Next-Generation Sequencing Reveals a Novel Emaravirus in Diseased Maple Trees From a German Urban Forest

Abstract

While the focus of plant virology has been mainly on horticultural and field crops as well as fruit trees, little information is available on viruses that infect forest trees. Utilization of next-generation sequencing (NGS) methodologies has revealed a significant number of viruses in forest trees and urban parks. In the present study, the full-length genome of a novel Emaravirus has been identified and characterized from sycamore maple (Acer pseudoplatanus) – a tree species of significant importance in urban and forest areas – showing leaf mottle symptoms. RNA-Seq was performed on the Illumina HiSeq2500 system using RNA preparations from a symptomatic and a symptomless maple tree. The sequence assembly and analysis revealed the presence of six genomic RNA segments in the symptomatic sample (RNA1: 7,074 nt-long encoding the viral replicase; RNA2: 2,289 nt-long encoding the glycoprotein precursor; RNA3: 1,525 nt-long encoding the nucleocapsid protein; RNA4: 1,533 nt-long encoding the putative movement protein; RNA5: 1,825 nt-long encoding a hypothetical protein P5; RNA6: 1,179 nt-long encoding a hypothetical protein P6). Two independent NGS sequencing runs from the same symptomatic maple tree detected the same genome segments. For one of these sequencing runs the cDNA library was prepared using a primer targeting the conserved genome terminal region, known to be shared between emaraviruses genome segments. We suggest, therefore, that the six identified genome segments represent the complete genome of a novel emaravirus from maple, which we tentatively name maple mottle-associated virus (MaMaV). Phylogenetic and sequence homology analyses place this virus on the distinct “subgroup a” clade within the Emaravirus genus along with – among others – rose rosette virus, Actinidia emaravirus 2, and fig mosaic virus. Validation RT-PCR assays performed on symptomatic and non-symptomatic trees suggest that MaMaV may be the symptom-inducing virus in the diseased trees. To our knowledge, this is the first time an Emaravirus is described from maple and is fully genetically characterized. With the discovery of MaMaV, the genus Emaravirus comprising negative-sense single-stranded viruses with very divergent genomes – that were until recently overlooked – has substantially increased counting 22 established and putative members.

Characterisation and Distribution of Karaka Ōkahu Purepure Virus—A Novel Emaravirus Likely to Be Endemic to New Zealand

“…Amino acid sequence analysis of the putative RdRp of known emaraviruses showed the emaraviruses comprise three major clades (clades I, II and III), with the largest clade (clade I) split into three subclades (subclades a, b and c). The observed branching pattern conforms to previous reports [ 52 , 53 , 54 , 55 ]. The earliest identified emaraviruses belong to Clade I, while more recent discoveries have expanded our understanding of emaravirus evolution with the identification of clades II and III.…”

Towards the Forest Virome: High-Throughput Sequencing Drastically Expands Our Understanding on Virosphere in Temperate Forest Ecosystems

“…The lack of virome complexity is rather surprising, when we consider the HTS results obtained from other wild as well as cultivated woody hosts. A possible explanation could be the age of the tree; it was 3 years old when it was sampled, thus it was exposed for only a short time to viral pathogens [74]. [182].…”

Towards the Forest Virome: Next-Generation-Sequencing Drastically Expands our Understanding on Virosphere in Temperate Forest Ecosystems

“…Among these, three virus genera are overwhelmingly represented. These are the genus Emaravirus with up to now four species (aspen mosaic-associated virus [26]; common oak ringspot-associated virus [27,28]; maple mottle-associated virus [29]; European mountain ash ringspot-associated virus [9]), the genus Badnavirus with two species (birch leafroll-associated virus [15]; chestnut mosaic virus [30]) and the genus Carlavirus with eight species (birch carlavirus [14]; blueberry scorch virus [31]; elderberry carlaviruses A, B, C, D, E [32][33]; elm carlavirus [34]). All the novel emara-and badnaviruses are found to be associated with the corresponding symptoms and are, consequently, plant pathogenic, while the role of the carlaviruses is not yet clarified.…”

“…has never been unambiguously described as a host for any well-characterized viral agent. Employing RNA-Seq methodology a novel emaravirus was recently reported in sycamore maple (A. pseudoplatanus) exhibiting mottle symptoms in Germany and was genetically characterized [29]. Maple mottle-associated virus comprises 6 RNA segments and evidence is provided that it may be the symptom-inducing virus in the diseased trees.…”