Identification of novel RNA viruses in alfalfa ( Medicago sativa ): an Alphapartitivirus , a Deltapartitivirus, and a Marafivirus

Kim, Hyein; Park, Dongbin; Hahn, Yoonsoo

doi:10.1016/j.gene.2017.09.069

Cited by 39 publications

(55 citation statements)

References 34 publications

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“…Upon the pathogens infection, bioactive JAs promote direct interaction between COI1 and JAZ proteins and then trigger the SCF-COI1 complex, resulting in poly-ubiquitination and degradation of the JAZ proteins. Ultimately, a variety of transcription factors could be activated for the expression of the JA-responsive genes [75]. Besides, MYC2 is a bHLH (basic helix-loop-helix) transcription factor and a positive regulator of JA responses [76].…”

Section: Discussionmentioning

confidence: 99%

Transcriptome analysis of Nicotiana benthamiana infected by Tobacco curly shoot virus

et al. 2018

Virol J

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BackgroundTobacco curly shoot virus (TbCSV) is a monopartite begomovirus associated with betasatellite (Tobacco curly shoot betasatellite, TbCSB), which causes serious leaf curl disease on tomato and tobacco in China. It is interesting that TbCSV induced severe upward leaf curling in Nicotiana benthamiana, but in the presence of TbCSB, symptoms changed to be downward leaf curling. However, the mechanism of interactions between viral pathogenicity, host defense, viral-betasatellite interactions and virus-host interactions remains unclear.MethodsIn this study, RNA-seq was used to analyze differentially expressed genes (DEGs) in N. benthamiana plants infected by TbCSV (Y35A) and TbCSV together with TbCSB (Y35AB) respectively.ResultsThrough mapping to N. benthamiana reference genome, 59,814 unigenes were identified. Transcriptome analysis revealed that a total of 4081 and 3196 DEGs were identified in Y35AB vs CK (control check) and Y35A vs CK, respectively. Both GO and KEGG analyses were conducted to classify the DEGs. Ten of the top 15 GO terms were enriched in both DEGs of Y35AB vs CK and Y35A vs CK, and these enriched GO terms mainly classified into three categories including biological process, cellular component and molecular function. KEGG pathway analysis indicated that 118 and 111 pathways were identified in Y35AB vs CK and Y35A vs CK, respectively, of which nine and six pathways were significantly enriched. Three major pathways in Y35AB vs CK involved in metabolic pathways, carbon metabolism and photosynthesis, while those in Y35A vs CK were related to Ribosome, Glyoxylate and dicarboxylate metabolism and DNA replication. We observed that 8 PR genes were significantly up-regulated and 44 LRR-RLK genes were significantly differentially expressed in Y35A treatment or in Y35AB treatment. In addition, 7 and 13 genes were identified to be significantly changed in biosynthesis and signal transduction pathway of brassinosteroid (BR) and jasmonic acid (JA) respectively.ConclusionsThese results presented here would be particularly useful to further elucidate the response of the host plant against virus infection.Electronic supplementary materialThe online version of this article (10.1186/s12985-018-1044-1) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Transcriptome analysis of Nicotiana benthamiana infected by Tobacco curly shoot virus

et al. 2018

Virol J

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“…On the nucleotide level, AVF has 78% identity with the newly identified and proposed alfalfa marafivirus MsMV1 [11], (BLASTN query coverage 80%, E-value = 0.0, accession № MF443260.1). The next closest species from the genus Marafivirus , per PASC tool [16], is oat blue dwarf virus isolate OBDV2r (50.2% identities, accession № GU396990), a member of the genus Marafivirus .…”

Section: Resultsmentioning

confidence: 99%

“…The first proposed species of the genus Marafivirus in alfalfa, MsMV1, was described only recently [11] and before that no members of this genus were identified in alfalfa. Although AVF is most closely related to MsMV1, it does represent a new species, based on the current demarcation criteria in the genus Marafivirus [8].…”

Section: Discussionmentioning

confidence: 99%

“…al. [11] for identification of MsMV1, originated from China and employed alfalfa standard varieties Maverick (FDC1) and CUF101 (FDC9) introduced to China from the United States.…”

Section: Discussionmentioning

confidence: 99%

“…Until very recently, marafiviruses were not reported to infect alfalfa. In 2018, the nucleotide sequence of the proposed Medicago sativa marafivirus 1 (MsMV1) was deduced from alfalfa transcriptomic data by Kim et al, [11]. These alfalfa transcriptomic data were previously deposited to NCBI and published by a different group of authors [12].…”

Section: Introductionmentioning

confidence: 99%

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Characterization of alfalfa virus F, a new member of the genus Marafivirus

et al. 2018

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Viral infections of alfalfa are widespread in major cultivation areas and their impact on alfalfa production may be underestimated. A new viral species, provisionally named alfalfa virus F (AVF), was identified using a virion-associated nucleic acid (VANA) metagenomics-based approach in alfalfa (Medicago sativa L.) samples collected in Southern France. The nucleotide sequence of the viral genome was determined by de-novo assembly of VANA reads and by 5’/3’ RACE with viral RNA extracted from enriched viral particles or with total RNA, respectively. The virus shares the greatest degree of overall sequence identity (~78%) with Medicago sativa marafivirus 1 (MsMV1) recently deduced from alfalfa transcriptomic data. The tentative nucleotide sequence of the AVF coat protein shares ~83% identity with the corresponding region of MsMV1. A sequence search of the predicted single large ORF encoding a polyprotein of 235kDa in the Pfam database resulted in identification of five domains, characteristic of the genus Marafivirus, family Tymoviridae. The AVF genome also contains a conserved “marafibox”, a 16-nt consensus sequence present in all known marafiviruses. Phylogenetic analysis of the complete nucleotide sequences of AVF and other viruses of the family Tymoviridae grouped AVF in the same cluster with MsMV1. In addition to 5’ and 3’ terminal extensions, the identity of the virus was confirmed by RT-PCRs with primers derived from VANA-contigs, transmission electron microscopy with virus-infected tissues and transient expression of the viral coat protein gene using a heterologous virus-based vector. Based on the criteria demarcating species in the genus Marafivirus that include overall sequence identity less than 80% and coat protein identity less than 90%, we propose that AVF represents a distinct viral species in the genus Marafivirus, family Tymoviridae.

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