The complete sequences of two divergent variants of the rhabdovirus raspberry vein chlorosis virus and the design of improved primers for virus detection

Jones, Sue; McGavin, W.J.; MacFarlane, Stuart A.

doi:10.1016/j.virusres.2019.03.004

Cited by 12 publications

(9 citation statements)

References 13 publications

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“…To further investigate the phylogenetic relationship of cytorhabdoviruses, we aligned 28 RdRP amino acid sequences (2374 aa in length, including gaps) from reference cytorhabdoviruses available in Genbank, including two sequences derived from transcriptomes of B. tabaci ( Table S2 ). The phylogenetic analysis shows that cytorhabdoviruses cluster in monophyletic groups according to its potential vector: aphid [ 35 , 36 , 37 , 38 , 39 ], planthopper [ 40 , 41 , 42 , 43 , 44 , 45 ], leafhopper [ 46 ], whitefly, and an undescribed vector ( Figure 6 ). As previously suggested [ 7 , 47 , 48 ], BaCV isolates and PpVE were closely related to B. tabaci TSA 2 (AKC57270.1), confirming that these viruses belong to the species Papaya cytorhabdovirus .…”

Section: Resultsmentioning

confidence: 99%

Transmission of the Bean-Associated Cytorhabdovirus by the Whitefly Bemisia tabaci MEAM1

Pinheiro-Lima

Pereira–Carvalho

Alves-Freitas

et al. 2020

Viruses

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The knowledge of genomic data of new plant viruses is increasing exponentially; however, some aspects of their biology, such as vectors and host range, remain mostly unknown. This information is crucial for the understanding of virus–plant interactions, control strategies, and mechanisms to prevent outbreaks. Typically, rhabdoviruses infect monocot and dicot plants and are vectored in nature by hemipteran sap-sucking insects, including aphids, leafhoppers, and planthoppers. However, several strains of a potentially whitefly-transmitted virus, papaya cytorhabdovirus, were recently described: (i) bean-associated cytorhabdovirus (BaCV) in Brazil, (ii) papaya virus E (PpVE) in Ecuador, and (iii) citrus-associated rhabdovirus (CiaRV) in China. Here, we examine the potential of the Bemisia tabaci Middle East-Asia Minor 1 (MEAM1) to transmit BaCV, its morphological and cytopathological characteristics, and assess the incidence of BaCV across bean producing areas in Brazil. Our results show that BaCV is efficiently transmitted, in experimental conditions, by B. tabaci MEAM1 to bean cultivars, and with lower efficiency to cowpea and soybean. Moreover, we detected BaCV RNA in viruliferous whiteflies but we were unable to visualize viral particles or viroplasm in the whitefly tissues. BaCV could not be singly isolated for pathogenicity tests, identification of the induced symptoms, and the transmission assay. BaCV was detected in five out of the seven states in Brazil included in our study, suggesting that it is widely distributed throughout bean producing areas in the country. This is the first report of a whitefly-transmitted rhabdovirus.

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Section: Resultsmentioning

confidence: 99%

Transmission of the Bean-Associated Cytorhabdovirus by the Whitefly Bemisia tabaci MEAM1

Pinheiro-Lima

Pereira–Carvalho

Alves-Freitas

et al. 2020

Viruses

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“…Two of the cytorhabdoviruses, AChV1 and SuSV1, whose genomes were only partially assembled, clustered phylogenetically in a monophyletic clade with ADV, ChYDaV, RVCV and SCV, all the viruses that contain a P6 accessory ORF between the G and L genes [ 66 , 67 , 68 , 69 ]. Given this clustering, it is likely that AChV1 and SuSV1 will have a similar genomic organization.…”

Section: Discussionmentioning

confidence: 99%

Illuminating the Plant Rhabdovirus Landscape through Metatranscriptomics Data

Bejerman

Dietzgen

Debat

2021

Viruses

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Rhabdoviruses infect a large number of plant species and cause significant crop diseases. They have a negative-sense, single-stranded unsegmented or bisegmented RNA genome. The number of plant-associated rhabdovirid sequences has grown in the last few years in concert with the extensive use of high-throughput sequencing platforms. Here, we report the discovery of 27 novel rhabdovirus genomes associated with 25 different host plant species and one insect, which were hidden in public databases. These viral sequences were identified through homology searches in more than 3000 plant and insect transcriptomes from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) using known plant rhabdovirus sequences as the query. The identification, assembly and curation of raw SRA reads resulted in sixteen viral genome sequences with full-length coding regions and ten partial genomes. Highlights of the obtained sequences include viruses with unique and novel genome organizations among known plant rhabdoviruses. Phylogenetic analysis showed that thirteen of the novel viruses were related to cytorhabdoviruses, one to alphanucleorhabdoviruses, five to betanucleorhabdoviruses, one to dichorhaviruses and seven to varicosaviruses. These findings resulted in the most complete phylogeny of plant rhabdoviruses to date and shed new light on the phylogenetic relationships and evolutionary landscape of this group of plant viruses. Furthermore, this study provided additional evidence for the complexity and diversity of plant rhabdovirus genomes and demonstrated that analyzing SRA public data provides an invaluable tool to accelerate virus discovery, gain evolutionary insights and refine virus taxonomy.

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“…Two of the cytorhabdoviruses, AChV1 and SuSV1, whose genomes were only partially assembled, clustered phylogenetically in a monophyletic clade with ADV, ChYDaV, RVCV and SCV, all viruses that contain a P6 accessory ORF between G and L genes (Bejerman et al, 2015; Jones et al, 2019; Koloniuk et al, 2018; Liu et al, 2021). Given this clustering, it is likely that AChV1 and SuSV1 will have a similar genomic organization.…”

Section: Discussionmentioning

confidence: 99%

Illuminating the plant rhabdovirus landscape through metatranscriptomics data

Bejerman

Dietzgen

Debat

2021

Preprint

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Rhabdoviruses infect a large number of plant species and cause significant crop diseases. They have a negative-sense, single-stranded unsegmented or bisegmented RNA genome. The number of plant-associated rhabdovirid sequences has grown in the last few years in concert with the extensive use of high-throughput sequencing platforms. Here we report the discovery of 26 novel rhabdovirus genomes associated with 24 different host plant species and one insect, which were hidden in public databases. These viral sequences were identified through homology searches in more than 3,000 plant and insect transcriptomes from the NCBI Sequence Read Archive (SRA) using known plant rhabdovirus sequences as query. Identification, assembly and curation of raw SRA reads resulted in sixteen viral genome sequences with full-length coding regions and ten partial genomes. Highlights of the obtained sequences include viruses with unique and novel genome organizations among known plant rhabdoviruses. Phylogenetic analysis showed that thirteen of the novel viruses were related to cytorhabdoviruses, one to alphanucleorhabdoviruses, five to betanucleorhabdoviruses, one to dichorhaviruses, and six to varicosaviruses. These findings resulted in the most complete phylogeny of plant rhabdoviruses to date and shed new light on the phylogenetic relationships and evolutionary landscape of this group of plant viruses. Furthermore, this study provides additional evidence for the complexity and diversity of plant rhabdovirus genomes and demonstrates that analyzing SRA public data provides an invaluable tool to accelerate virus discovery, gain evolutionary insights and refine virus taxonomy.

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The complete sequences of two divergent variants of the rhabdovirus raspberry vein chlorosis virus and the design of improved primers for virus detection

Cited by 12 publications

References 13 publications

Transmission of the Bean-Associated Cytorhabdovirus by the Whitefly Bemisia tabaci MEAM1

Transmission of the Bean-Associated Cytorhabdovirus by the Whitefly Bemisia tabaci MEAM1

Illuminating the Plant Rhabdovirus Landscape through Metatranscriptomics Data

Illuminating the plant rhabdovirus landscape through metatranscriptomics data

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