Location: Crops Pathology and Genetics ResearchTitle: Detection of a new luteovirus in imported nectarine trees: A case study to propose adoption of metagenomics in post-entry quarantine
|Bag, Sudeep - University Of California|
|Al Rwahnih, Maher - University Of California|
|Rowhani, Adib - University Of California|
|Uyemoto, Jerry - US Department Of Agriculture (USDA)|
Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/16/2015
Publication Date: 6/1/2015
Publication URL: http://apsjournals.apsnet.org/doi/full/10.1094/PHYTO-09-14-0262-R
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.
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.