A novel member of the Tombusviridae from a wild legume, Gompholobium preissii

Koh, Shu Hui; Ong, Jamie W.L.; Admiraal, Ryan; Sivasithamparam, Krishnapillai; Jones, Michael G. K.; Wylie, Stephen J.

doi:10.1007/s00705-016-2992-7

Cited by 3 publications

(2 citation statements)

References 27 publications

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“…The presence of scaffolds with the highest sequence match to viruses from a total of 23 genera indicated that the population of viruses in this host are greatly diverse. This is in agreement with the findings of diverse viral species in previous studies of various wild plant species through viral metagenomics [ 21 , 22 , 23 , 24 , 25 ]. A greater virus diversity was further observed in the viral population of wild V. corymbosum native to Florida, as shown by the number of viral genera, which is almost twice more than those of cultivated viromes.…”

Section: Discussionsupporting

confidence: 93%

Discovery of Known and Novel Viruses in Wild and Cultivated Blueberry in Florida through Viral Metagenomic Approaches

Olmstead

Varsani

Polston

et al. 2021

Viruses

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Southern highbush blueberry (interspecific hybrids of Vaccinium corymbosum L.) is cultivated near wild V. corymbosum as well as closely related species in Florida, USA. The expansion of blueberry cultivation into new areas in Florida and deployment of new cultivars containing viruses can potentially increase the diversity of viruses in wild and cultivated V. corymbosum. In this study, viral diversity in wild and cultivated blueberries (V. corymbosum) is described using a metagenomic approach. RNA viromes from V. corymbosum plants collected from six locations (two cultivated and four wild) in North Central Florida were generated by high throughput sequencing (HTS) and analyzed using a bioinformatic analysis pipeline. De novo assembled contigs obtained from viromes of both commercial and wild sites produced sequences with similarities to plant virus species from a diverse range of families (Amalgaviridae, Caulimoviridae, Endornaviridae, Ophioviridae, Phenuiviridae, and Virgaviridae). In addition, this study has enabled the identification of blueberry latent virus (BlLV) and blueberry mosaic associated ophiovirus (BlMaV) for the first time in Florida, as well as a tentative novel tepovirus (blueberry virus T) (BlVT) in blueberry. To the best of our knowledge, this is the first study that compares viral diversity in wild and cultivated blueberry using a metagenomic approach.

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Section: Discussionsupporting

confidence: 93%

Discovery of Known and Novel Viruses in Wild and Cultivated Blueberry in Florida through Viral Metagenomic Approaches

Olmstead

Varsani

Polston

et al. 2021

Viruses

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“…Similarly, within the family Tombusviridae, PASC output showed substantial overlaps between the inter-genera and within-genus distances for Alphanecrovirus and Gammacarmovirus (pink and yellow bars, respectively) (Supplementary Fig. 3a, right), even though the two genera have been classified by a phylogenetic analysis based on the RNA-dependent RNA polymerase (RdRP) protein and the CP 49,50 . However, VISTA effectively captured the divergences between these different genera, generating pairwise distance distributions that clearly separated bars of different colors, evident by distinct valleys (Supplementary Fig.…”

Section: Discussionmentioning

confidence: 98%

Fast and accurate taxonomic classification for viral genomes with VISTA

Bao,

Zhang,

Guo

et al. 2023

Preprint

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The exponential growth of viral genome sequences in public databases has created a pressing need for a universal, scalable, and automated taxonomic framework to facilitate comprehensive virus studies. Here, we present VISTA (Virus Sequence-based Taxonomy Assignment), a novel computational tool for virus taxonomy featuring a pairwise sequence comparison system and an automatic demarcation threshold identification framework. VISTA leverages physio-chemical property sequences, k-mer profiles and selected features to construct a comprehensive distance-based framework for taxonomic clustering. Through a systematic comparison with the Pairwise Sequence Comparison (PASC), we demonstrate that VISTA achieves significantly improved separation for taxonomic groups, establishes more objective taxonomic demarcation thresholds, and runs at a substantially faster speed. We successfully applied VISTA to the class Caudoviricetesand 38 other virus families, indicating that our approach is robust, scalable, and capable of providing taxonomy assignments for both prokaryotic and eukaryotic viruses. Moreover, the application of VISTA to 679 unclassified phage genomes recovered from metagenomic data identified 46 novel virus families. VISTA is available as both a command line tool and a user-friendly web portal at https://ngdc.cncb.ac.cn/vista.

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