Analyses of virus/viroid communities in nectarine trees by next-generation sequencing and insight into viral synergisms implication in host disease symptoms

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.

Updating the Quarantine Status of Prunus Infecting Viruses in Australia

“…Like many other studies [69][70][71][72], mixed infections of two or more viruses were also detected in 24/100 Prunus trees tested. PNRSV occurred in all mixed infections which is not surprising given that PNRSV is easily transmitted by pollen and vegetatively, and was the most frequently detected virus [67,68].…”

Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution

“…Several platforms for second-generation sequencing have been developed by different companies such as Roche 454, Illumina, Solid and Ion Torrent (Bleidorn, 2016;Goodwin et al, 2016;Heather and Chain, 2016;Villamor et al, 2019). In addition to detection of new plant viruses and viroids, HTS is being used for studies on epidemiology, synergistic interactions between viruses, and genetic diversity and evolutionary mechanisms of virus populations (Kehoe et al, 2014;Hadidi et al, 2016;Pecman et al, 2017;Roossinck, 2017;Tan et al, 2019;Xu et al, 2019).…”

Identification of Plant Viruses Infecting Pear Using RNA Sequencing

“…Metatranscriptomic analysis of the virome of a major pear cultivar (SG) in Korea was performed. NGS is a recently emerged tool for virus detection and screening and has been used to discover numerous viruses, viral strains, and viral pathogens responsible for conditions of unknown etiologies ( Jo et al, 2018a ; Roossinck et al, 2015 ; Xu et al, 2019 ). Rapid virus discovery using NGS is considered a modern approach to prevent the outbreaks of novel viral diseases resulting from climate change, introduction via trade, and deterioration of natural ecosystems.…”

“…Detection of viruses using classic methods, such as ELISA and RT-PCR, is often limited in terms of identifying novel virus species ( Jeong et al, 2014 ; Ji et al, 2013 ). In addition to increasing the rate of virus discovery, NGS has been used to detect viruses and viroids in various fruit trees, including citrus, and peach ( Jo et al, 2018b , 2020 ; Xu et al, 2019 ).…”