Abstract
High-throughput sequencing has dramatically broadened the possibilities for plant virus research and diagnostics, enabling discovery of new or obscure viruses, and virus strains and rapid sequencing of their genomes. In this research, we employed high-throughput sequencing to discover a new virus infecting tomato, Henbane mosaic virus (Potyvirus, Potyviridae), which was first discovered at the beginning of 20th century in the United Kingdom in cultivated henbane. A field tomato plant with severe necrotic symptoms of unknown etiology was sampled in Slovenia and high-throughput sequencing analysis using small RNA and ribosomal RNA depleted total RNA approaches revealed a mixed infection with Potato virus M (Carlavirus, Betaflexiviridae), Southern tomato virus (Amalgavirus, Amalgamaviridae) and henbane mosaic virus in the sample. The complete genomic sequence of henbane mosaic virus was assembled from the sequencing reads. By re-inoculation of the infected material on selected test plants, henbane mosaic virus was isolated and a host range analysis was performed, demonstrating the virus was pathogenic on several plant species. Due to limited metadata in public repositories, the taxonomic identification of the virus isolate was initially putative. Thus, in the next step, we used small RNA sequencing to determine genomic sequences of four historic isolates of the virus, obtained from different virus collections. Phylogenetic analyses performed using this new sequence information enabled us to taxonomically position Henbane mosaic virus as a member of the Potyvirus genus within the chili veinal mottle virus phylogenetic cluster and define the relationship of the new tomato isolate with the historic ones, indicating the existence of at least four putative strains of the virus. The first detection of henbane mosaic virus in tomato and demonstration of its pathogenicity on this host is important for plant protection and commercial tomato production. Since the virus was initially present in a mixed infection, and its whole genome was not sequenced, it has probably been overlooked in routine diagnostics. This study confirms the applicability of a combination of high-throughput sequencing and classic plant virus characterization methods for identification and phylogenetic classification of obscure viruses and historical viral isolates, for which no or limited genome sequence data is available.
Highlights
The immense sequence data generating potential of highthroughput sequencing (HTS) has enabled an accelerated discovery of new virus species in recent years (Barba et al, 2013; Massart et al, 2014; Adams and Fox, 2016) and increased resolution of viral population and evolution studies (Kutnjak et al, 2017)
In the present research we address another angle of this problem; we used HTS to detect and sequence the genome of a known plant virus, namely henbane mosaic virus (HMV, genus Potyvirus, family Potyviridae), which had a poorly characterized genome, despite being the subject of several biological studies in the past
The increased rate of virus discovery, brings new challenges, especially considering the biological characterization of the newly detected viral sequences. The latter is crucial to establish their importance, i.e., their impact on agriculture and trade (Massart et al, 2017) or their natural ecosystems. Since this process comprises laborious classical virology techniques, in many cases, the biological characterization of rapidly discovered new viral species is lagging behind their discovery, often due to time constrains
Summary
The immense sequence data generating potential of highthroughput sequencing (HTS) has enabled an accelerated discovery of new virus species in recent years (Barba et al, 2013; Massart et al, 2014; Adams and Fox, 2016) and increased resolution of viral population and evolution studies (Kutnjak et al, 2017). In the present research we address another angle of this problem; we used HTS to detect and sequence the genome of a known plant virus, namely henbane mosaic virus (HMV, genus Potyvirus, family Potyviridae), which had a poorly characterized genome, despite being the subject of several biological studies in the past. The virus was later reported in the United Kingdom in Atropa belladonna (Smith, 1945) and in Datura stramonium (Bradley, 1952). P. alkekengi was considered the main host and the new strain was labeled as HMV-A (Lovisolo and Bartels, 1970). The suggested main host plants for HMV are different species from the Solanaceae family (Govier and Plumb, 1972). Its particles are filamentous in shape (Govier and Plumb, 1972) with a length, estimated by electron microscopy to be approximately 850 nm (Lovisolo and Bartels, 1970)
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.
