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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » National Germplasm Resources Laboratory » Research » Publications at this Location » Publication #346258

Research Project: Characterizing and Detecting Pathogens to Ensure Safe Exchange of Plant Germplasm

Location: National Germplasm Resources Laboratory

Title: Discovery and molecular characterization of a new luteovirus identified by high-throughput sequencing from apple

Author
item Liu, Huawei - China Agricultural University
item Wu, Liping - Nanchang University
item Nikolaevera, Ekaterina - Pennsylvania Department Of Agriculture
item Peter, Kari - Pennsylvania State University
item Liu, Zongrang
item Mollov, Dimitre
item Cao, Mengji - Southwest University
item Li, Ruhui

Submitted to: Virology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/6/2018
Publication Date: 5/15/2018
Citation: Liu, H., Wu, L., Nikolaevera, E., Peter, K., Liu, Z., Mollov, D.S., Cao, M., Li, R. 2018. Discovery and molecular characterization of a new luteovirus identified by high-throughput sequencing from apple. Virology Journal. https://doi.org/10.1186/s12985-018-0998-3.
DOI: https://doi.org/10.1186/s12985-018-0998-3

Interpretive Summary: Apple (Malus domestica) is the most widely cultivated fruit tree worldwide. The U.S. is the world’s second-largest producer of the crop, with a wholesale value of $4 billion. Apple trees are propagated by grafting and thus prone to accumulating viral pathogens. ‘Rapid Apple Decline’ (RAD) is a newly emerging problem of young, dwarf apple trees in the northeastern USA. The affected trees show trunk necrosis, and develop bark cracking and cankers, before collapsing over a short duration (weeks). In this study, three common apple viruses and a new luteovirus were identified from RAD trees. The complete genomic sequence of the new luteovirus was obtained, and a molecular detection method was developed. Limited sampling detected the luteovirus from apple trees in some, but not all, affected orchards. The study provides the information necessary to name and classify the virus, and develop detection methods for it. Additional research is needed to determine the role of viruses in RAD.

Technical Abstract: ‘Rapid Apple Decline’ (RAD) is a newly emerging problem of young, dwarf apple trees in the northeastern USA. The affected trees show trunk necrosis, bark cracking and canker formation before collapsing in the summer. In this study, a new luteovirus and three common viruses were identified from apple trees in RAD-affected orchards using high throughput sequencing (HTS) technology. The HTS derived detections were verified by RT-PCR. The complete genomic sequence of the new luteovirus, named as Apple luteovirus 1 (ALV-1), was determined to be 6,001 nucleotides. The arrangement and structure of the ALV-1 genome resembles those of other luteoviruses, containing six hallmark open reading frames (ORF) of the genus Luteovirus encoding proteins involved in replication (P1 and P1-P2 fusion protein), virion assembly (CP), movement (P3a and P4) and aphid transmission (P3-P5 fusion protein). Two additional ORFs, one nested within ORF1 and another within ORF5, were found and are unique among luteoviruses. Sequence comparisons and phylogenetic analyses show that ALV-1 is a new species of the genus Luteovirus in the family Luteoviridae. RT-PCR results showed that the virus was common in the affected blocks. The virus has been graft transmitted to virus-free apple seedlings. Molecular characterization of ALV-1 provides important information to further investigate the causes of RAD.