Autor: Professor Murilo Zerbini (DFP/UFV)
Data: Terça, 03/10/23, às 16h
Local: Anfiteatro do DFP

Resumo: A significant proportion of the global virome is comprised of RNA viruses. Studies on the dynamics of plant viruses tend to focus on economically important plants, creating a bias towards agricultural systems in detriment of the natural world. Studying viruses found in wild plants is therefore vital to obtain an unbiased view on the diversity of plant viruses. Viral metagenomics, based on the use of high-throughput sequencing (HTS), has revolutionized virus discovery and our understanding of the Earth’s virome diversity. Oxford Nanopore sequencing platforms have emerged as attractive options as they can quickly generate reads with more than 10,000 nucleotides. We applied a geometagenomics approach to characterize viral communities in two ecosystems with different levels of human intervention: the UFV-Rio Paranaiba (UFV-CRP) campus and the Parque Estadual da Serra do Brigadeiro (PESB), both located in the state of Minas Gerais. A total of 427 plant samples were collected, consisting of mostly cultivated plants at UFV-CRP and uncultivated plants at PESB. dsRNA was extracted and sequenced with an Oxford Nanopore MinION device. Three approaches were used to identify and classify the virome of each sample: (i) detection of viral RdRp palm domain with PalmScan, (ii) profile HMMs for viral RdRp, and (iii) a novel tool, geNomad, that identifies viral and plasmid genomes from nucleotide sequences. PalmScan identified sequences related to viral polymerases, but it was not possible to identify the viruses. Using profile HMMs and geNomad we were able to identify and classify viral sequences mostly at the family level. We found viral sequences at both regions, but the highest number of sequences classified as viral was observed at PESB. At UFV-CRP, 46.6% of the sequences were classified as belonging to the order Patatavirales, 17.7% as other viruses and 35.7% were not classified. At PESB, only 59.3% were classified and 40.7% could not be classified. The greater percentage of unclassified sequences from PESB likely reflects the fact that most of the samples are from uncultivated plants. Other approaches are being tested to identify and classify these novel viral sequences. Nanopore sequencing was shown to be a viable, quick, and cost-effective approach for metagenomics-based plant virus discovery.