A virome from ornamental flowers in an Australian rural town

Wylie, Stephen J.; Tran, T. T.; Nguyen, Duy; Koh, Shu Hui; Chakraborty, Angana; Xü, Wei; Jones, Michael G. K.; Li, H.

doi:10.1007/s00705-019-04317-7

Cited by 12 publications

(6 citation statements)

References 29 publications

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“…BVMoV is a species within the genus Bevemovirus (Seo et al, 2017). The next similar sequences were polyproteins of various macluraviruses (genus Macluravirus) such as the narcissus latent virus (QDC21212.1), cardamom mosaic virus (YP_009508901.1), and Chinese yam necrotic mosaic virus (YP_006590058.1), with 32%-34% identity in an approximately 2700-aa overlap (Kondo and Fujita, 2012;Elangovan et al, 2019;Wylie et al, 2019). Thus, SaPlV1 is the most closely related to BVMoV and possibly, a novel member of the genus Bevemovirus.…”

Section: Genome Sequence Of Striga-associated Poty-like Virus 1 (Saplv1)mentioning

confidence: 99%

Two novel poty-like viruses identified from the transcriptome data of purple witchweed (Striga hermonthica)

Choi¹,

Shin²,

Shirasu³

et al. 2022

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Section: Genome Sequence Of Striga-associated Poty-like Virus 1 (Saplv1)mentioning

confidence: 99%

Two novel poty-like viruses identified from the transcriptome data of purple witchweed (Striga hermonthica)

Choi¹,

Shin²,

Shirasu³

et al. 2022

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“…Moreover, partial segments of a cogu-like virus were discovered when the virome of ornamental flowers was analyzed by HTS ( Wylie et al, 2019 ). However, it will be necessary to complete the genome characterization and perform further analyses of these viruses to confirm if they are in fact plant-infecting viruses or arthropod-infecting viruses whose RNA was co-purified along with the plant RNA.…”

Section: Negative-sense Single-stranded Rna Virus Diversity and Taxomentioning

confidence: 99%

The Plant Negative-Sense RNA Virosphere: Virus Discovery Through New Eyes

2020

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The use of high-throughput sequencing (HTS) for virus diagnostics, as well as the importance of this technology as a valuable tool for discovery of novel viruses has been extensively investigated. In this review, we consider the application of HTS approaches to uncover novel plant viruses with a focus on the negative-sense, single-stranded RNA virosphere. Plant viruses with negative-sense and ambisense RNA (NSR) genomes belong to several taxonomic families, including Rhabdoviridae, Aspiviridae, Fimoviridae, Tospoviridae, and Phenuiviridae. They include both emergent pathogens that infect a wide range of plant species, and potential endophytes which appear not to induce any visible symptoms. As a consequence of biased sampling based on a narrow focus on crops with disease symptoms, the number of NSR plant viruses identified so far represents only a fraction of this type of viruses present in the virosphere. Detection and molecular characterization of NSR viruses has often been challenging, but the widespread implementation of HTS has facilitated not only the identification but also the characterization of the genomic sequences of at least 70 NSR plant viruses in the last 7 years. Moreover, continuing advances in HTS technologies and bioinformatic pipelines, concomitant with a significant cost reduction has led to its use as a routine method of choice, supporting the foundations of a diverse array of novel applications such as quarantine analysis of traded plant materials and genetic resources, virus detection in insect vectors, analysis of virus communities in individual plants, and assessment of virus evolution through ecogenomics, among others. The insights from these advancements are shedding new light on the extensive diversity of NSR plant viruses and their complex evolution, and provide an essential framework for improved taxonomic classification of plant NSR viruses as part of the realm Riboviria. Thus, HTS-based methods for virus discovery, our 'new eyes,' are unraveling in real time the richness and magnitude of the plant RNA virosphere.

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“…The virome concept emerged in parallel with the general microbiome concept ( Wylie et al., 2012 ; Berg et al., 2020 ). Virome analyses can include the study of viruses in a single host, or at multiple scales, such as host plants or vector species, the set of hosts within a location, or environmental samples such as from water or soil ( Kreuze et al., 2009 ; Al Rwahnih et al., 2011 ; Rosario et al., 2015 ; Leke et al., 2016 ; Hadad et al., 2019 ; Wylie et al., 2019 ; Alcalá-Briseño et al., 2020 ; Bacnik et al., 2020 ; Britt et al., 2020 ; Kwok et al., 2020 ; Fontenele et al., 2021 ). Implementing HTS allowed virome analysis to thrive through viral metagenomics, combined with new sampling options (i.e., individual, bulked, and mixed samples) and expanded virus sequence databases.…”

Section: Introduction To the Plant Viromementioning

confidence: 99%

Translating virome analyses to support biosecurity, on-farm management, and crop breeding

et al. 2023

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Virome analysis via high-throughput sequencing (HTS) allows rapid and massive virus identification and diagnoses, expanding our focus from individual samples to the ecological distribution of viruses in agroecological landscapes. Decreases in sequencing costs combined with technological advances, such as automation and robotics, allow for efficient processing and analysis of numerous samples in plant disease clinics, tissue culture laboratories, and breeding programs. There are many opportunities for translating virome analysis to support plant health. For example, virome analysis can be employed in the development of biosecurity strategies and policies, including the implementation of virome risk assessments to support regulation and reduce the movement of infected plant material. A challenge is to identify which new viruses discovered through HTS require regulation and which can be allowed to move in germplasm and trade. On-farm management strategies can incorporate information from high-throughput surveillance, monitoring for new and known viruses across scales, to rapidly identify important agricultural viruses and understand their abundance and spread. Virome indexing programs can be used to generate clean germplasm and seed, crucial for the maintenance of seed system production and health, particularly in vegetatively propagated crops such as roots, tubers, and bananas. Virome analysis in breeding programs can provide insight into virus expression levels by generating relative abundance data, aiding in breeding cultivars resistant, or at least tolerant, to viruses. The integration of network analysis and machine learning techniques can facilitate designing and implementing management strategies, using novel forms of information to provide a scalable, replicable, and practical approach to developing management strategies for viromes. In the long run, these management strategies will be designed by generating sequence databases and building on the foundation of pre-existing knowledge about virus taxonomy, distribution, and host range. In conclusion, virome analysis will support the early adoption and implementation of integrated control strategies, impacting global markets, reducing the risk of introducing novel viruses, and limiting virus spread. The effective translation of virome analysis depends on capacity building to make benefits available globally.

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A virome from ornamental flowers in an Australian rural town

Cited by 12 publications

References 29 publications

Two novel poty-like viruses identified from the transcriptome data of purple witchweed (Striga hermonthica)

Two novel poty-like viruses identified from the transcriptome data of purple witchweed (Striga hermonthica)

The Plant Negative-Sense RNA Virosphere: Virus Discovery Through New Eyes

Translating virome analyses to support biosecurity, on-farm management, and crop breeding

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