Near-complete genome sequence and seed transmission evaluation of <i>Physalis rugose mosaic virus</i> from southern Brazil

Savi, Amanda; Gorayeb, Eduardo Silva; Nascimento, Samara Campos; Faria, Caroline Bolson de; Fajardo, Thor Vinícius Martins; Nhani Junior, Antônio; Bogo, Amauri; Casa, Ricardo Trezzi; Silva, Fabio Nascimento da

doi:10.1590/0103-8478cr20200702

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CROP PROTECTION • Cienc. Rural 51 (4) • 2021 • https://doi.org/10.1590/0103-8478cr20200702 copy

Near-complete genome sequence and seed transmission evaluation of Physalis rugose mosaic virus from southern Brazil

Sequência do genoma completo e avaliação da transmissão por sementes do Physalis rugose mosaic virus no sul do Brasil

Authorship SCIMAGO INSTITUTIONS RANKINGS

ABSTRACT:

Physalis rugose mosaic virus (PhyRMV) causes severe damage to Physalis peruviana L., affecting vegetative parameters, fruit quantity and quality. The aim of this study was to perform a molecular characterization of PhyRMV associated with P. peruviana from commercial fields in the municipality of Lages, Santa Catarina State, Southern Brazil, and to evaluate its transmission by seeds. Plants displaying mosaic, dwarfism, and leaf malformation symptoms were collected from P. peruviana. Double-stranded RNA was extracted and submitted to cDNA library synthesis and high-throughput sequencing (HTS). For the virus transmission assay, seeds from PhyRMV-infected plants were used, and viral infection in seedlings was verified using symptomatic and molecular diagnosis. PhyRMV RNA has 4162 nucleotides (nts) and a genomic organization similar to that of other sobemoviruses and shares 97% nt identity with the previously characterized PhyRMV Piracicaba isolate. Results indicated the unlikely transmission of PhyRMV by physalis seeds.

Key words:
characterization; PhyRMV; Sobemovirus

Authorship

Amanda Savi

Programa de Pós-Graduação em Produção Vegetal, Universidade do Estado de Santa Catarina (UDESC), 88520-000, Lages, SC, Brasil. Universidade do Estado de Santa Catarina (UDESC)BrazilLages, SC, BrazilPrograma de Pós-Graduação em Produção Vegetal, Universidade do Estado de Santa Catarina (UDESC), 88520-000, Lages, SC, Brasil.

https://orcid.org/0000-0001-9628-3305

Eduardo Silva Gorayeb

https://orcid.org/0000-0001-8594-6070

Samara Campos Nascimento

https://orcid.org/0000-0001-7329-2540

Caroline Bolson de Faria

https://orcid.org/0000-0001-8916-7824

Thor Vinícius Martins Fajardo

Embrapa Uva e Vinho, Bento Gonçalves, RS, Brasil.Embrapa Uva e VinhoBrazilBento Gonçalves, RS, BrazilEmbrapa Uva e Vinho, Bento Gonçalves, RS, Brasil.

https://orcid.org/0000-0001-6621-5192

Antônio Nhani Junior

Embrapa Informática Agropecuária, Campinas, SP, Brasil.Embrapa Informática AgropecuáriaBrazilCampinas, SP, BrazilEmbrapa Informática Agropecuária, Campinas, SP, Brasil.

https://orcid.org/0000-0002-3096-4009

Amauri Bogo

https://orcid.org/0000-0002-2766-2042

Ricardo Trezzi Casa

https://orcid.org/0000-0003-3563-8525

Fabio Nascimento da Silva ^*E-mail: fabio.silva@udesc.br. *Corresponding author.

https://orcid.org/0000-0002-6187-5033

E-mail: fabio.silva@udesc.br. ^*Corresponding author.

DECLARATION OF CONFLICTS OF INTERESTS

The authors declare that there is no conflict of interest. The funding entities had no influence on the study design; nor in the collection, analysis or interpretation of the data; in the writing of the manuscript, nor in the decision to publish the results.

AUTHORS’ CONTRIBUTIONS

FNS, ESG and AS conceived and designed experiments. EGS, AS, SCN, and CBF performed the experiments; TVMF performed double-strand RNA extraction; ANJ, FNS and AS performed sequence analysis and bioinformatics; FNS, RTC and AB supervised and coordinated the greenhouse experiments and data analysis; FNS and AS prepared the draft of the manuscript. All authors critically revised the manuscript and approved of the final version.

SCIMAGO INSTITUTIONS RANKINGS

Embrapa Uva e Vinho, Bento Gonçalves, RS, Brasil.Embrapa Uva e VinhoBrazilBento Gonçalves, RS, BrazilEmbrapa Uva e Vinho, Bento Gonçalves, RS, Brasil.

Embrapa Informática Agropecuária, Campinas, SP, Brasil.Embrapa Informática AgropecuáriaBrazilCampinas, SP, BrazilEmbrapa Informática Agropecuária, Campinas, SP, Brasil.

Figures | Tables

Figures (2)
Tables (1)

Thumbnail

Figure 1
(A) Physalis peruviana infected by physalis rugose mosaic virus (PhyRMV) showing mosaic, malformation and blister symptoms (left), and dwarfism (right). (B) Electrophoretic analyses of the PCR products for the detection of PhyRMV from original samples collected. MM: 1 kb molecular ladder; C-: not-infected P. peruviana (negative control); C+: PhyRMV-infected P. peruviana (positive control); 1: original dsRNA extracted from P. peruviana leaves. (C) Phylogenetic relationship based on the alignment of the PhyRMV near-complete genome and other members of the genus Sobemovirus. General Time Reversible (GTR) model with gamma distribution (G) was used and bootstrap support of 8,000 replications. The alignment for phylogeny was performed with the MUSCLE tool available in the MEGA X program. The numbers on the branches indicate the bootstrap values. Members of the Sobemovirus genus are: artemisia virus A (ArtVA; JN620802), blueberry shoestring virus (BSSV; LC081344), cocksfoot mottle virus (CfMV; L40905), cymbidium chlorotic mosaic virus (CyCMV; LC019764), imperata virus (IYMV; AM990928), lucerne transient streak virus (LTSV; JQ782213), papaya lethal yellowing virus (PLYV; JX123318), rice yellow mottle virus (RYMV; MG599280), rottboellia yellow mottle virus (RoMoV; KC577469), ryegrass mottle virus (RGMoV; AB040446), sesbania mosaic virus (SeMV; AY004291), solanum nodiflorum mottle virus (SNMoV; KC577470), southern bean mosaic virus (SBMV; AF055887), southern cowpea mosaic virus (SCPMV; M23021), sowbane mosaic virus (SoMV; AM940437), soybean yellow common mosaic virus (SYCMV; JF495127), subterranean clover mottle virus (SCMoV; AF208001), turnip rosette virus (TRoV; AY177608), velvet tobacco mottle virus (VTMoV; HM754263), and physalis rugose mosaic virus (PhyRMV; MK681145). The arrow indicates the isolate characterized in this study.

Thumbnail

Figure 2
Sequences comparisons between genomes of physalis rugose mosaic virus (PhyRMV) Brazilian isolates. Map of nucleotide and amino acid substitutions in PhyRMV genome. Nucleotide and amino acids substitution are indicated following the order: isolated characterized in this study/Piracicaba isolate. Red lines indicate nonsynonymous nucleotide substitutions (dN) and grey lines indicate synonymous nucleotide substitutions (dS). Nucleotide positions are numbered according to sequence of the PhyRMV characterized in this study (MN782300).

Thumbnail

Table 1
Transmission rate of seeds to Physalis peruviana seedlings.

Figure 1 (A) Physalis peruviana infected by physalis rugose mosaic virus (PhyRMV) showing mosaic, malformation and blister symptoms (left), and dwarfism (right). (B) Electrophoretic analyses of the PCR products for the detection of PhyRMV from original samples collected. MM: 1 kb molecular ladder; C-: not-infected P. peruviana (negative control); C+: PhyRMV-infected P. peruviana (positive control); 1: original dsRNA extracted from P. peruviana leaves. (C) Phylogenetic relationship based on the alignment of the PhyRMV near-complete genome and other members of the genus Sobemovirus. General Time Reversible (GTR) model with gamma distribution (G) was used and bootstrap support of 8,000 replications. The alignment for phylogeny was performed with the MUSCLE tool available in the MEGA X program. The numbers on the branches indicate the bootstrap values. Members of the Sobemovirus genus are: artemisia virus A (ArtVA; JN620802), blueberry shoestring virus (BSSV; LC081344), cocksfoot mottle virus (CfMV; L40905), cymbidium chlorotic mosaic virus (CyCMV; LC019764), imperata virus (IYMV; AM990928), lucerne transient streak virus (LTSV; JQ782213), papaya lethal yellowing virus (PLYV; JX123318), rice yellow mottle virus (RYMV; MG599280), rottboellia yellow mottle virus (RoMoV; KC577469), ryegrass mottle virus (RGMoV; AB040446), sesbania mosaic virus (SeMV; AY004291), solanum nodiflorum mottle virus (SNMoV; KC577470), southern bean mosaic virus (SBMV; AF055887), southern cowpea mosaic virus (SCPMV; M23021), sowbane mosaic virus (SoMV; AM940437), soybean yellow common mosaic virus (SYCMV; JF495127), subterranean clover mottle virus (SCMoV; AF208001), turnip rosette virus (TRoV; AY177608), velvet tobacco mottle virus (VTMoV; HM754263), and physalis rugose mosaic virus (PhyRMV; MK681145). The arrow indicates the isolate characterized in this study.

Figure 2 Sequences comparisons between genomes of physalis rugose mosaic virus (PhyRMV) Brazilian isolates. Map of nucleotide and amino acid substitutions in PhyRMV genome. Nucleotide and amino acids substitution are indicated following the order: isolated characterized in this study/Piracicaba isolate. Red lines indicate nonsynonymous nucleotide substitutions (dN) and grey lines indicate synonymous nucleotide substitutions (dS). Nucleotide positions are numbered according to sequence of the PhyRMV characterized in this study (MN782300).

Table 1 Transmission rate of seeds to Physalis peruviana seedlings.

Experiment	---------Infectivity (% infected plants)^a----------		Transmission rate (% infected seedlings) ^b
	C-	C+
1	0/10 (0)	20/20 (100)	0/200 (0)
2	0/10 (0)	20/20 (100)	0/200 (0)
3	0/10 (0)	20/20 (100)	0/200 (0)

^a Number of infected plants/number of inoculated plants, verified by RT-PCR amplification of viral genomic fragments at 30 days after inoculation; P. peruviana inoculated only with buffer were used as a negative control. C- and C+ correspond to the negative and positive controls, respectively. From the plants used as a C+, seeds were collected for the transmission test;
^b Number of infected seedlings/ number of seedlings evaluated, verified by RT-PCR amplification of viral genomic fragments at 50 days after the emergency.

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Near-complete genome sequence and seed transmission evaluation of <i>Physalis rugose mosaic virus</i> from southern Brazil

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[1] E-mail: fabio.silva@udesc.br. ^*Corresponding author.