Molecular and biological properties of two putative new cytorhabdoviruses infecting <i>Trifolium pratense</i>

Fráňová, Jana; Sarkisová, Tatiana; Jakešová, Hana; Koloniuk, Igor

doi:10.1111/ppa.13065

Cited by 14 publications

(10 citation statements)

References 36 publications

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“…At least one transmembrane domain was identified in each P’ protein predicted in the genomes of a group of cytorhabdoviruses discovered in this study, consistent with a previous analysis of other cytorhabdoviruses which also identified at least one transmembrane domain in every P’ protein (Franova et al, 2019). Interestingly, this overprinted accessory protein is encoded by every cytorhabdovirus that appears to be aphid-transmitted.…”

Section: Discussionsupporting

confidence: 91%

“…At least one transmembrane domain has been predicted in every cytorhabdovirus with an accessory P6 ORF. Transmembrane domains were also predicted in the accessory ORF between G and L genes of other cytorhabdoviruses (Ding et al, 2019; Franova et al, 2019; Yang et al, 2017). Thus, the protein encoded by this small ORF may have membrane-associated functions similar to viroporins in vertebrate rhabdoviruses (Joubert et al 2014).…”

Section: Discussionmentioning

confidence: 99%

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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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Section: Discussionsupporting

confidence: 91%

Section: Discussionmentioning

confidence: 99%

Illuminating the plant rhabdovirus landscape through metatranscriptomics data

Bejerman

Dietzgen

Debat

2021

Preprint

View full text Add to dashboard Cite

show abstract

“…At least one transmembrane domain was identified in each P′ protein predicted in the genomes of a group of cytorhabdoviruses discovered in this study, consistent with a previous analysis of other cytorhabdoviruses, which also identified at least one transmembrane domain in every P′ protein [ 65 ]. Interestingly, this overprinted accessory protein is encoded by every cytorhabdovirus that appears to be aphid-transmitted.…”

Section: Discussionsupporting

confidence: 91%

Illuminating the Plant Rhabdovirus Landscape through Metatranscriptomics Data

Bejerman

Dietzgen

Debat

2021

Viruses

View full text Add to dashboard Cite

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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“…The StrV-1-1/2017(B) isolate is maintained to date on cuttings of P. floridana in a greenhouse as recently described [41]. The freeze-dried leaves were deposited in UPOC collection funded by the Ministry of Agriculture of the Czech Republic as a part of the National Program of Genepool Conservation of Microorganisms and Small Animals of Economic Importance () under accession number UPOC-VIR-044.…”

Section: Resultsmentioning

confidence: 99%

Molecular and Biological Characterization of a New Strawberry Cytorhabdovirus

Fráňová

Přibylová

Koloniuk

2019

Viruses

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Virus diseases of strawberry present several complex problems. More than 25 viruses have been described in the genus Fragaria thus far. Here, we describe a novel rhabdovirus, tentatively named strawberry virus 1 (StrV-1), that infects F. ananassa and F. vesca plants. Genomic sequences of three distinct StrV-1 genotypes co-infecting a single F. ananassa host were obtained using combined Illumina and Ion Proton high-throughput sequencing. StrV-1 was transmitted to herbaceous plants via Aphis fabae and A. ruborum, further mechanically transmitted to Nicotiana occidentalis 37B and sub-inoculated to N. benthamiana, N. benthamiana DCL2/4i, N. occidentalis 37B, and Physalis floridana plants. Irregular chlorotic sectors on leaf blades and the multiplication of calyx leaves seem to be the diagnostic symptoms for StrV-1 on indexed F. vesca clones. StrV-1 was detected in asymptomatic grafted plants and in 49 out of 159 field strawberry samples via RT-PCR followed by Sanger sequencing. The bacilliform shape of the virions, which have a cytoplasm-limited distribution, their size, and phylogenetic relationships support the assignment of StrV-1 to a distinct species of the genus Cytorhabdovirus. Acyrthosiphon malvae, A. fabae, and A. ruborum were shown to transmit StrV-1 under experimental conditions.

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Molecular and biological properties of two putative new cytorhabdoviruses infecting Trifolium pratense

Cited by 14 publications

References 36 publications

Illuminating the plant rhabdovirus landscape through metatranscriptomics data

Illuminating the plant rhabdovirus landscape through metatranscriptomics data

Illuminating the Plant Rhabdovirus Landscape through Metatranscriptomics Data

Molecular and Biological Characterization of a New Strawberry Cytorhabdovirus

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