Transcriptome Mining Expands Knowledge of RNA Viruses across the Plant Kingdom

Mifsud, Jonathon C O; Gallagher, Rachael V.; Holmes, Edward C.; Geoghegan, Jemma L.

doi:10.1128/jvi.00260-22

Cited by 50 publications

(71 citation statements)

References 112 publications

(128 reference statements)

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“…The predictions of moss ssRNA-containing beny-like virus infecting D. scoparium (this study) and another moss-infecting virus, Leucodon julaceus associated beny-like virus [ 40 ], raise the question of whether the virus cell-to-cell movement in mosses can occur in a way similar to that in higher plants. The available published data suggest that macromolecular trafficking in mosses is quite similar to that in flowering plants and includes trafficking through plasmodesmata having obvious structural similarity to those in seed plants [ 41 , 42 ], which is in agreement with our finding that the moss viruses code for transport module was typical for viruses of higher plants.…”

Section: Discussionmentioning

confidence: 99%

Bioinformatic Analysis Predicts a Novel Genetic Module Related to Triple Gene and Binary Movement Blocks of Plant Viruses: Tetra-Cistron Movement Block

Morozov

Solovyev

2022

Biomolecules

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Previous studies have shown that the RNA genomes of some plant viruses encode two related genetic modules required for virus movement over the host body, containing two or three genes and named the binary movement block (BMB) and triple gene block (TGB), respectively. In this paper, we predict a novel putative-related movement gene module, called the tetra-cistron movement block (TCMB), in the virus-like transcriptome assemblies of the moss Dicranum scoparium and the Antarctic flowering plant Colobanthus quitensis. These TCMBs are encoded by smaller RNA components of putative two-component viruses related to plant benyviruses. Similar to the RNA2 of benyviruses, TCMB-containing RNAs have the 5′-terminal coat protein gene and include the RNA helicase gene which is followed by two small overlapping cistrons encoding hydrophobic proteins with a distant sequence similarity to the TGB2 and TGB3 proteins. Unlike TGB, TCMB also includes a fourth 5′-terminal gene preceding the helicase gene and coding for a protein showing a similarity to the double-stranded RNA-binding proteins of the DSRM AtDRB-like superfamily. Additionally, based on phylogenetic analysis, we suggest the involvement of replicative beny-like helicases in the evolution of the BMB and TCMB movement genetic modules.

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Section: Discussionmentioning

confidence: 99%

Bioinformatic Analysis Predicts a Novel Genetic Module Related to Triple Gene and Binary Movement Blocks of Plant Viruses: Tetra-Cistron Movement Block

Morozov

Solovyev

2022

Biomolecules

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“…The awareness on the importance of virus diseases, especially amid an on-going COVID-19 pandemic 1 , increased research interest on the exploration of virus diversity across ecosyst ems, assisted by high-throughput sequencing (HTS) [2][3][4] , and by exploring global nucleotide databases [5][6][7] . In agroecosystems, viruses are ubiquitous microbes associated with eukaryotic hosts including crop and weed plants, fungi, oomycetes, arthropods, and nematodes, as well as prokaryotes such as bacteria 8,9 .…”

Section: Introductionmentioning

confidence: 99%

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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“…Nevertheless, a minuscule portion, probably a small fraction of one percent of the virosphere has been characterized so far [3]. Therefore, we have a limited knowledge of the vast world virome, with its remarkable diversity and including every potential host organism assessed so far [4][5][6]. Data mining of publically available transcriptome datasets has become an efficient and inexpensive strategy to unlock the diversity of the plant virosphere [5].…”

Section: Introductionmentioning

confidence: 99%

“…Until 2017, LBVaV was the only identified and extensively characterized varicosavirus [12][13][14], then, in 2017 and 2018, two novel varicosaviruses were identified through high-throughput sequencing (HTS) [15][16]. However, in 2021 and 2022, there was a five-fold increase in the number of reported varicosaviruses, with 12 out 15 discovered through data mining of publically available transcriptome datasets [6,9,[17][18], while the other three were identified using HTS [19][20][21] (Suppl. Fig.…”

Section: Introductionmentioning

confidence: 99%

“…On the other hand, the only unsegmented varicosavirus described so far has 5 ORFs, in the order 3’-N-Protein 2-Protein 3– Protein 4–L-5’ [9]. Varicosaviruses appear to have a diverse host range including dicots, monocots, gymnosperms, ferns, and liverworts [6, 9]. The vector of a sole member, lettuce big vein-associated virus (LBVaV) has been characterized, which is the chytrid fungus Olpidium spp .…”

Section: Introductionmentioning

confidence: 99%

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Unlocking the hidden genetic diversity of varicosaviruses, the neglected plant rhabdoviruses

Bejerman

Dietzgen

Debat

2022

Preprint

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The genus Varicosavirus is one of six genera of plant-infecting rhabdoviruses. Varicosaviruses have non-enveloped flexuous rod-shaped virions and a negative-sense, single-stranded RNA genome. A distinguishing feature of varicosaviruses, that is shared with dichorhaviruses, is a bi-segmented genome. Before 2017, a sole varicosavirus was known and characterized, then two more varicosaviruses were identified through high-throughput sequencing in 2017 and 2018. More recently, the number of known varicosaviruses has substantially increased in concert with the extensive use of high-throughput sequencing platforms and data mining approaches. The novel varicosaviruses revealed not only sequence diversity but also plasticity in terms of genome architecture, including a virus with a tentatively unsegmented genome. Here, we report the discovery of 45 novel varicosavirus genomes, which were identified in publicly available metatranscriptomic data. Identification, assembly, and curation of raw Sequence Read Archive reads resulted in 39 viral genome sequences with full-length coding regions and 6 with nearly complete coding regions. Highlights of the obtained sequences include eight varicosaviruses with unsegmented genomes, linked to a phylogenetic clade associated with gymnosperms. These findings resulted in the most complete phylogeny of varicosaviruses to date and shed new light on the phylogenetic relationships and evolutionary landscape of this group of plant rhabdoviruses. Thus, the extensive use of sequence data mining for virus discovery has allowed unlocking of the hidden genetic diversity of varicosaviruses, the largely neglected plant rhabdoviruses. Keywords: plant rhabdovirus; varicosaviruses, genome architecture, virus taxonomy; metatranscriptomics

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Transcriptome Mining Expands Knowledge of RNA Viruses across the Plant Kingdom

Abstract: Our knowledge of plant viruses is mainly limited to those infecting economically important host species. In particular, we know little about those viruses infecting basal plant lineages such as the ferns, lycophytes, bryophytes, and charophytes.

Cited by 50 publications

References 112 publications

Bioinformatic Analysis Predicts a Novel Genetic Module Related to Triple Gene and Binary Movement Blocks of Plant Viruses: Tetra-Cistron Movement Block

Bioinformatic Analysis Predicts a Novel Genetic Module Related to Triple Gene and Binary Movement Blocks of Plant Viruses: Tetra-Cistron Movement Block

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

Unlocking the hidden genetic diversity of varicosaviruses, the neglected plant rhabdoviruses

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