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.
Highlights
Viruses of forest trees have been, until recently, only slightly characterized due to two main reasons; (a) biased sampling based on a restricted focus on agricultural crops and fruit trees viruses (Büttner et al, 2013) and (b) a general bias against the identification of the most divergent genomes (Zhang et al, 2018)
All sequences differed from the corresponding variant generated from the original sequence from Acer + (2014) by 0.3–1.6% and by 0.4–1.1% in the cases of the RT-PCR products amplified by primer-pair RNA1aF/R and RNA1bF/R, respectively (Supplementary Table 2)
The six newly identified RNA segments are attributed to a novel Emaravirus species based on the following: (a) The multipartite genome is composed of six single-stranded RNA molecules; (b) All six RNAs share a fully conserved stretch of 13 nt at their 5 and 3 termini; (c) Each segment of the genome encodes a single protein, which shows sequence identity with homologous proteins of other emaraviruses; (d) In all phylogenetic trees generated with amino acid sequences, maple mottle-associated virus (MaMaV) is only distantly related phylogenetically to the emaraviruses currently represented in the GenBank fulfilling the current species demarcation criteria of emaraviruses to show more than 25% aa divergence of RNA1-RNA3 encoded proteins (Elbeaino et al, 2018)
Summary
Viruses of forest trees have been, until recently, only slightly characterized due to two main reasons; (a) biased sampling based on a restricted focus on agricultural crops and fruit trees viruses (Büttner et al, 2013) and (b) a general bias against the identification of the most divergent genomes (Zhang et al, 2018). Due to the utilization of generation sequencing (NGS), forest virology has gained a significant momentum in identifying viruses infecting forest trees. A birch virome was unraveled revealing a complex of novel and known viruses (Rumbou et al, 2020), while a novel badnavirus associated with the birch leaf-roll disease was identified and genetically characterized (Rumbou et al, 2018). (von Bargen et al, 2018) It is apparent, that the application of NGS tools has substantially increased the rate of virus discovery in forest and urban green ecosystems
Sign-in/Register to view highlights & summary 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.
