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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
item Sudarshana, Mysore

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/1/2015
Publication Date: 7/1/2015
Publication URL:
Citation: 2015. Detection of a new luteovirus in imported nectarine Trees: A case study to propose adoption of metagenomics in post-entry quarantine. Phytopathology. 105(6):840-846.

Interpretive Summary:

Technical Abstract: In spring 2013, five year-old nectarine (Prunus persica) trees, grafted on peach rootstock Nemaguard, were found stunted in a propagation block in California. These trees had been propagated from budwood of three nectarine cultivars imported from France and cleared through the post-entry quarantine procedure. 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. To investigate the etiological agent, dsRNA was extracted from bark scrapings from the scion and rootstock portions, and a cDNA library was prepared and sequenced using the Illumina platform. BLAST analysis of the contigs generated by the de novo assembly of sequence reads indicated the presence of a novel luteovirus. Complete sequence of the viral genome was determined by sequencing of three overlapping cDNA clones generated by RT-PCR and by rapid amplification of the 5'- and 3'- termini. The virus genome was comprised of 4,991 nucleotides with a gene organization similar to members of the genus Luteovirus (family Luteoviridae). The presence of the virus, tentatively named ‘Nectarine stem pitting-associated virus’, was confirmed in symptomatic trees by RT-PCR. Discovery of a new virus in nectarine trees after post2entry quarantine indicates the importance of including (i) metagenomic analysis by next generation sequencing approach as an essential tool to assess the plant health status, and (ii) examination of the woody cylinders as part of the indexing process.