Illuminating the plant rhabdovirus landscape through metatranscriptomics data

Bejerman, Nicolás; Dietzgen, Ralf G.; Debat, Humberto Julio

doi:10.1101/2021.05.13.443957

Cited by 17 publications

(14 citation statements)

References 76 publications

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“…In weeds, six new rhabdoviruses were detected, primarily associated with Asteraceae species. Our observations added to the discoveries made in other studies, e.g., a recent discovery of 27 new viruses that are phylogenetically-related to plant rhabdoviruses through homology searches in the transcriptome shotgun assembly database of NCBI [86]. Some rhabdoviruses are known to replicate in its arthropod vector as well [87], thus, further infectivity tests are needed to confirm their infectivity and pathogenicity in associated plant hosts.…”

Section: Discussionmentioning

confidence: 80%

In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem

Rivarez

Pecman

Bačnik

et al. 2022

Preprint

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Viruses influence plants in agroecosystems, where their pathogenic nature in crops is primarily studied. Within the same systems, their diversity in non-crop plants and role outside the disease perspective is less known. To better understand their diversity and ecology, we performed an extensive virome exploration focusing on tomatoes and diverse weed species within or surrounding tomato farms. We detected 126 viruses, wherein 80 were novel (70 exclusively from weeds), and demonstrated infectivity of a novel tobamovirus in solanaceous hosts. Diversities of predominantly detected tomato viruses were variable, in some cases, with patterns comparable to global isolates of same species. We phylogenetically analyzed and taxonomically classified novel viruses and showed links between a subgroup of phylogenetically-related rhabdoviruses and a group of taxonomically-related host plants. Around one-third of viruses (n=10) detected in tomatoes were also detected in weeds, which might indicate possible role of weeds as inoculum reservoirs. We showed that even in a relatively well studied agroecosystem, a large part of plant viromes can still be unknown. Extensive biological and ecological insights generated from such holistic agroecosystem virome exploration will aid in anticipating possible emergences of plant virus diseases, and would serve as baseline for post-discovery characterization studies.

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Section: Discussionmentioning

confidence: 80%

In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem

Rivarez

Pecman

Bačnik

et al. 2022

Preprint

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“…Finally, the recently discovered gymnosperm varicose-like Pinus flexilis virus 1 in the family Rhabdoviridae contains an unsegmented genome organisation that differs from the typical bi-segmented structure of the varicosaviruses (25, 103). We find the bi-segmented structure in varicosavirus-like viruses for the first time in ferns and liverworts (TfVV and MgVV) which predate the gymnosperms.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome Mining Reveals a Spectrum of RNA Viruses in Primitive Plants

Mifsud

Gallagher

Holmes

et al. 2022

Preprint

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Current knowledge of plant viruses stems largely from those affecting economically important plants. Yet, plant species in cultivation represent a small and bias subset of the plant kingdom. Here, we describe virus diversity and abundance from a survey of 1079 transcriptomes from species across the breadth of the plant kingdom (Archaeplastida) by analysing open-source data from the One Thousand Plant Transcriptomes Initiative (1KP). We identified 104 potentially novel viruses, of which 40% comprised single-stranded positive-sense RNA viruses across eight orders, including members of the Hepelivirales, Tymovirales, Cryppavirales, Martellivirales and Picornavirales. One-third of the newly described viruses comprised double-stranded RNA viruses from the orders Durnavirales and Ghabrivirales. The remaining were negative-sense RNA viruses from the Rhabdoviridae, Aspiviridae, Yueviridae, Phenuiviridae and the newly proposed Viridisbunyaviridae. Our analysis considerably expands the known host range of 13 virus families to include lower plants (e.g., Benyviridae and Secoviridae) and four virus families to include algae hosts (e.g., Tymoviridae and Chrysoviridae). The discovery of the first 30 kDa movement protein in a non-vascular plant, suggests that the acquisition of plant virus movement proteins occurred prior to the emergence of the plant vascular system. More broadly, however, a co-phylogeny analysis revealed that the evolutionary history of these families is largely driven by cross-species transmission events. Together, these data highlight that numerous RNA virus families are associated with older evolutionary plant lineages than previously thought and that the scarcity of RNA viruses found in lower plants to date likely reflects a lack of investigation rather than their absence.

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“…On the other hand, ClEV forms a distinct subgroup of enamoviruses alongwith CVEV and pepper enamovirus. Interestingly, a cytorhabdovirus-Trachyspermum ammi virus 1 [2] and a putative tymovirus-Kava virus 1 [1] were identi ed in the same Bioprojects from where TaPV and PmPV, respectively were discovered in the current study.…”

Section: Main Textmentioning

confidence: 91%

“…In recent times, plant RNA datasets and contigs available in NCBI-Sequence Read Archive (SRA) and Transcriptome Shotgun Assembly (TSA) databases, respectively have emerged as one of the major resources for the discovery of putative novel viruses [2,7,22,23]. Such identi ed novel viruses could be regarded as bona de ones based on the report by Simmonds and colleagues [25] who suggested the incorporation of viruses that were identi ed only from metagenomic data into the o cial taxonomy scheme of the International Committee on Taxonomy of Viruses (ICTV) for comprehensive characterization of global virome.…”

Section: Main Textmentioning

confidence: 99%

Exploration of plant transcriptomes reveals five putative novel poleroviruses and an enamovirus

Sidharthan

Nagendran²,

Baranwal³

2022

Virus Genes

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Transcriptome datasets available in public domain serve as valuable resource for identi cation and characterization of novel viral genomes. Poleroviruses are economically important plant-infecting RNA viruses belonging to the family Luteoviridae. In the present study, we explored the plant transcriptomes available in public domain and identi ed ve putative novel poleroviruses tentatively named as Foeniculum vulgare polerovirus (FvPV), Kalanchoe marnieriana polerovirus (KmPV), Paspalum notatum polerovirus (PnPV), Piper methysticum polerovirus (PmPV), Trachyspermum ammi polerovirus (TaPV) and a novel enamovirus named as Celmisia lyallii enamovirus (ClEV) in Foeniculum vulgare, Kalanchoe marnieriana, Paspalum notatum, Piper methysticum, Trachyspermum ammi and Celmisia lyallii, respectively. Coding-complete genomes (5.56−5.74 kb) of CIEV, KmPV, PnPV, PmPV and TaPV were recovered while only the partial genome of FvPV could be recovered. The genome organization of identi ed viruses except ClEV is 5'−P0−P1−P2−P3a−P3−P4−P5−3' while that of ClEV is 5'−P0−P1−P2−P3− P5−3'. Phylogenetic analysis and genome organization revealed the relatedness of FvPV, KmPV, PnPV, PmPV and TaPV to other poleroviruses and ClEV to other enamoviruses.

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Illuminating the plant rhabdovirus landscape through metatranscriptomics data

Cited by 17 publications

References 76 publications

In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem

In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem

Transcriptome Mining Reveals a Spectrum of RNA Viruses in Primitive Plants

Exploration of plant transcriptomes reveals five putative novel poleroviruses and an enamovirus

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