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Title: Detection of a new luteovirus in imported nectarine trees: A case study to propose adoption of metagenomics in post-entry quarantine

item BAG, SUDEEP - University Of California
item AL RWAHNIH, MAHER - University Of California
item Li, Ashley
item Gonzalez, Asaul
item ROWHANI, ADIB - University Of California
item UYEMOTO, JERRY - US Department Of Agriculture (USDA)
item Sudarshana, Mysore

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/16/2015
Publication Date: 6/1/2015
Publication URL:
Citation: Bag, S., Al Rwahnih, M., Li, A., Gonzalez, A., Rowhani, A., Uyemoto, J.K., Sudarshana, M.R. 2015. Detection of a new luteovirus in imported nectarine trees: A case study to propose adoption of metagenomics in post-entry quarantine. Phytopathology. 105:840-846.

Interpretive Summary:

Technical Abstract: In spring 2013, nectarine (Prunus persica) trees produced from budwood, imported from France, after post-entry quarantine clearance, grafted onto Nemaguard seedlings were found not growing vigorously in a propagation block in California. Examination of the canopy failed to reveal any obvious symptoms. However, examination of the trunks, after stripping the bark, revealed extensive pitting on the woody cylinder. Bark scrapings from the scion and rootstock portions were obtained and nucleic acid fraction enriched for dsRNA extracted, cDNA prepared, and sequenced on an Illumina platform. Analysis of the contigs generated by de novo assembly of the sequence reads using BLAST indicated the presence of the sequence of a novel luteovirus. Complete sequencing of the genome, using overlapping cDNA clones generated by RT-PCR and by 5'- and 3'-RACE, indicated that the virus genome was comprised of 5,132 nucleotides with a gene organization similar to the members of the genus Luteovirus (family Luteoviridae). The presence of the new virus was confirmed in symptomatic trees by RT-PCR and was named ‘Nectarine stem pitting-associated virus’. Discovery of a new virus in a stone fruit tree after post-entry quarantine by next generation sequencing indicates the importance of including (1) metagenomics approach as an essential tool to assess plant health status and (2) examination of woody cylinders as part of the indexing process.