Diverse genomoviruses representing twenty-nine species identified associated with plants

Fontenele, Rafaela S.; Roumagnac, Philippe; Richet, Cécile; Kraberger, Simona; Stainton, Daisy; Aleamotu’a, Maketalena; Filloux, Denis; Bernardo, Pauline; Harkins, Gordon William; McCarthy, James K.; Charles, Lachlan S.; Lamas, N. S.; Abreu, E. F. M.; Abreu, Rayane A.; Batista, Graciete B.; Lacerda, A. L. M.; Salywon, Andrew M.; Wojciechowski, Martin F.; Majure, Lucas C.; Martin, Darren P.; Ribeiro, S. G.; Lefeuvre, Pierre; Varsani, Arvind

doi:10.1007/s00705-020-04801-5

Cited by 13 publications

(2 citation statements)

References 123 publications

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“…DNA viruses of the family Genomoviridae were also detected in C. brasiliensis . This group of ssDNA viruses is considered a sister group of the family Geminiviridae and has the potential to cause fungal hypovirulence, identified in different environmental samples associated with plants and animals, including in Brazil infecting common beans and citrus ( Lamas et al, 2016 ; Chabi-Jesus et al, 2020 ; Fontenele et al, 2020 ; Varsani and Krupovic, 2021 ). Phylogenetic analysis of the putative viral sequence suggests its association with viruses from the family Genomoviridae , indicating a close relationship to chicken genomovirus mg4 and other viruses of the genus Gemycircularvirus .…”

Section: Discussionmentioning

confidence: 99%

Expanding the environmental virome: Infection profile in a native rainforest tree species

et al. 2022

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Agroforestry systems (AFS) for cocoa production combine traditional land-use practices with local biodiversity conservation, resulting in both ecological and agricultural benefits. The cacao-cabruca AFS model is widely implemented in regions of the Brazilian Atlantic Forest. Carpotroche brasiliensis (Raddi) A. Gray (Achariaceae) is a tree found in cabruca landscapes that is often used for reforestation and biotechnological applications. Despite its importance, we still lack information about viruses circulating in C. brasiliensis, particularly considering the possibility of spillover that could affect cocoa production. In our study, we analyzed the Carpotroche brasiliensis virome from Atlantic Forest and cacao-cabruca AFS regions using metatranscriptomics from several vegetative and reproductive organs. Our results revealed a diverse virome detecting near-complete or partial coding sequences of single- and double-stranded DNA and RNA viruses classified into at least six families (Botourmiaviridae, Bromoviridae, Caulimoviridae, Genomoviridae, Mitoviridae, and Rhabdoviridae) plus unclassified elements. We described with high confidence the near-complete and the partial genomes of two tentative novel viruses: Carpotroche-associated ilarvirus and Carpotroche-associated genomovirus, respectively. Interestingly, we also described sequences likely derived from a rhabdovirus, which could represent a novel member of the genus Gammanucleorhabdovirus. We observed higher viral diversity in cacao-cabruca AFS and reproductive organs of C. brasiliensis with preferential tropism to fruits, which could directly affect production. Altogether, our results provide data to better understand the virome in this unexplored agroecological interface, such as cacao-cabruca AFS and forest ecosystem, providing information on the aspects of virus–plant interactions.

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Section: Discussionmentioning

confidence: 99%

Expanding the environmental virome: Infection profile in a native rainforest tree species

et al. 2022

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“…The known diversity of viruses associated with cacti has mostly been restricted to RNA viruses belonging to the single-stranded RNA virus families Alphaflexiviridae, Betaflexiviridae, Puribunyaviridae, Tombusviridae and Virgaviridae [8][9][10][11][12][13][14], but through recent research efforts, DNA viruses that either infect or are associated with cacti have been identified [15][16][17][18].…”

Section: Introductionmentioning

confidence: 99%

New World Cactaceae Plants Harbor Diverse Geminiviruses

Fontenele

Salywon

Majure

et al. 2021

Viruses

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The family Cactaceae comprises a diverse group of typically succulent plants that are native to the American continent but have been introduced to nearly all other continents, predominantly for ornamental purposes. Despite their economic, cultural, and ecological importance, very little research has been conducted on the viral community that infects them. We previously identified a highly divergent geminivirus that is the first known to infect cacti. Recent research efforts in non-cultivated and asymptomatic plants have shown that the diversity of this viral family has been under-sampled. As a consequence, little is known about the effects and interactions of geminiviruses in many plants, such as cacti. With the objective to expand knowledge on the diversity of geminiviruses infecting cacti, we used previously acquired high-throughput sequencing results to search for viral sequences using BLASTx against a viral RefSeq protein database. We identified two additional sequences with similarity to geminiviruses, for which we designed abutting primers and recovered full-length genomes. From 42 cacti and five scale insects, we derived 42 complete genome sequences of a novel geminivirus species that we have tentatively named Opuntia virus 2 (OpV2) and 32 genomes of an Opuntia-infecting becurtovirus (which is a new strain of the spinach curly top Arizona virus species). Interspecies recombination analysis of the OpV2 group revealed several recombinant regions, in some cases spanning half of the genome. Phylogenetic analysis demonstrated that OpV2 is a novel geminivirus more closely related to viruses of the genus Curtovirus, which was further supported by the detection of three recombination events between curtoviruses and OpV2. Both OpV2 and Opuntia becurtoviruses were identified in mixed infections, which also included the previously characterized Opuntia virus 1. Viral quantification of the co-infected cactus plants compared with single infections did not show any clear trend in viral dynamics that might be associated with the mixed infections. Using experimental Rhizobium-mediated inoculations, we found that the initial accumulation of OpV2 is facilitated by co-infection with OpV1. This study shows that the diversity of geminiviruses that infect cacti is under-sampled and that cacti harbor diverse geminiviruses. The detection of the Opuntia becurtoviruses suggests spill-over events between viruses of cultivated species and native vegetation. The threat this poses to cacti needs to be further investigated.

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Family Genomoviridae: 2021 taxonomy update

Varsani

Krupovìč

2021

Arch Virol

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The family Genomoviridae (phylum Cressdnaviricota, class Repensiviricetes, order Geplafuvirales) includes viruses with circular single-stranded DNA genomes encoding two proteins, the capsid protein and the rolling-circle replication initiation protein. The genomes of the vast majority of members in this family have been sequenced directly from diverse environmental or animal-and plant-associated samples, but two genomoviruses have been identified infecting fungi. Since the last taxonomic update of the Genomoviridae, a number of new members of this family have been sequenced. Here, we report on the most recent taxonomic update, including the creation of one new genus, Gemytripvirus, and classification of ~420 new genomoviruses into 164 new species. We also announce the adoption of the "Genus + freeform epithet" binomial system for the naming of all 236 officially recognized species in the family Genomoviridae. The updated taxonomy presented in this article has been accepted by the International Committee on Taxonomy of Viruses (ICTV).

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Diverse genomoviruses representing twenty-nine species identified associated with plants

Cited by 13 publications

References 123 publications

Expanding the environmental virome: Infection profile in a native rainforest tree species

Expanding the environmental virome: Infection profile in a native rainforest tree species

New World Cactaceae Plants Harbor Diverse Geminiviruses

Family Genomoviridae: 2021 taxonomy update

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