Abstract
In the past decade, high-throughput sequencing (HTS) has had a major impact on virus diversity studies as well as on diagnosis, providing an unbiased and more comprehensive view of the virome of a wide range of organisms. Rather than the serological and molecular-based methods, with their more “reductionist” view focusing on one or a few known agents, HTS-based approaches are able to give a “holistic snapshot” of the complex phytobiome of a sample of interest. In grapevine for example, HTS is powerful enough to allow for the assembly of complete genomes of the various viral species or variants infecting a sample of known or novel virus species. In the present study, a total RNAseq-based approach was used to determine the full genome sequences of various grapevine fanleaf virus (GFLV) isolates and to analyze the eventual presence of other viral agents. From four RNAseq datasets, a few complete grapevine-infecting virus and viroid genomes were de-novo assembled: (a) three GFLV genomes, 11 grapevine rupestris stem-pitting associated virus (GRSPaV) and six viroids. In addition, a novel viral genome was detected in all four datasets, consisting of a single-stranded, positive-sense RNA molecule of 6033 nucleotides. This genome displays an organization similar to Tymoviridae family members in the Tymovirales order. Nonetheless, the new virus shows enough differences to be considered as a new species defining a new genus. Detection of this new agent in the original grapevines proved very erratic and was only consistent at the end of the growing season. This virus was never detected in the spring period, raising the possibility that it might not be a grapevine-infecting virus, but rather a virus infecting a grapevine-associated organism that may be transiently present on grapevine samples at some periods of the year. Indeed, the Tymoviridae family comprises isometric viruses infecting a wide range of hosts in different kingdoms (Plantae, Fungi, and Animalia). The present work highlights the fact that even though HTS technologies produce invaluable data for the description of the sanitary status of a plant, in-depth biological studies are necessary before assigning a new virus to a particular host in such metagenomic approaches.
Highlights
Grapevine is one of the oldest domesticated crops and has been cultivated for more than seven millennia in a wide range of geographical areas (McGovern, 2003)
Grapevine material used in this study came from a virus’ corecollection maintained in an open-field by the Institut National de la Recherche Agronomique (INRA) in its Colmar research center (48.064457 lat., 7.334899 long.) (Table S2)
RNASeq datasets obtained from a collection of Gewurztraminer grapevines singly infected by grapevine fanleaf virus (GFLV) isolates were first analyzed by directly mapping total cleaned reads (Table S3) onto a curated collection of grapevine viruses’ reference sequences
Summary
Grapevine is one of the oldest domesticated crops and has been cultivated for more than seven millennia in a wide range of geographical areas (McGovern, 2003). The most prominent advance would likely be the adaptation of Koch’s original postulates, morphing from the simplistic “1 pathogen = 1 disease” equation to considering microbial interactions and their adaptation dynamics in order for the host to develop a disease, sometimes referred to as the “pathobiome” concept (Stecher et al, 2012; Byrd and Segre, 2016) After this first descriptive step, more work is needed in the field of etiology and functional genomics, in order to better understand the interactions between the microbiota, the pathogens and the host that might trigger the expression of disease and to precisely understand to which agents the pathobiome concept is most relevant
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