.  Results The results showed that Illumina sequencing respectively. They showed the presence, in Burkina Faso, of a complex of at least six species of RNA viruses, all the six are new species in Burkina Faso. It also allowed the detection of Epicoccum nigrum ourmia-like virus 2, Plasmopara viticola lesion associated ourmia-like virus 34, and Epicoccum nigrum ourmia-like virus 2 on tomato for the first time in the world.  Conclusion Overall, this study highlights the fact that our knowledge of the structure and function of RNA viruses' populations is still incomplete and the need to continue efforts towards establishing the host range for more effective control of these viruses.