Detection of global soybean viruses in metagenomic sequence data using Microbe Finder (MiFi®) & Thrips variability on soybean

• Ano de defesa: 2022
• Autor(a) principal: Ribeiro-Junior, Marcos Roberto [UNESP]
• Tipo de documento: Tese
• Tipo de acesso: Acesso aberto
• Idioma: eng
• Instituição de defesa: Universidade Estadual Paulista (Unesp)
• Palavras-chave em Português: next-generation sequencing; Thysanoptera; Glycine max; EDNA; sequenciamento de nova geração
• Link de acesso: http://hdl.handle.net/11449/238296

Soybean (Glycine max) is an important crop worldwide used as a source of oilseed and protein. Nevertheless, each year, soybean growers lose significant yields to diseases caused by viruses and damage caused by thrips, therefore, precise diagnosis is crucial for management. Passiflora virus Y (PaVY) was detected naturally infecting soybean for the first time in Brazil and the complete genome sequencing shows a 9679nt long virus that shares 84.4% nt identity with a previously reported PaVY isolate from Passiflora spp. The virus was successfully transmitted by Myzus persicae, and sap transmitted to indicator hosts. Electronic probes (e-probes) ranging from 19-60 nucleotides in length were designed for the 46 viruses that infect soybean using MiProbe within MiFi® platform. In silico results validate the usage of e-probes to detect up to 46 viruses in metagenomic soybean data. In vitro analyses revelated nine viruses present in Brazilian HTS Illumina soybean samples. The curated soybean virus e-probes are free of access for diagnostics through MiDetect within the MiFi® platform. Nine thrips species, collected from 20 different plant species in Brazil, including soybean, were identified by sequencing partial COI gene. Specific primers based on COI and 28S sequences were obtained for Caliothrips phaseoli and Frankliniella occidentalis species, respectively. Bayesian phylogenetic analyses demonstrated that specimens of the same species were clustered under their respective clade, but not necessarily under the same genus clade. Our results demonstrate that PCR and sequencing can be used for identification of well described species, but traditional taxonomy is still necessary for the identification of new species and must be combined with molecular techniques.