Complete genome sequence of patchouli chlorosis-associated cytorhabdovirus, a new cytorhabdovirus infecting patchouli plants in Brazil

Kauffmann, C. M.; Boari, A. de J.; Silva, João Marcos Fagundes; Blawid, Rosana; Nagata, Tatsuya

doi:10.1007/s00705-022-05594-5

Cited by 6 publications

(7 citation statements)

References 9 publications

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“…In the last few years, several novel cytorhabdoviruses which do not induce visible disease symptoms have been reported in HTS studies (Bejerman et al, 2020; Belete et al, 2023; Bolus et al, 2021; Kauffmann et al, 2022; Kopke et al, 2023; Lee et al, 2022; Liu et al, 2021; Medberry et al, 2022; Petrzik et al, 2022; Safarova et al, 2022; Wu et al, 2023). Moreover, many novel cytorhabdoviruses were identified when metatranscriptomic data publicly available at the Transcriptome Shotgun Assembly (TSA) sequence databases was mined (Bejerman et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

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

Bejerman,

Dietzgen,

Debat

2023

Preprint

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Cytorhabdoviruses (genusCytorhabdovirus, familyRhabdoviridae) are plant-infecting viruses with enveloped, bacilliform virions. Established members of the genusCytorhabdovirushave 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 familyRhabdoviridae. 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 (familyFimoviridae) 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 genusCytorhabdovirusinto 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.

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Section: Discussionmentioning

confidence: 99%

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

Bejerman,

Dietzgen,

Debat

2023

Preprint

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“…In the last few years, several novel cytorhabdoviruses that do not induce visible disease symptoms have been reported in HTS studies [91][92][93][94][95][96][97][98][99][100][101]. Moreover, many novel cytorhabdoviruses were identified when metatranscriptomic data publicly available at the Transcriptome Shotgun Assembly (TSA) sequence databases was mined [9].…”

Section: Discovery Of Novel Cytorhabdo-like Viruses Expands Their Div...mentioning

confidence: 99%

“…The exception was one virus associated with the host Pogostemon, known as "patchouly chlorosis-associated cytorhabdovirus", which was found to have a truncated G gene. It was speculated that this truncation may be linked to the fact that patchouli plants are primarily propagated vegetatively and may not require a functional G protein [94]. One distinctive feature of alphacytorhabdoviruses is the presence of an overlapping ORF within the P-encoding ORF, named P' in most of their proposed members (65/71).…”

Section: Proposed New Genus Alphacytorhabdovirusmentioning

confidence: 99%

Novel Tri-Segmented Rhabdoviruses: A Data Mining Expedition Unveils the Cryptic Diversity of Cytorhabdoviruses

Bejerman,

Dietzgen,

Debat

2023

Viruses

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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 viruses with tri-segmented genomes were also identified. This finding represents the first tri-segmented viruses in the family Rhabdoviridae, and they should be classified in a novel genus within this family for which we suggest the name “Trirhavirus”. 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 the 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.

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“…Infections caused by viruses can lead to a decrease in plant development and oil content in patchouli plants (Sugimura et al., 1995). In the world, patchouli plants have been reported naturally infected by viruses belonging to the genera Cytorhabdovirus , Fabavirus , Potyvirus , Potexvirus and Necrovirus (Kauffmann et al., 2022; Kitajima, 2020; Sastry et al., 2019).…”

Section: Figurementioning

confidence: 99%

“…In Brazil, patchouli plants have been naturally identified infected with the potexvirus patchouli virus X (PatVX), the alphanecrovirus tobacco necrosis virus (TNV), the tobravirus pepper ringspot virus (PepRSV) and a cytorhabdovirus and nucleorhabdovirus not completely characterized (Kitajima, 2020). Recently, patchouli plants showing symptoms of vein chlorosis and chlorosis spots were found to be infected with a cytorhabdovirus tentatively named patchouli chlorosis‐associated cytorhabdovirus (PCaCV) (Kauffmann et al., 2022).…”

Section: Figurementioning

confidence: 99%

Biological and molecular characterization of bidens mosaic virus infecting patchouli (Pogostemon cablin) in Brazil

Martines,

Favara,

Marubayashi

et al. 2023

Journal of Phytopathology

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Six patchouli (Pogostemon cablin Benth.) plants showing symptoms of viral infection were found in Brazil. Transmission electron microscopy revealed flexuous particles and characteristic pinwheel‐shaped cytoplasmic inclusions of potyvirus in sap and cells of symptomatic leaves. Potyvirus infection was confirmed through RT‐PCR, using universal primers followed by nucleotide sequencing. The obtained sequences, comprising part of the CP gene and the 3′ non‐translated region, showed 97.71%–97.87% identity with an isolate of bidens mosaic virus (BiMV). The nucleotide sequences of the CP, HC‐Pro and CI genes of BiMV isolates from patchouli plants were obtained through RT‐PCR with specific primers followed by nucleotide sequencing. The obtained sequences showed 95.78%–97.1% identities with BiMV isolates from Brazil. One BiMV isolate from a patchouli infected plant was sap‐transmitted to different plant species. Chenopodium amaranticolor exhibited local lesions, Bidens pilosa developed leaf mosaic, and Nicotiana benthamiana exhibited chlorosis and stunting. The BiMV isolate was transmitted from infected patchouli plant to B. pilosa using Myzus persicae aphids. This is the first confirmation of patchouli infected with BiMV in Brazil. Further studies are necessary to assess the incidence of this potyvirus in commercial patchouli crops, as well as the damage caused to plant development and the quantity and quality of essential oils produced.

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Complete genome sequence of patchouli chlorosis-associated cytorhabdovirus, a new cytorhabdovirus infecting patchouli plants in Brazil

Cited by 6 publications

References 9 publications

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

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

Novel Tri-Segmented Rhabdoviruses: A Data Mining Expedition Unveils the Cryptic Diversity of Cytorhabdoviruses

Biological and molecular characterization of bidens mosaic virus infecting patchouli (Pogostemon cablin) in Brazil

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