Diversity of polerovirus‐associated<scp>RNAs</scp>in the virome of wild and cultivated carrots

Schönegger, Deborah; Babalola, Bisola Mercy; Marais, Armelle; Faure, Chantal; Candresse, Thierry

doi:10.1111/ppa.13623

Cited by 3 publications

(3 citation statements)

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“…These self-replicating subviral agents depend on helper viruses of the family Solemoviridae for aphid transmission and have recently been classified as tombus-like associated RNAs (tlaRNAs) due to their phylogenetic affinities with members of the Tombusviridae family [ 37 ]. A detailed description of their diversity, distribution and preferential association with either wild or cultivated carrots within this metagenomic study has recently been published [ 38 ]. Moreover, two novel hammerhead ribozyme containing single-stranded circular satellite RNAs, carrot red leaf virus satellite 1 (CtRLV Sat1) and carrot red leaf virus satellite 2 (CtRLV Sat2) have also been identified in Spanish and French carrot populations and reported in detail recently [ 39 ].…”

Section: Resultsmentioning

confidence: 99%

“…In addition, six different umbraviruses, three known (CMoV, CMoMV, WCMoV) and three new or potentially new (CaUV2 and CaUV3, CaUV1) were detected in different carrot populations in France, often in complex co-infections, when single plants were analyzed. The carrot virome was equally rich in subviral agents, with four different tombus-like-associated RNAs identified in French and Spanish carrot populations [ 38 ]. In addition, both linear and small circular, hammerhead-containing satellite RNAs [ 39 ] were detected.…”

Section: Discussionmentioning

confidence: 99%

“…The results confirmed that plants were frequently coinfected by different known and novel poleroviruses, umbraviruses and associated subviral agents, suggesting complex and flexible interactions. Indeed, while arracacha latent virus E (ALVE, genus Enamovirus ) was not observed in French or Spanish carrot viromes, arracacha latent virus E-associated RNA (ALVEaRNA) was frequently identified, often in coinfection with CtRLV, which likely fulfils a helper virus role, thus indicating some degree of plasticity in the association between different helper and dependent viruses [ 38 ]. Co-infections likely explain that several tentative recombination events could be detected among members of the Polerovirus genus, including a statistically highly significant recombination in the CP-readthrough (CP-RT) protein involving WCtRLV, CtRLV and the novel CaPV1.…”

Section: Discussionmentioning

confidence: 99%

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Carrot populations in France and Spain host a complex virome rich in previously uncharacterized viruses

et al. 2023

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High-throughput sequencing (HTS) has proven a powerful tool to uncover the virome of cultivated and wild plants and offers the opportunity to study virus movements across the agroecological interface. The carrot model consisting of cultivated (Daucus carota ssp. sativus) and wild carrot (Daucus carota ssp. carota) populations, is particularly interesting with respect to comparisons of virus communities due to the low genetic barrier to virus flow since both population types belong to the same plant species. Using a highly purified double-stranded RNA-based HTS approach, we analyzed on a large scale the virome of 45 carrot populations including cultivated, wild and off-type carrots (carrots growing within the field and likely representing hybrids between cultivated and wild carrots) in France and six additional carrot populations from central Spain. Globally, we identified a very rich virome comprising 45 viruses of which 25 are novel or tentatively novel. Most of the identified novel viruses showed preferential associations with wild carrots, either occurring exclusively in wild populations or infecting only a small proportion of cultivated populations, indicating the role of wild carrots as reservoir of viral diversity. The carrot virome proved particularly rich in viruses involved in complex mutual interdependencies for aphid transmission such as poleroviruses, umbraviruses and associated satellites, which can be the basis for further investigations of synergistic or antagonistic virus-vector-host relationships.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Carrot populations in France and Spain host a complex virome rich in previously uncharacterized viruses

et al. 2023

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Pollen-mediated gene flow from wild carrots (Daucus carota L. subsp. carota) affects the production of commercial carrot seeds (Daucus carota L. subsp. sativus) internationally and in New Zealand in the context of climate change: A systematic review

Godwin,

Pieralli,

Sofkova-Bobcheva

et al. 2024

Science of The Total Environment

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Identification of a novel recombinant polerovirus and other emergent viruses and tombusvirus-like associated RNA species associated with carrot motley dwarf disease in the United States

Erickson,

Ter Horst,

Carlson

et al. 2024

Front. Microbiol.

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Carrot motley dwarf (CMD) is a viral disease complex caused by co-infection of the polerovirus carrot red leaf virus with the umbraviruses carrot mottle virus or carrot mottle mimic virus, and/or a tombusvirus like associated RNA (tlaRNA), which depend on co-infection with a helper polerovirus to gain aphid transmissibility. In 2020 and 2021 carrot samples from Washington, United States (U.S.), and parsley and cilantro samples from California, U.S., exhibiting typical symptoms of CMD were submitted for diagnosis. Initial RT-PCR diagnostic assays identified the typical CMD viruses in the carrot samples, however only the umbraviruses and tlaRNAs were detected in the parsley and cilantro samples; as such, these samples were retested with another RT-PCR assay for generic polerovirus detection. Unexpectedly, the poleroviruses Torilis crimson leaf virus (TorCLV) and fennel motley virus were identified. Subsequent RNA sequencing analysis was conducted to confirm these results and look for other emergent viruses. In addition to confirming the diagnostic results, the recently described polerovirus Foeniculum vulgare polerovirus, the umbraviruses Pastinaca umbravirus 1 and wild carrot mottle virus, and the tlaRNA Arracacha latent virus E associated RNA were identified, making this the first report of these viruses and tlaRNA in the U.S. Using phylogenetic and pairwise identity comparisons and RDP4 recombination analyses, we also identified a putative novel polerovirus, for which we propose the name parsley polerovirus, that appears to be a recombinant between carrot polerovirus 1, sharing 92% amino acid (aa) identity with the RNA dependent RNA polymerase in the 5′ gene block, and TorCLV, sharing >98% aa identity with the capsid protein in the 3 gene block. This work adds to the growing list of polerovirus species exhibiting recombination between the 5′ and 3′ gene blocks, and highlights the unique, variable, and dynamic associations that can occur in polerovirus, umbravirus, and tlaRNA disease complexes.

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Diversity of polerovirus‐associatedRNAsin the virome of wild and cultivated carrots

Cited by 3 publications

References 22 publications

Carrot populations in France and Spain host a complex virome rich in previously uncharacterized viruses

Carrot populations in France and Spain host a complex virome rich in previously uncharacterized viruses

Pollen-mediated gene flow from wild carrots (Daucus carota L. subsp. carota) affects the production of commercial carrot seeds (Daucus carota L. subsp. sativus) internationally and in New Zealand in the context of climate change: A systematic review

Identification of a novel recombinant polerovirus and other emergent viruses and tombusvirus-like associated RNA species associated with carrot motley dwarf disease in the United States

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