Skip to main content
SpringerLink
Log in

Analyzes of mealybug (Pseudococcus longispinus) virome reveal grapevine viruses diversity

  • Short Communication
  • Published:
Tropical Plant Pathology Aims and scope Submit manuscript

Abstract

The long-tailed mealybug, Pseudococcus longispinus, is an important insect pest in grapevine growing areas in several countries, including Brazil. Metagenomic analysis of nucleic acids extracted from insect vectors makes it possible to study the diversity of insect viruses in addition to plant pathogenic viruses. In this study, insects (Ps. longispinus) were collected, and pooled throughout a plot of virus disease symptomatic vines, cultivated in growing beds, and analyzed by high throughput sequencing (HTS). The complete genome of grapevine leafroll-associated virus 2 and 3 (GLRaV-2 and -3) and a partial sequence of grapevine virus A (GVA) with two complete ORFs (coat protein and RNA-binding protein) were assembled from mealybug extracts and exhibited high nucleotide identities, up to 99%, with previously characterized homologous Brazilian isolates from grapevines. This information was validated by the detection of these viruses in the original symptomatic vines (N=76), from where mealybugs were collected, equivalent to an incidence of 34.2%, 89.5% and 36.8% for GLRaV-2, GLRaV-3 and GVA, respectively. Although one of these viruses is not transmitted by mealybugs (GLRaV-2), prospection of plant viruses infecting grapevine plants by analyzing the metagenome of insects could represent a relevant alternative to improve monitoring of viral diseases aiming at the management and control of viral diseases in vineyards or cultivation fields. This work is the first analysis of the Ps. longispinus virome in Brazil focusing on grapevine viruses.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Data availability

All sequencing data obtained in this study were included in the manuscript and/or submitted to the GenBank database under the accession numbers OR502861, OR640977, OR546046 and, OR613005 and BioProject PRJNA1020893.

References

  • Ahmed AR, Apori SO, Karim AA (2023) Mealybug vectors: a review of their transmission of plant viruses and their management strategies. AIMS Agriculture and Food 8:736–761

    Article  Google Scholar 

  • Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. Available at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Accessed 23 Oct 2023

  • Basso MF, Fajardo TVM, Saldarelli P (2017) Grapevine virus diseases: economic impact and current advances in viral prospection and management. Revista Brasileira de Fruticultura 39:e-411

    Article  Google Scholar 

  • Beuning LL, Murphy P, Wu E, Batchelor TA, Morris BAM (1999) Molecular-based approach to the differentiation of mealybug (Hemiptera: Pseudococcidae) species. Journal of Economic Entomology 92:463–472

    Article  CAS  PubMed  Google Scholar 

  • Bhat AI, Rao GP (2020) Transmission of viruses through mealybugs. Characterization of plant viruses. Springer Protocols Handbooks Humana Press, New York, pp 95–98

    Chapter  Google Scholar 

  • Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications. BMC Bioinformatics 10:421

    Article  PubMed  PubMed Central  Google Scholar 

  • Canaguier A, Grimplet J, Di Gaspero G, Scalabrin S, Duchêne E, Choisne N, Mohellibi N, Guichard C, Rombauts S, Le Clainche I, Bérard A, Chauveau A, Bounon R, Rustenholz C, Morgante M, Le Paslier MC, Brunel D, Adam-Blondon AF (2017) A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3). Genomics Data 14:56–62

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen S, Zhou Y, Chen Y, Gu J (2018) Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884–i890

    Article  PubMed  PubMed Central  Google Scholar 

  • Dubiela CR, Fajardo TVM, Souto ER, Nickel O, Eiras M, Revers LF (2013) Simultaneous detection of Brazilian isolates of grapevine viruses by TaqMan real-time RT-PCR. Tropical Plant Pathology 38:158–165

    Article  Google Scholar 

  • Fajardo TVM, Bertocchi AA, Nickel O (2020) Determination of the grapevine virome by high-throughput sequencing and grapevine viruses detection in Serra Gaúcha, Brazil. Revista Ceres 67:156–163

    Article  CAS  Google Scholar 

  • Fajardo TVM, Peres CA, Nickel O (2023) Real-time RT-PCR high-resolution melting curve analysis to detect and differentiate Brazilian variants of grapevine viruses. Ciência e Técnica Vitivinícola 38:188–195

    Article  Google Scholar 

  • Fuchs M (2020) Grapevine viruses: a multitude of diverse species with simple but overall poorly adopted management solutions in the vineyard. Journal of Plant Pathology 102:643–653

    Article  Google Scholar 

  • Fuchs M (2023) Grapevine virology highlights: 2018-2023. Proceedings of the 20th congress of the international council for the study of virus and virus-like diseases of the grapevine, Thessaloniki, Greece, pp 18–26. Available at https://icvg.org/data/ICVG20Abstracts.pdf. Accessed 5 Mar 2024 

  • Grohs DS, Almança MAK, Fajardo TVM, Halleen F, Miele A (2017) Advances in propagation of grapevine in the world. Revista Brasileira de Fruticultura 39:e-760

    Article  Google Scholar 

  • Herrbach E, Alliaume A, Prator CA, Daane KM, Cooper ML, Almeida RPP (2017) Vector transmission of grapevine leafroll-associated viruses. In: Meng B, Martelli GP, Golino DA, Fuchs M (eds) Grapevine viruses: molecular biology, diagnostics and management. Springer, Cham, pp 483–503

    Chapter  Google Scholar 

  • Jarugula S, Alabi OJ, Martin RR, Naidu RA (2010) Genetic variability of natural populations of Grapevine leafroll-associated virus 2 in Pacific Northwest vineyards. Phytopathology 100:698–707

    Article  CAS  PubMed  Google Scholar 

  • Kaur N, Hasegawa DK, Ling K-S, Wintermantel WM (2016) Application of genomics for understanding plant virus-insect vector interactions and insect vector control. Phytopathology 106:1213–1222

    Article  CAS  PubMed  Google Scholar 

  • Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution 35:1547–1549

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kuniyuki H, Gioria R, Rezende JAM, Willink CG, Novo JPS, Yuki VA (2006) Transmissão experimental do grapevine virus B pela cochonilha Pseudococcus longispinus Targioni-Tozzetti (Hemiptera: Pseudococcidae). Summa Phytopathologica 32:151–155

    Article  Google Scholar 

  • La Notte P, Buzkan N, Choueiri E, Minafra A, Martelli GP (1997) Acquisition and transmission of grapevine virus A by the mealybug Pseudococcus longispinus. Journal of Plant Pathology 79:79–85

    Google Scholar 

  • Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nature Methods 9:357–359

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948

    Article  CAS  PubMed  Google Scholar 

  • Li D, Luo R, Liu C-M, Leung C-M, Ting H-F, Sadakane K, Yamashita H, Lam T-W (2016) MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods 102:3–11

    Article  CAS  PubMed  Google Scholar 

  • Maliogka VI, Martelli GP, Fuchs M, Katis NI (2015) Control of viruses infecting grapevine. Advances in Virus Research 91:175–227

    Article  CAS  PubMed  Google Scholar 

  • Mannini F, Digiaro M (2017) The effects of viruses and viral diseases on grapes and wine. In: Meng B, Martelli GP, Golino DA, Fuchs M (eds) Grapevine viruses: Molecular biology, diagnostics and management. Springer, Cham, pp 453–482

    Chapter  Google Scholar 

  • Maree HJ, Pirie MD, Oosthuizen K, Bester R, Rees DJG, Burger JT (2015) Phylogenomic analysis reveals deep divergence and recombination in an economically important grapevine virus. PLoS One 10:e0126819

    Article  PubMed  PubMed Central  Google Scholar 

  • Martinez-Mercado MA, Jesús JLD, Galindo-Sánchez CE, Saavedra-Flores A, Carrillo-Tripp J (2022) Novel viral RNA genomes of the vine mealybug Planococcus ficus. Journal of General Virology 103:3

    Article  Google Scholar 

  • McGreal B, Sandanayaka M, Chooi KM, MacDiarmid R (2019) Development of sensitive molecular assays for the detection of grapevine leafroll-associated virus 3 in an insect vector. Archives of Virology 164:2333–2338

    Article  CAS  PubMed  Google Scholar 

  • O’Leary NA, Wright MW, Brister JR, Ciufo S et al (2016) Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Research 44:D733–D745

    Article  PubMed  Google Scholar 

  • Osman F, Rowhani A (2008) Real-time RT-PCR (TaqMan) assays for the detection of viruses associated with Rugose wood complex of grapevine. Journal of Virological Methods 154:69–75

    Article  CAS  PubMed  Google Scholar 

  • Osman F, Leutenegger C, Golino D, Rowhani A (2007) Real-time RT-PCR (TaqMan) assays for the detection of Grapevine leafroll associated viruses 1–5 and 9. Journal of Virological Methods 141:22–29

    Article  CAS  PubMed  Google Scholar 

  • Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C (2017) Salmon provides fast and bias-aware quantification of transcript expression. Nature Methods 14:417–419

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rott ME, Jelkmann W (2001) Characterization and detection of several filamentous viruses of cherry: adaptation of an alternative cloning method (DOP-PCR) and modification of an RNA extraction protocol. European Journal of Plant Pathology 107:411–420

    Article  CAS  Google Scholar 

  • Rubio L, Galipienso L, Ferriol I (2020) Detection of plant viruses and disease management: Relevance of genetic diversity and evolution. Frontiers in Plant Science 11:1092

    Article  PubMed  PubMed Central  Google Scholar 

  • Schoelz J, Volenberg D, Adhab M, Fang Z, Klassen V, Spinka C, Al Rwahnih M (2021) A survey of viruses found in grapevine cultivars grown in Missouri. American Journal of Enology and Viticulture 72:73–84

    Article  CAS  Google Scholar 

  • Song Y, Hanner RH, Meng B (2021) Probing into the effects of grapevine leafroll-associated viruses on the physiology, fruit quality and gene expression of grapes. Viruses 13:593

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tsai C-W, Rowhani A, Golino DA, Daane KM, Almeida RPP (2010) Mealybug transmission of grapevine leafroll viruses: An analysis of virus-vector specificity. Phytopathology 100:830–834

    Article  PubMed  Google Scholar 

  • Van der Auwera GA, O’Connor BD (2020) Genomics in the Cloud: Using Docker, GATK, and WDL in Terra. O’Reilly Media, USA

    Google Scholar 

  • Vončina D, Jagunić M, De Stradis A, Diaz-Lara A, Al Rwahnih M, Šćepanović M, Almeida RPP (2024) New host plant species of grapevine virus A identified with vector-mediated infections. Plant Disease 108:125–130

    Article  PubMed  Google Scholar 

  • Wilm A, Aw PPK, Bertrand D, Yeo GHT, Ong SH, Wong CH, Khor CC, Petric R, Hibberd ML, Nagarajan N (2012) LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Research 40:11189–11201

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wistrom CM, Blaisdell GK, Wunderlich LR, Botton M, Almeida RPP, Daane KM (2017) No evidence of transmission of grapevine leafroll-associated viruses by phylloxera (Daktulosphaira vitifoliae). European Journal of Plant Pathology 147:937–941

    Article  CAS  Google Scholar 

  • Wu Q, Habili N, Kinoti WM, Tyerman SD, Rinaldo A, Zheng L, Constable FE (2023a) A metagenomic investigation of the viruses associated with Shiraz Disease in Australia. Viruses 15:774

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu Q, Habili N, Tyerman SD, Rinaldo A, Little A, Constable FE (2023b) First detection of five previously unreported grapevine viruses in Australia. Australasian Plant Disease Notes 18:27

    Article  Google Scholar 

  • Xiao H, Liu Z, Wang N, Long Q, Cao S, Huang G, Liu W, Peng Y, Riaz S, Walker AM, Gaut BS (2023) Adaptive and maladaptive introgression in grapevine domestication. Proceedings of the National Academy of Sciences, USA 120:e2222041120

    Article  CAS  Google Scholar 

  • Zhou Y, Minio A, Massonnet M, Solares E, Lv Y, Beridze T, Cantu D, Gaut BS (2019) The population genetics of structural variants in grapevine domestication. Nature Plants 5:965–979

    Article  PubMed  Google Scholar 

Download references

Acknowledgements

This study was supported by Embrapa, project 22.16.04.035.00.00. Authors thank Marcos F. Vanni for technical support and Vera M. Quecini (Embrapa Uva e Vinho, Brazil) for some bioinformatics HTS analyzes.

Author information

Authors and Affiliations

  1. Embrapa Uva e Vinho, Bento Gonçalves, RS, 95.701-008, Brazil

    Thor Vinícius Martins Fajardo & Osmar Nickel

  2. Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, 70.770-917, Brazil

    Priscila Grynberg & Roberto Coiti Togawa

  3. Institute for Integrative Systems Biology (I2SysBio), 46980, Paterna, Valencia, Spain

    João Marcos Fagundes Silva

  4. Departamento de Agronomia, Universidade do Estado de Santa Catarina, Lages, SC, 88.520-000, Brazil

    Fabio Nascimento da Silva

Authors
  1. Thor Vinícius Martins Fajardo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Priscila Grynberg
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Roberto Coiti Togawa
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. João Marcos Fagundes Silva
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Fabio Nascimento da Silva
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Osmar Nickel
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Conceptualization: TVMF and ON; methodology: TVMF and ON; formal analysis and investigation: TVMF; HTS and bioinformatics analyzes: PG, RCT, JMFS and FNS; writing - original draft preparation: TVMF and ON; writing - review and editing: TVMF, PG, RCT, JMFS, FNS and ON; funding acquisition: TVMF; resources: TVMF, ON and FNS; supervision: TVMF.

Corresponding author

Correspondence to Thor Vinícius Martins Fajardo.

Ethics declarations

Conflict of interest

The authors declare no competing interests.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Fajardo, T.V.M., Grynberg, P., Togawa, R.C. et al. Analyzes of mealybug (Pseudococcus longispinus) virome reveal grapevine viruses diversity. Trop. plant pathol. (2024). https://doi.org/10.1007/s40858-024-00647-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s40858-024-00647-3

Keywords

Search

Navigation