Skip to main content
ARS Home » Northeast Area » Washington, D.C. » National Arboretum » Floral and Nursery Plants Research » Research » Publications at this Location » Publication #328793

Title: Deep sequencing analysis of apple infecting viruses in Korea

item CHO, IN-SOOK - Rural Development Administration - Korea
item IGORI, DAVVAJARAL - University Of Science And Technology Of China
item LIM, SEUNG-MO - University Of Science And Technology Of China
item CHOI, GUG-SEOUN - Rural Development Administration - Korea
item Hammond, John
item LIM, HYOUN-SUB - Chungnam National University
item MOON, JAE-SUN - University Of Science And Technology Of China

Submitted to: Plant Pathology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/23/2016
Publication Date: 5/23/2016
Citation: Cho, I., Igori, D., Lim, S., Choi, G., Hammond, J., Lim, H., Moon, J. 2016. Deep sequencing analysis of apple infecting viruses in Korea. Plant Pathology Journal . 32(5):441-451.

Interpretive Summary: Virus infection causes losses of yield and quality in many crops, and infections of multiple viruses tend to accumulate in crops such as fruit trees that are vegetatively propagated. The visible symptoms expressed by single and mixed infections are often visually indistinguishable, but mixed infections are typically more damaging than single infections; new viruses may also be introduced into the crop and spread by grafting onto previously un-infected rootstocks. Screening plants from commercial orchards is a means of determining virus presence and prevalence, which is the first step in control. Recently developed deep sequencing techniques have the capability of detecting all viruses present in the crop, including viruses not previously known to occur in the crop and region. Application of deep sequencing to samples of apple trees showing small leaves and/or slowed growth from commercial orchards in Korea revealed the presence of various combinations of from two to five viruses; two of these viruses had not previously been detected in Korea. These results demonstrate the power of the deep sequencing technique to identify the viruses present in fruit tree stocks showing signs of poor growth or low productivity. Identification of two viruses not previously known to occur in Korea will allow future testing for these viruses in certification programs designed to improve the health and productivity of fruit trees, to the benefit of nursery stock producers and fruit farmers.

Technical Abstract: Deep sequencing of viruses isolated from eight symptomatic apple trees in Korea has generated 52 contigs derived from five viruses: Apple chlorotic leaf spot virus (ACLSV), Apple stem grooving virus (ASGV), Apple stem pitting virus (ASPV), Apple green crinkle associated virus (AGCaV) and Apricot latent virus (ApLV). The assembled contigs showed 68-99% sequence identity compared to the reference sequences of the five respective viral genomes. Sequences of ASPV and ASGV were the most abundantly represented by the 52 contigs assembled. The presence of the five viruses in the samples was confirmed by RT-PCR using specific primers based on the sequences of each assembled contig. All five viruses were detected in three of the samples, whereas all samples had mixed infections with at least two viruses. The most frequently detected virus was ASPV, followed by ASGV, ApLV, ACLSV and AGCaV. AGCaV was identified in assembled contigs ID 1012480 and 93549, which showed 82% and 78% nucleotide sequence identity with ORF1 of AGCaV isolate Aurora-1. ApLV was identified in three assembled contigs, ID 65587, 1802365 and 116777, which showed 77%, 78% and 76% nucleotide sequence identity, respectively, with ORF1 of ApLV isolate LA2. Deep sequencing assays were shown to be a valuable and powerful tool for detection and identification of known and unknown viromes in infected apple trees, here identifying ApLV and AGCaV in commercial orchards in Korea for the first time.