Poster: Molecular & Cellular Plant-Microbe Interactions: Proteomics/Metabolomics/Genomics
Root transcriptome analysis reveals viral diversity in two species of blueberry
N. SAAD (2) , J. Olmstead (1), R. Alcalá-Briseño (2), A. Varsani (3), J. Polston (2) (1) Horticultural Sciences Department, University of Florida, U.S.A.; (2) Department of Plant Pathology, University of Florida, U.S.A.; (3) School of Biological Sciences,
A growing number of metagenomics based approaches have been used for the elucidation of viral diversity in insects, cultivated plants, and water in agricultural production systems. However, while the generation of plant transcriptomes has greatly increased over the last few years, their use for data mining viral sequences has been largely unexplored. In this study, blueberry root transcriptomes (8 libraries each of Vaccinium arboreum and V. corymbosum x V. darrowi ‘Emerald’) were analyzed using bioinformatic analyses for plant viral sequences. De novo assembly of ‘Emerald’ libraries yielded a complete viral genome of the Blueberry red ringspot virus (BRRV), genus Soymovirus, family Caulimoviridae, a plant virus with a dsDNA genome. BRRV was detected by PCR in 100% and 25% of the ‘Emerald’ and V. arboreum samples, respectively. Since sequences of species in the Caulimoviridae are known to be present as integrants in their hosts, back to back primers were designed to detect the episomal form of BRRV genome. The episomal form of BRRV was detected in root tissue of ‘Emerald’ but not V. arboreum, which indicated that the BRRV sequences in V. arboreum are most likely those of integrants. In addition, BLASTx analysis of 16 blueberry libraries revealed contigs that match sequences in 20 virus genera and 10 families. Overall, this study demonstrates the feasibility of using available host transcriptome data for mining viral sequences.