Skip to main content
SpringerLink
Log in

Further genomic characterization of pineapple mealybug wilt-associated viruses using high-throughput sequencing

  • Original Article
  • Published:
Tropical Plant Pathology Aims and scope Submit manuscript

Abstract

In this study, we describe the further genomic characterization of several pineapple mealybug wilt-associated virus (PMWaV) members of the genus Ampelovirus, family Closteroviridae, using high-throughput sequencing (HTS). PMWaV-2 is a necessary factor in the complex etiology of mealybug wilt disease of pineapple (MWP). The complete PMWaV-1 genome was described previously, but the genomes of PMWaV-2, PMWaV-3, and putative PMWaV-4 and PMWaV-5 species lack complete characterization. To further study MWP etiology through genomic characterization of PMWaVs, a cDNA library from total RNA of pineapple plants was generated and underwent HTS. A PMWaV-4 genome of 12,932 nucleotides was assembled from the HTS data. Proteins from the PMWaV-4 genome shared high amino acid similarity to those of PMWaV-1. The RNA-dependent RNA polymerase (RdRp), heat shock protein 70 homolog (HSP70h), and coat protein (CP) proteins of PMWaV-4 shared 88, 87, and 85% amino acid identity, respectively, to those of PMWaV-1 (AF414119) indicating PMWaV-4 is a distinct strain of PMWaV-1 but not a distinct ampelovirus species. Therefore, we suggest that PMWaV-4 be designated PMWaV-1 strain 4 (MN539275). Further, we used HTS to obtain a new isolate of PMWaV-1 (MN539276) and supplemented the available sequences of the genomes of PMWaV-2 (MN539272 and MN539273) and PMWaV-3 (MN539274) in their 5′-terminal regions.

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

Similar content being viewed by others

References

  • Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Cech M, Chilton J, Clements D, Coraor N, Eberhard C, Gruning B, Guerler A, Hillman-Jackson J, Von Kuster G, Rasche E, Soranzo N, Turaga N, Taylor J, Nekrutenko A, Goecks J (2016) The galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Research 44:W3–W10

    Article  CAS  Google Scholar 

  • Alvarez RA, Martin RR, Quito-Avila DF (2015) First report of pineapple mealybug wilt associated virus-1 in Ecuador. New Disease Reports 31:15

    Article  Google Scholar 

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

  • Borroto EG, Cintra M, González J, Borroto C, Oramas P (1998) First report of a closterovirus-like particle associated with pineapple plants (Ananas comosus cv. Smooth Cayenne) affected with pineapple mealybug wilt in Cuba. Plant Disease 82:263–263

    Article  Google Scholar 

  • Carter W (1951) The feeding sequence of Pseudococcus brevipes-(ckl) in relation to mealybug wilt of pineapples in Hawaii. Phytopathology 41:769–780

    Google Scholar 

  • Carter W (1952) Injuries to plants caused by insect toxins. II. The Botanical Review 18:680–721

    Article  CAS  Google Scholar 

  • Carter W (1963) Mealybug wilt of pineapple; a reappraisal. Annals of the New York Academy of Sciences 105:741–764

    Article  Google Scholar 

  • Dey KK, Borth WB, Melzer MJ, Wang ML, Hu JS (2015) Analysis of pineapple mealybug wilt associated virus-1 and -2 for potential RNA silencing suppressors and pathogenicity factors. Viruses 7:969–995

    Article  CAS  Google Scholar 

  • Dey K, Green JC, Melzer MJ, Borth W, Hu J (2018a) Mealybug wilt of pineapple and associated viruses. Horticulturae 4:52

    Article  Google Scholar 

  • Dey K, Sugikawa J, Kerr C, Melzer MJ (2018b) Air potato (Dioscorea bulbifera) plants displaying virus-like symptoms are co-infected with a novel potyvirus and a novel ampelovirus. Virus Genes 55:117–121

    Article  Google Scholar 

  • Gambley C, Steele V, Geering A, Thomas J (2008) The genetic diversity of ampeloviruses in Australian pineapples and their association with mealybug wilt disease. Australasian Plant Pathology 37:95–105

    Article  CAS  Google Scholar 

  • Gonsalves A, Sether D, Ullman D, Hu J (1992) Detection of pineapple closterovirus, a possible cause of mealybug wilt of pineapple. I International Pineapple Symposium 334:411–416

    Google Scholar 

  • Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nature Biotechnology 29:644–652

    Article  CAS  Google Scholar 

  • Gunasinghe U, German T (1986) Association of virus-particles with mealybug-wilt of pineapple. Phytopathology 10:1073

    Google Scholar 

  • Gunasinghe U, German T (1987) Further chacterization of virus associated with mealybug-wilt of pineapple. Phytopathology 12:1776

    Google Scholar 

  • Gunasinghe U, German T (1989) Purification and partial characterization of a virus from pineapple. Phytopathology 79:1337–1341

    Article  Google Scholar 

  • Henschel R, Lieber M, Wu L, Nista P, Haas BJ, LeDuc RD (2012) Trinity RNA-Seq assembler performance optimization. In: Proceedings of the conference on extreme science and engineering discovery environment, article 45

  • Hernandez-Rodriguez L, Ramos-Gonzalez PL, Garcia-Garcia G, Zamora V, Peralta-Martin AM, Peña I, Perez JM, Ferriol X (2014) Geographic distribution of mealybug wilt disease of pineapple and genetic diversity of viruses infecting pineapple in Cuba. Crop Protection 65:43–50

    Article  Google Scholar 

  • Illingworth JF (1931) Preliminary report on evidence that mealy bugs are an important factor in pineapple wilt. Journal of Economic Entomology 24:877–889

    Article  Google Scholar 

  • Ito K (1962) Additional immunological evidence supporting the virus nature of mealybug wilt. Pineapple Research Institute News 10:158–162

    Google Scholar 

  • Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A (2012) Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649

    Article  Google Scholar 

  • Larsen LD (1910) Diseases of pineapple. Bulletin of the Experiment Station of the Hawaii Sugar Planters’ Association. Division of Pathology and Physiology 10:1–72

    Google Scholar 

  • Le SQ, Gascuel O (2008) An improved general amino acid replacement matrix. Molecular Biology and Evolution 25:1307–1320

    Article  CAS  Google Scholar 

  • Maliogka VI, Dovas CI, Katis NI (2008) Evolutionary relationships of virus species belonging to a distinct lineage within the Ampelovirus genus. Virus Research 135:125–135

    Article  CAS  Google Scholar 

  • Martelli GP, Agranovsky AA, Bar-Joseph M, Boscia D, Candresse T, Coutts RHA, Dolja VV, Hu JS, Jelkmann W, Karasev AV, Martin RR, Minafra A, Namba S, Vetten HJ (eds) (2011) Family Closteroviridae, ninth report of the international Commitee on taxonomy of viruses. Virus taxonomy. Elsevier-Academic Press, Amsterdam, p 996

    Google Scholar 

  • Martelli GP, Abou Ghanem-Sabanadzovic N, Agranovsky AA, Al Rwahnih M, Dolja VV, Dovas CI, Fuchs M, Gugerli P, Hu JS, Jelkmann W, Katis NI, Maliogka VI, Melzer MJ, Menzel W, Minafra A, Rott ME, Rowhani A, Sabanadzovic S, Saldarelli P (2012) Taxonomic revision of the family Closteroviridae with special reference to the grapevine leafroll-associated members of the genus Ampelovirus and the putative species unassigned to the family. Journal of Plant Pathology 94:7–19

    Google Scholar 

  • Melzer M, Karasev A, Sether D, Hu J (2001) Nucleotide sequence, genome organization and phylogenetic analysis of pineapple mealybug wilt-associated virus-2. Journal of General Virology 82:1–7

    Article  CAS  Google Scholar 

  • Melzer M, Sether D, Karasev A, Borth W, Hu J (2008) Complete nucleotide sequence and genome organization of pineapple mealybug wilt-associated virus-1. Archives of Virology 153:707–714

    Article  CAS  Google Scholar 

  • Peron FN, Calloni R, Ventura JA, Fernandes PMB (2019) Bioinformatics approach to the study of the molecular behaviour of mealybug wilt of pineapple. Acta Horticulture 1239:177–184

    Article  Google Scholar 

  • Sether D, Hu J (2002) Closterovirus infection and mealybug exposure are necessary for the development of mealybug wilt of pineapple disease. Phytopathology 92:928–935

    Article  CAS  Google Scholar 

  • Sether D, Ullman D, Hu J (1996) Detection of pineapple closterovirus in pineapple plants and mealybugs using monoclonal antibodies. Plant Pathology 45:829–836

    Article  Google Scholar 

  • Sether D, Liu X, Wang M, Zee F, Ullman D, Hu J (1997) Use of a tissue blotting immunoassay to examine the distribution of pineapple closterovirus in Hawaii. Plant Disease 81:1150–1154

    Article  Google Scholar 

  • Sether D, Ullman D, Hu J (1998) Transmission of pineapple mealybug wilt-associated virus by two species of mealybug (Dysmicoccus spp.). Phytopathology 88:1224–1230

    Article  CAS  Google Scholar 

  • Sether D, Karasev A, Okumura C, Arakawa C, Zee F, Kislan M, Busto J, Hu J (2001) Differentiation, distribution, and elimination of two different pineapple mealybug wilt-associated viruses found in pineapple. Plant Disease 85:856–864

    Article  CAS  Google Scholar 

  • Sether DM, Melzer MJ, Busto J, Zee F, Hu JS (2005a) Diversity and mealybug transmissibility of ampeloviruses in pineapple. Plant Disease 89:450–456

    Article  CAS  Google Scholar 

  • Sether D, Melzer M, Subere C, Hu J (2005b) Pineapple mealybug wilt associated viruses 1, 3, and 4, and grapevine leafroll associated viruses 4, 5, 6, and 9 are a distinct group in the genus Ampelovirus. In: XIII international congress of virology, Washington, DC. American Society for Microbiology, pp 121–122

  • Sether DM, Melzer MJ, Borth WB, Hu J (2009) Genome organization and phylogenetic relationship of pineapple mealybug wilt associated virus-3 with family Closteroviridae members. Virus Genes 38:414–420

    Article  CAS  Google Scholar 

  • Yu N, Luo Z, Fan H, Zhang Z, Li X, Wang J, Liu Z, He F (2015) Complete genomic sequence of a pineapple mealybug wilt-associated virus-1 from Hainan Island, China. European Journal of Plant Pathology 141:611–615

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The research was supported in part by grants from the United State Department of Agriculture National Institute of Food and Agriculture, Hatch HAW09025-H (1001478), and the United State Department of Agriculture -Agricultural Research Service (58-5320-4-012). We appreciate Adriana E. Larrea-Sarmiento for her technical assistance.

Author information

Authors and Affiliations

  1. Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, USA

    James C. Green, Alejandro Olmedo-Velarde, Michael J. Melzer, Islam Hamim, Wayne B. Borth & John S. Hu

  2. Department of Plant Pathology, University of California, Davis, CA, USA

    Maher A. Rwahnih

  3. Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh, Bangladesh

    Islam Hamim

  4. United States Department of Agriculture, Agricultural Research Service, Pacific Basin, Agricultural Research Center, Hilo, HI, USA

    Tracie M. Brower & Marisa Wall

Authors
  1. James C. Green
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Maher A. Rwahnih
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Alejandro Olmedo-Velarde
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Michael J. Melzer
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Islam Hamim
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Wayne B. Borth
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Tracie M. Brower
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Marisa Wall
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. John S. Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

JG, MAR and JH planed and designed the experimental work. JG and MAR executed the experimental work. JG, AOV, and MAR conducted data analyses. JG, AOV, MM, IH, WB, MW, TM, and JH wrote the manuscript.

Corresponding author

Correspondence to John S. Hu.

Ethics declarations

Conflict of interest

The authors declare that they have no conflicts of interest.

Human and animal rights

This article does not contain any studies with human participants or animals performed by any of the authors.

Additional information

Section Editor: Michael Goodin

Publisher’s note

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

Electronic supplementary material

Fig. S1

Agarose gel electrophoresis of RT-PCR products for PMWaVs. Pineapple accessions samples were collected from the United States Department of Agriculture, Agricultural Research Service (USDA-ARS), National Clonal Germplasm Repository (NCGR) at the Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center (PBARC) in Hilo HI, USA. (a) PMWaV-1, expected product size 590 bp; (b) PMWaV-2, expected product size 610 bp; (c) PMWaV-3, expected product size 499 bp; and (d) PMWaV-4, expected product size, 435 bp. Lanes: L, molecular ladder 100 bp; 1, HANA 17; 2, HANA 21; 3, HANA 46; 4, HANA 49; 5, HANA 156; 6, HANA 158; 7, HANA 160; 8, HANA 187; NTC, non-template control. (PNG 1544 kb)

High Resolution Image (TIF 484 kb)

Fig. S2

Agarose gel electrophoresis of RT-PCR products for partial fragments of RNA-dependent RNA polymerase (RdRp), heat shock protein 70 homolog (HSP70h), coat protein (CP) and ORF1a genes from PMWaV-4. (a) RT-PCR products of RdRP, HSP70 (HSP) and CP using primers 1944/1945, 1946/1947 and 1948/1949, respectively. Three technical replicates per gene were included in this RT-PCR assay. (b) RT-PCR products of partial fragments of ORF1a targeting positions 258-731 (primers 1932/1933), 94-553 (primers 1934/1935) and 798-1426 (primers 1936/1937) from a 1,522-nucleotide contig from a HTS assembly from HANA 160 infected with PMWaV-4. Six technical replicates were included in this RT-PCR assay. (PNG 180 kb)

High Resolution Image (TIF 61 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Green, J.C., Rwahnih, M.A., Olmedo-Velarde, A. et al. Further genomic characterization of pineapple mealybug wilt-associated viruses using high-throughput sequencing. Trop. plant pathol. 45, 64–72 (2020). https://doi.org/10.1007/s40858-019-00330-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s40858-019-00330-y

Keywords

Search

Navigation