title: Unusual RNA plant virus integration in the soybean genome leads to the production of small RNAs.
abstract: Horizontal gene transfer (HGT) is known to be a major force in genome evolution. The acquisition of genes from viruses by eukaryotic genomes is a well-studied example of HGT, including rare cases of non-retroviral RNA virus integration. The present study describes the integration of cucumber mosaic virus RNA-1 into soybean genome. After an initial metatranscriptomic analysis of small RNAs derived from soybean, the de novo assembly resulted a 3029-nt contig homologous to RNA-1. The integration of this sequence in the soybean genome was confirmed by DNA deep sequencing. The locus where the integration occurred harbors the full RNA-1 sequence followed by the partial sequence of an endogenous mRNA and another sequence of RNA-1 as an inverted repeat and allowing the formation of a hairpin structure. This region recombined into a retrotransposon located inside an exon of a soybean gene. The nucleotide similarity of the integrated sequence compared to other Cucumber mosaic virus sequences indicates that the integration event occurred recently. We described a rare event of non-retroviral RNA virus integration in soybean that leads to the production of a double-stranded RNA in a similar fashion to virus resistance RNAi plants.
authors.affiliation: Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil. Electronic address: guicf13@gmail.com.
authors.forename: Guilherme Cordenonsi
authors.initials: GC
authors.lastname: da Fonseca
authors.affiliation: Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil.
authors.forename: Luiz Felipe Valter
authors.initials: LFV
authors.lastname: de Oliveira
authors.affiliation: Laboratório Nacional de Computação Científica, LNCC, Petropolis, RJ, Brazil.
authors.forename: Guilherme Loss
authors.initials: GL
authors.lastname: de Morais
authors.affiliation: Empresa Brasileira de Pesquisa Agropecuária, EMBRAPA, Londrina, PR, Brazil.
authors.forename: Ricardo Vilela
authors.initials: RV
authors.lastname: Abdelnor
authors.affiliation: Empresa Brasileira de Pesquisa Agropecuária, EMBRAPA, Londrina, PR, Brazil.
authors.forename: Alexandre Lima
authors.initials: AL
authors.lastname: Nepomuceno
authors.affiliation: Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland, Australia.
authors.forename: Peter M
authors.initials: PM
authors.lastname: Waterhouse
authors.affiliation: Fasteris SA, Plan-les-Ouates, Switzerland.
authors.forename: Laurent
authors.initials: L
authors.lastname: Farinelli
authors.affiliation: Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil; Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil. Electronic address: rogerio.margis@ufrgs.br.
authors.forename: Rogerio
authors.initials: R
authors.lastname: Margis
mesh_terms: D001483:Base Sequence; D017799:Cucumovirus / Q000502:physiology; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D018745:Genome, Plant; D010802:Phylogeny; D010942:Plant Viruses / Q000502:physiology*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics* / Q000378:metabolism; D013025:Glycine max / Q000235:genetics* / Q000821:virology*; D016662:Virus Integration / Q000502:physiology*
chemical_list: D012333:RNA, Messenger; D018749:RNA, Plant
keywords: Cucumber mosaic virus; Horizontal gene transfer; RNA plant virus; Soybean; Transposon