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Rubus yellow net virus (RYNV) belongs to genus Badnavirus. Badnaviruses are found in plants as endogenous, inactive or activatable sequences, and/or in episomal (infectious and active) forms. To assess the state of RYNV in Rubus germplasm, we sequenced the genomes of various cultivars and mined eight raspberry whole genome datasets. Bioinformatics analysis revealed the presence of a diverse array of endogenous RYNV (endoRYNV) sequences that differ significantly in their structure; some lineages have nearly complete, yet non-functional genomes whereas others have rudimentary, short sequence fragments. We developed assays to genotype the main lineages as well as the only known episomal lineage present in the United States. This study discloses the widespread presence of endoRYNVs in commercial raspberries, likely because breeding efforts have focused on a limited pool of germplasm that harbored endoRYNVs. • Rubus yellow net virus (RYNV) endogenous genomes (endoRYNV) differ significantly in their structure. • There are seven major endoRYNVs lineages identified in raspberry. • All integration events occurred before or during 19th century. • EndoRYNVs are widespread in commercial raspberries. • No endoRYNVs were identified in blackberry. [ABSTRACT FROM AUTHOR]

Environmental research in agriculture is today largely reactive, focused on problems at small scales and conducted within narrow disciplinary boundaries. This approach has worked to abate a number of environmental problems created by agriculture, but it has not provided effective solutions for many of the most recalcitrant ones. Furthermore, the approach fails to position agriculture to deliver new environmental benefits that the public and policymakers increasingly demand. A new vision is needed for environmental research in agriculture--one that is anticipatory; promotes long-term, systems-level research at multiple scales, better incorporates important interactions between the biophysical and social sciences, and provides for the proper evaluation of deployed solutions. Achieving this vision will require major changes in funding strategies, in institutional reward structures, and in policies that presently inhibit collaborations across disciplinary and institutional boundaries. It is, nevertheless, time to act. [ABSTRACT FROM AUTHOR]