Abstract
We analyzed virus and viroid communities in five individual trees of two nectarine cultivars with different disease phenotypes using next-generation sequencing technology. Different viral communities were found in different cultivars and individual trees. A total of eight viruses and one viroid in five families were identified in a single tree. To our knowledge, this is the first report showing that the most-frequently identified viral and viroid species co-infect a single individual peach tree, and is also the first report of peach virus D infecting Prunus in China. Combining analyses of genetic variation and sRNA data for co-infecting viruses/viroid in individual trees revealed for the first time that viral synergisms involving a few virus genera in the Betaflexiviridae, Closteroviridae, and Luteoviridae families play a role in determining disease symptoms. Evolutionary analysis of one of the most dominant peach pathogens, peach latent mosaic viroid (PLMVd), shows that the PLMVd sequences recovered from symptomatic and asymptomatic nectarine leaves did not all cluster together, and intra-isolate divergent sequence variants co-infected individual trees. Our study provides insight into the role that mixed viral/viroid communities infecting nectarine play in host symptom development, and will be important in further studies of epidemiological features of host-pathogen interactions.
Highlights
Peach is one of the most widely grown fruit crops in China, and nectarine (Prunus persica cv. nectarina) is an important cultivar of peach
The Illumina reads obtained from sequencing the five cDNA libraries, which were prepared using RNA extracted from the scion parts of the grafted trees, yielded between 22,434,184 and 30,438,485 raw sRNA reads per library
We found that samples T01 and T02 from greenhouse #1 had the highest number of virus/viroid-associated reads, with 5.53% and 9.60% of the clean sRNA reads, respectively, while the virus/viroid-associated reads in samples T03, T04, and T05 ranged from 1.11% to 2.71% (Table S1)
Summary
Peach is one of the most widely grown fruit crops in China, and nectarine (Prunus persica cv. nectarina) is an important cultivar of peach. Next-generation sequencing (NGS) approaches have opened new avenues in recent years for the identification of viruses and viroids (including novel pathogens), and this technology is well suited for large-scale pathogen surveys, because it can increase the speed at which a wide range of known pathogens are detected, and because it can be used to detect newly-emerging or potential pathogens for which other diagnostic tools are not yet available[3,4,5,6]. Several NGS-based strategies have been developed to overcome problems with traditional approaches, and these have resulted in the identification of known and novel viruses in peach These include two novel luteoviruses, nectarine stem-pitting-associated virus www.nature.com/scientificreports/. We used NGS technology to study the viral communities in nectarine trees with different disease phenotypes We identified both known and novel viruses and viroids, and performed comparative analyses of the potential contribution of the pathogens to disease symptoms. Our results will extend the range and kinds of virus and viroid species that infect peach trees, and provide insight into the viral synergisms and the agents that might be associated with disease symptoms in nectarine
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
