title: Detection of a New Luteovirus in Imported Nectarine Trees: A Case Study to Propose Adoption of Metagenomics in Post-Entry Quarantine.
abstract: In spring 2013, 5-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, double-stranded RNA 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 reverse transcription-polymerase chain reaction (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 post-entry 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.
authors.affiliation: First, second, and fifth authors: Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616; and third, fourth, sixth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616.
authors.forename: Sudeep
authors.initials: S
authors.lastname: Bag
authors.affiliation: First, second, and fifth authors: Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616; and third, fourth, sixth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616.
authors.forename: Maher
authors.initials: M
authors.lastname: Al Rwahnih
authors.affiliation: First, second, and fifth authors: Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616; and third, fourth, sixth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616.
authors.forename: Ashley
authors.initials: A
authors.lastname: Li
authors.affiliation: First, second, and fifth authors: Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616; and third, fourth, sixth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616.
authors.forename: Asaul
authors.initials: A
authors.lastname: Gonzalez
authors.affiliation: First, second, and fifth authors: Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616; and third, fourth, sixth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616.
authors.forename: Adib
authors.initials: A
authors.lastname: Rowhani
authors.affiliation: First, second, and fifth authors: Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616; and third, fourth, sixth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616.
authors.forename: Jerry K
authors.initials: JK
authors.lastname: Uyemoto
authors.affiliation: First, second, and fifth authors: Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616; and third, fourth, sixth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616.
authors.forename: Mysore R
authors.initials: MR
authors.lastname: Sudarshana
mesh_terms: D001483:Base Sequence; D002140:California; D005602:France; D016679:Genome, Viral / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D017793:Luteovirus / Q000235:genetics* / Q000302:isolation & purification; D056186:Metagenomics; D008969:Molecular Sequence Data; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology*; D018547:Plant Stems / Q000821:virology; D027861:Prunus / Q000821:virology*; D011790:Quarantine; D012330:RNA, Double-Stranded / Q000235:genetics; D017422:Sequence Analysis, DNA; D014197:Trees
chemical_list: D012330:RNA, Double-Stranded