Biology subjects

Bejerman, N.

Publications and source records attributed to Bejerman, N..

At least 19 recordsLinked to original sources

bioRxiv2026

Systematic genome analysis enables long-overdue taxonomic reorganization of genus Orthoflavivirus; potential assignment of over 50 new species

Members of the Orthoflavivirus genus in the family Flaviviridae are primarily vector-transmitted RNA viruses infecting humans, other mammals and birds, including major pathogens such as tick borne encephalitis, West Nile, Zika and dengue viruses. Vector-borne flaviviruses are assigned to the Euflavivirus subgenus of orthoflaviviruses, with more divergent largely unclassified insect-specific flaviviruses, including cell fusing agent virus assigned to the second subgenus, Fusivirus. The currently classified 57 orthoflavivirus species have traditionally been assigned descriptively on the basis of their genome and antigenic relatedness, ecology and host and vector tropisms, although many more orthoflavi-like viruses remain unassigned. To investigate whether species might be demarcated using a fixed genetic divergence threshold, we examined distributions of pairwise distances in NS5 and E genes (which encode the RNA-dependent RNA polymerase and envelope protein, respectively) of classified orthoflaviviruses. Demarcation thresholds of 0.1 in the two regions would be most parsimonious with current euflavivirus classification. Exceptions include species in the tick-borne encephalitis virus complex with divergences below the threshold, and dengue virus types currently assigned to a single species that are substantially above. Application of the proposed thresholds would provide the means to establish 25 new euflavivirus and 33 new fusivirus species and reconcile several anomalies and inconsistencies in the current species taxonomy. The use of a species demarcation threshold brings consistency with the classification of viruses in other families. A robust and evolutionarily consistent framework furthermore enables taxonomic assignments of the numerous currently unassigned orthoflaviviruses that lack the phenotypic descriptions required for the current species definition.

microbiology↗

bioRxiv2026

Data mining sheds light on a novel family of plant-associated negative-sense RNA viruses linked to lispiviruses

Large-scale mining of public transcriptomic datasets can reveal viral diversity that remains invisible to conventional virus-surveillance approaches, while increasingly powerful structure-prediction methods provide a complementary route to characterizing highly divergent viral proteins. Here, we combine sequence detection, phylogenetic analysis, structural prediction, and host-association analyses to investigate the cryptic diversity and biology of a new clade of plant-associated lispi-like viruses. Analyses of RNA-sequencing datasets identified and enabled assembly of 87 lispi-like virus genomes associated with 75 plant hosts, expanding the known diversity of this new group by approximately 40-fold. The viruses share a conserved four-cistron genome organization, 3'-N-P2-P3-L-5'. Structural analyses provide functional insights into the four conserved proteins. P1 (N) adopts a canonical negative-strand RNA virus nucleocapsid architecture with conserved RNA-interacting residues and a predicted RNA-packaging configuration. P2 is exceptionally divergent; although a subset of structures resembles the ITPase/HAM1 fold. P3 forms a conserved trimeric coiled-coil architecture reminiscent of a viral fusion-protein stalk, but lacks the family-wide sequence features expected of a canonical membrane glycoprotein. P4 contains a structurally resolved Mononegavirales-type RNA-dependent-RNA-polymerase (RdRp) core with invariant catalytic motifs, including the characteristic GDN signature, whereas its accessory regions are substantially more divergent. Phylogenetic insights form a distinct monophyletic lineage sister to the predominantly invertebrate-associated Lispiviridae, supporting their recognition as a new proposed family Masuviridae, comprising 15 tentative genera. Genus-level clustering is accompanied by marked differences in host association, ranging from strong specialization to broader host ranges. Retrospective screening of public sequencing libraries further identified lispi-like virus sequences in 1,536 libraries representing 134 plant species, 11 plant families and 182 geographic locations, highlighting a substantial and geographically widespread cryptic virome. Together, these results establish Masuviridae as a deeply divergent lineage of plant-associated negative-sense RNA viruses and illustrate how the integration of sequence, structural, and large-scale transcriptomic analyses can move viral dark matter from detection towards evolutionary and functional characterization.

microbiology↗

bioRxiv2026

Novel RNA viruses reveal a complex mycovirome in the smut fungus Thecaphora thlaspeos

Mycoviruses are widespread in fungi, yet their diversity and host associations remain poorly explored in many lineages, including smut fungi. Here, we report the discovery of the first eight novel RNA viruses infecting the Brassicaceae-associated smut fungus Thecaphora thlaspeos. Using transcriptomic datasets derived from fungal mycelium and host plant controls, we identified dsRNA viral genomes supported by consistent read abundance, high genome coverage, and codon usage patterns closely matching those of the fungal host. All genomes are monosegmented and bicistronic, encoding capsid protein and polymerase genes in compact arrangements. Genome annotation and phylogenetic analyses based on the predicted RNA polymerase classified these viruses within the genera Totivirus and Eimeriavirus. Comparative analyses across fungal strains revealed intraspecific variation in virome composition, suggesting that host genetic background may influence viral community structure and that multiple dsRNA infection is common. Together, these findings expand the known diversity of mycoviruses in Ustilaginomycotina and identify T. thlaspeos as a host of a complex RNA virome. This work establishes a foundation for future studies on virus prevalence, transmission, and potential impacts on fungal biology and plant pathogenesis.

microbiology↗

bioRxiv2025

Implementation of an Artificial Rearing System and Molecular Identification of Gyropsylla spegazziniana (Lizer & Trelles) (Hemiptera: Psylloidea: Aphalaridae)

Gyropsylla spegazziniana, commonly known as the yerba mate psyllid, is one of the main pests affecting Ilex paraguariensis (yerba mate) production. To date, this pest has only been characterized morphologically, and no efficient artificial rearing system has been developed. In this study, we implemented a successful artificial rearing protocol under controlled conditions, a key step for further investigations. In addition, a fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI), one of the most widely used markers for phylogenetic characterization in insects, was amplified and sequenced, enabling the first molecular identification of this pest. The obtained data confirmed the previously proposed taxonomic position of G. spegazziniana, which was based on morphological traits, as a member of the family Aphalaridae. This study lays the foundation for future research on this economically important pest species of yerba mate.

ecology↗

bioRxiv2025

Expanding the known nucleorhabdovirus world: the final chapter in a trilogy exploring the hidden diversity of plant-associated rhabdoviruses

Nucleorhabdoviruses, classified into four distinct genera within the family Rhabdoviridae (subfamily Betarhabdovirinae), are plant-infecting viruses, characterized by nucleus-associated, enveloped, bacilliform virions. Nucleorhabdoviruses possess an unsegmented, single-stranded, negative-sense RNA genome (ca. 12-15.2 kb) that encodes six to eight proteins. Here, by exploring large publicly available metatranscriptomics datasets, we report the identification and genomic characterization of 47 novel viruses with genetic and evolutionary hallmarks of nucleorhabdoviruses. These viruses are associated with 45 distinct host plant species and were previously hidden in public database. Our findings significantly broaden the known host range of nucleorhabdoviruses, including the first nucleorhabdovirus associated with ferns and the first gammanucleorhabdoviruses linked to dicot hosts. Genetic divergence and evolutionary analyses suggest that all these novel viruses likely represent members of novel species. Phylogenetic reconstruction indicates that ten novel viruses are related to alphanucleorhabdoviruses, 25 to betanucleorhabdoviruses, eight to deltanucleorhabdoviruses and four to gammanucleorhabdoviruses. This study constitutes the final chapter in a trilogy chronicling a data mining expedition into the cryptic diversity of plant-associated rhabdoviruses, a journey that began with varicosaviruses and continued with cytorhabdoviruses. These new findings yield the most comprehensive phylogeny of nucleorhabdoviruses to date, significantly expanding our genomic understanding and illuminating the phylogenetic relationships and evolutionary dynamics of this virus group. Further, this work underscores the value of large-scale sequence data mining in advancing our understanding of the hidden world of plant rhabdoviruses.

microbiology↗

bioRxiv2025

Grapevine holobiome metatranscriptomics provides a glimpse into the wood mycovirome

Given the agronomic and economic importance of viticulture, grapevine has been shown to host the largest number of viruses among plants to date. Nevertheless, studies assessing the grapevine-associated holobiont remain scarce. In this context, the viral component of this ecological niche is understudied. In this work, through metatranscriptomics of wood samples from individual grapevines that were either healthy or exhibited symptoms of grapevine trunk disease from Argentina, we provide a glimpse into the wood linked virome. Virus discovery from high-throughput sequencing data resulted in the identification and reconstruction of 123 novel virus sequences. Genetic and phylogenetic insights suggest that these sequences correspond to 78 novel virus species. Structural and functional annotation of the viruses showed a great diversity of genomic organizations, with the presence of dsRNA, ssRNA(-) and ssRNA(+) viruses belonging to more than 15 virus families. A significant number of viruses (66%) were linked to the recently accepted families Botourmiaviridae, Narnaviridae and Mitoviridae. Some highly divergent viruses resembling narnaviruses, ophioviruses, deltaflexiviruses and bunyaviruses could be accommodated within new genera or even new virus families. The differential detection and variable RNA levels across samples suggest complex dynamics and prevalence patterns of those novel viruses. The viral profile described here provides a first insight into the multifaceted South American grapevine wood holobiont mycovirome.

microbiology↗

bioRxiv2024

RNA virus discovery sheds light on the virome of a major vineyard pest, the European grapevine moth (Lobesia botrana)

The European grapevine moth (Lobesia botrana) poses a significant threat to vineyards worldwide, causing extensive economic losses. While its ecological interactions and control strategies are well-studied, its associated viral diversity remains unexplored. Here, we employ high-throughput sequencing data mining to comprehensively characterize the L. botrana virome, revealing novel and diverse RNA viruses. We characterized four new viral members belonging to distinct families, with evolutionary cues of cypoviruses (Reoviridae), sobemo-like viruses (Solemoviridae), phasmaviruses (Phasmaviridae), and carmotetraviruses (Carmotetraviridae). Phylogenetic analysis of the cypoviruses places them within the genus in affinity with other moth viruses, suggesting a potential ecological roles and host range within Lepidoptera. The bi-segmented and highly divergent sobemo-like virus showed a distinctive evolutionary trajectory of its encoding proteins at the periphery of recently reported invertebrate Sobelivirales. Notably, the presence of a novel phasmavirus, typically associated with mosquitoes, expands the known host range and diversity of this family to moths. Furthermore, the identification of a carmotetravirus branching in the same cluster of providence virus, a lepidopteran virus which replicates in plants, raises questions regarding the biological significance of this moth virus and grapevine. We further explored viral sequences in several publicly available transcriptomic datasets of the moth, indicating potential prevalence across distinct conditions. These results underscore the existence of a complex virome within L. botrana and lays the foundation for future studies investigating the ecological roles, evolutionary dynamics, and potential biocontrol applications of these viruses on the L. botrana--vineyard ecosystem.

microbiology↗

bioRxiv2024

Insights into the RNA virome of the corn leafhopper Dalbulus maidis, a major emergent threat of Maize in Latin America

The maize leafhopper (Dalbulus maidis) is a significant threat to maize crops in tropical and subtropical regions, causing extensive economic losses. While its ecological interactions and control strategies are well-studied, its associated viral diversity remains largely unexplored. Here, we employ high-throughput sequencing data mining to comprehensively characterize the D. maidis RNA virome, revealing novel and diverse RNA viruses. We characterized six new viral members belonging to distinct families, with evolutionary cues of beny-like viruses (Benyviridae), bunya-like viruses (Bunyaviridae) iflaviruses (Iflaviridae), orthomyxo-like viruses (Orthomyxoviridae), and rhabdoviruses (Rhabdoviridae). Phylogenetic analysis of the iflaviruses places them within the genus Iflavirus in affinity with other leafhoppers-associated iflaviruses. The five-segmented and highly divergent orthomyxo-like virus showed a relationship with other insect associated orthomyxo-like viruses. The rhabdo virus is related with a leafhopper associated rhabdo-like virus. Furthermore, the beny-like virus belonged to a cluster of insect-associated beny-like viruses, while the bi-segmented bunya-like virus was related with other bi-segmented insect-associated bunya-like viruses. These results highlight the existence of a complex virome linked to D. maidis and paves the way for future studies investigating the ecological roles, evolutionary dynamics, and potential biocontrol applications of these viruses on the D. maidis--maize pathosystem.

microbiology↗

bioRxiv2023

Novel tri-segmented rhabdoviruses: A data mining expedition unveils the cryptic diversity of cytorhabdoviruses

Cytorhabdoviruses (genus Cytorhabdovirus, family Rhabdoviridae) are plant-infecting viruses with enveloped, bacilliform virions. Established members of the genus Cytorhabdovirus have unsegmented single-stranded negative-sense RNA genomes (ca. 10-16 kb) which encode four to ten proteins. Here, by exploring large publicly available metatranscriptomics datasets, we report the identification and genomic characterization of 93 novel viruses with genetic and evolutionary cues of cytorhabdoviruses. Strikingly, five unprecedented cytorhabdoviruses with tri-segmented genomes were also identified. This finding represents the first tri-segmented viruses in the family Rhabdoviridae. Interestingly, the nucleocapsid and polymerase were the only typical rhabdoviral proteins encoded by those tri-segmented viruses, whereas in three of them, a protein similar to the emaravirus (family Fimoviridae) silencing suppressor was found, while the other predicted proteins had no matches in any sequence databases. Genetic distance and evolutionary insights suggest that all these novel viruses may represent members of novel species. Phylogenetic analyses, of both novel and previously classified plant rhabdoviruses, provide compelling support for the division of the genus Cytorhabdovirus into three distinct genera. This proposed reclassification not only enhances our understanding of the evolutionary dynamics within this group of plant rhabdoviruses but also illuminates the remarkable genomic diversity they encompass. This study not only represents a significant expansion of genomics of cytorhabdoviruses that will enable future research on the evolutionary peculiarity of this genus, but also shows the plasticity in the rhabdovirus genome organization with the discovery of tri-segmented members with a unique evolutionary trajectory.

microbiology↗

bioRxiv2023

Two novel flavi-like viruses shed light on the plant infecting koshuviruses

The family Flaviviridae is composed of viruses with a positive sense single-stranded RNA genome and includes viruses that are important veterinary and human pathogens. Most members of the family are arthropod and vertebrate-infecting viruses but more recently flavi-like divergent viruses have been identified in marine invertebrate and vertebrate hosts. The striking discovery of gentian Kobu-sho-associated virus (GKaV) expanded the host range of flaviviruses to plants, which was complemented by a recently reported flavi-like virus in carrot, suggesting they could be grouped in a proposed Koshovirus genus. Here, we report the identification in transcriptomic datasets and characterization of two novel RNA viruses from the flowering plants Coptis teeta and Sonchus asper, which have genetic and evolutionary affinity to koshoviruses. These two new viruses are members of novel species which were dubbed Coptis flavi-like virus 1 (CopV1) and Sonchus flavi-like virus 1 (SonV1) and with a viral monopartite RNA of ca. 24 kb, likely have the longest genomes among plant-associated RNA viruses yet. Structural and functional annotations of the polyproteins of all koshoviruses resulted in the detection not only of the expected helicase and RNA-dependent RNA polymerase, but also several additional divergent domains such as AlkB oxigenase, Trypsin-like serine protease, methyltransferase, and envelope E1 flavi-like domains. Phylogenetic analysis groups in a monophyletic clade CopV1, SonV1, GKaV and the carrot flavi-like virus robustly supporting the recently proposed genus Koshovirus of plant infecting flavi-like viruses.

microbiology↗

bioRxiv2023

Expanding the repertoire of the plant infecting ophioviruses

Ophioviruses (genus Ophiovirus, family Aspiviridae) are plant-infecting viruses with non-enveloped, filamentous, naked nucleocapsid virions. Members of genus Ophiovirus have a segmented single-stranded negative-sense RNA genome (ca. 11.3-12.5 kb), encompassing three or four linear segments. These segments encode in total four to seven proteins in sense and antisense orientation, both in the viral and complementary strands. The genus Ophiovirus includes seven species with viruses infecting both monocots and dicots, mostly trees, shrubs and some ornamentals. From a genomic perspective, as of today, there are complete genomes available for only four species. Here, by exploring large metatranscriptomics publicly available datasets, we report the identification and molecular characterization of 33 novel viruses with genetic and evolutionary cues of ophioviruses. Genetic distance and evolutionary insights suggest that all the detected viruses could correspond to members of novel species, which expand ca. 4.5-fold the current diversity of ophioviruses. The detected viruses increase the tentative host range of ophioviruses for the first time to mosses, liverwort and ferns. In addition, viruses were linked to several Asteraceae, Orchidaceae and Poaceae crops/ornamental plants. Phylogenetic analyses showed a novel clade of mosses, liverworts and fern ophioviruses, characterized by long branches suggesting still plenty unsampled hidden diversity within the genus. This study represents a significant expansion of genomics of ophioviruses, opening the grounds to future works on the molecular and evolutionary peculiarity of this virus genus.

microbiology↗

bioRxiv2022

An unwanted association: the threat to papaya crops by a novel potexvirus in northwest Argentina

An emerging virus isolated from papaya (Carica papaya) crops in northwestern (NW) Argentina was sequenced and characterized using next-generation sequencing. The resulting genome is 6,667-nt long and encodes five open reading frames in an arrangement typical of other potexviruses. This virus appears to be a novel member within the genus Potexvirus. Blast analysis of RNA-dependent RNA polymerase (RdRp) and coat protein (CP) genes showed the highest amino acid sequence identity (67% and 71%, respectively) with pitaya virus X. Based on nucleotide sequence similarity and phylogenetic analysis, the name papaya virus X is proposed for this newly characterized potexvirus that was mechanically transmitted to papaya plants causing chlorotic patches and severe mosaic symptoms. RT-PCR based detection of papaya virus X (PapVX) revealed that it is widely present in papaya crops from NW Argentina. The prevalence of PapVX, which seems to be restricted to the NW region of Argentina, and the fact that it has only been detected in this region could be associated with a recent emergence or adaptation of this virus to papaya in NW Argentina.

microbiology↗

bioRxiv2022

A glimpse into the DNA virome of the unique "living fossil" Welwitschia mirabilis

Here, we report the identification and characterization of four novel DNA viruses associated with Welwitschia mirabilis. Complete circular virus-like sequences with affinity to Caulimoviridae members and geminiviruses were detected and characterized from Welwitschia mirabilis genomic data. The two newly Caulimoviridae-like viruses have been tentatively named as Welwitschia mirabilis virus 1 and 2 (WMV1-WMV2); whereas the two identified geminiviruses were named as Welwitschia mirabilis associated geminivirus A and B (WMaGVA-WMaGVB). Phylogenetic analysis suggests that WMV1-2 belong to a proposed genus of Caulimoviridae-infecting gymnosperms. WMaGVA-B are phylogenetically related with both mastreviruses and capulaviruses and likely represent a distinct evolutionary lineage within geminiviruses.

microbiology↗

bioRxiv2021

Exploring the tymovirids landscape through metatranscriptomics data

Tymovirales is an order of viruses with positive-sense, single-stranded RNA genomes that mostly infect plants, but also fungi and insects. The number of tymovirid sequences has been growing in the last few years with the extensive use of high-throughput sequencing platforms. Here we report the discovery of 31 novel tymovirid genomes associated with 27 different host plant species, which were hidden in public databases. These viral sequences were identified through a homology searches in more than 3,000 plant transcriptomes from the NCBI Sequence Read Archive (SRA) using known tymovirids sequences as query. Identification, assembly and curation of raw SRA reads resulted in 29 viral genome sequences with full-length coding regions, and two partial genomes. Highlights of the obtained sequences include viruses with unique and novel genome organizations among known tymovirids. Phylogenetic analysis showed that six of the novel viruses were related to alphaflexiviruses, seventeen to betaflexiviruses, two to deltaflexiviruses and six to tymoviruses. These findings resulted in the most complete phylogeny of tymovirids to date and shed new light on the phylogenetic relationships and evolutionary landscape of this group of viruses. Furthermore, this study illustrates the complexity and diversity of tymovirids genomes and demonstrates that analyzing SRA public data provides an invaluable tool to accelerate virus discovery and refine virus taxonomy.

microbiology↗

bioRxiv2021

Biological, Molecular And Phiysiological Characterization Of Four Soybean mosaic virus Isolates Present In Argentine Soybean Crops

Soybean mosaic virus (SMV) causes systemic infections in soybean plants, leading to chlorotic mosaic and producing significant yield losses. The virus is widely distributed in all soybean production areas in the world. In Argentina, three geographical isolates were identified: Marcos Juarez (MJ), Manfredi (M), and North Western Argentina (NOA), and another isolate named "Planta Vinosa" (PV), which causes severe necrosis symptoms in some cultivars. Here, the biological, molecular and physiological characterization of these isolates was performed for the first time. Three of the four isolates showed a low genetic divergence in the evaluated genes (P1, CI and CP). Although SMV-NOA and SMV-PV had high homology at the sequence level, they showed wide differences in pathogenicity, seed mottling and the ability of transmission by seeds or aphids, as well as in physiological effects. SMV-NOA caused early alterations (before symptom appearance, BS) in {Phi}PSII and MDA content in leaves with respect to the other isolates. After the appearance of macroscopic symptoms (late symptoms, LS), SMV-M caused a significant increase in the content of MDA, total soluble sugars, and starch with respect to the other isolates. Thus, early alterations of {Phi}PSII and soluble sugars might have an impact on late viral symptoms. Likewise, SMV-MJ developed more severe symptoms in the susceptible Davis cultivar than in DM 4800. Therefore, our results show differences in genome, biological properties and physiological effects among SMV isolates as well as different interactions of SMV-MJ with two soybean cultivars.

plant biology↗

bioRxiv2020

Molecular characterization of a novel cytorhabdovirus with a unique genomic organization infecting yerba mate (Ilex paraguariensis) in Argentina

The genome of a novel rhabdovirus was detected in yerba mate (Ilex paraguariensis St. Hil.). The newly identified virus, tentatively named yerba mate virus A (YmVA), has a genome of 14,961 nucleotides. Notably, eight open reading frames were identified in the antigenomic orientation of the negative-sense, single-stranded viral RNA, including two novel accessory genes, in the order 3-N-P-3-4-M-G-L-8-5. Sequence identity of the encoded proteins as well as phylogenetic analysis suggest that YmVA is a new member of the genus Cytorhabdovirus, family Rhabdoviridae. YmVA unique genomic organization and phylogenetic relationships indicate that this virus likely represents a distinct evolutionary lineage within the cytorhabdoviruses.

microbiology↗

bioRxiv2019

Phylodynamics of sunflower chlorotic mottle virus, a re-emerging pathosystem

Distribution and epidemiological patterns of sunflower chlorotic mottle virus (SCMoV) in sunflower (Helianthus annuus L.) growing areas in Argentina were studied from 2006 to 2017. The virus was detected exclusively in the Pampas region (Entre Rios, Santa Fe, Cordoba, La Pampa and Buenos Aires provinces). Phylodynamic analyses performed using the coat protein gene of SCMoV isolates from sunflower and weeds dated the most recent common ancestor (MRCA) back to 1887 (HPD95% = 1572-1971), which coincides with the dates of sunflower introduction in Argentina. The MRCA was located in the south of Buenos Aires province and was associated with sunflower host (posterior probability for the ancestral host, ppah= 0.98). The Bayesian phylodynamic analyses revealed the dispersal patterns of SCMoV, suggesting a link between natural host diversity, crop displacement by human activities and virus spread.

plant biology↗

bioRxiv2019

Redefining the medicago sativa alphapartitivirus genome sequences

In alfalfa samples analyzed by hightroughput sequencing, four de novo assembled contigs encoding gene products showing identities to alphapartitiviruses proteins were found based on BlastX analysis. The predicted amino acid (aa) sequences of two contigs presented 99-100% identity to the RNA-dependent RNA polymerase (RdRp) and the capsid protein (CP) of the recently reported medicago sativa alphapartitivirus 1 (MsAPV1). In addition, the remaining two contigs shared only 56% (CP) and 70% (RdRp) pairwise aa identity with the proteins of MsAPV1, suggesting that these samples presented also a novel Alphapartitivirus species. Further analyses based on complete genome segments termini and the presence/absence of alphapartitivirus RNA in several samples and public alfalfa RNA datasets corroborated the identification of two different alphapartitivirus members. Our results also likely indicate that the reported MsAPV1 genome was previously reconstructed with genome segments of two different alphapartitiviruses. Overall, we not only revisited the MsAPV1 genome sequence but also report a new tentative alphapartitivirus species, which we propose the name medicago sativa alphapartitivirus 2. In addition, the RT-PCR detection of both MsAPV1 and MsAPV2 in several alfalfa cultivars suggests a broad distribution of both viruses.

microbiology↗