Advertisement

Virus Genes

pp 1–7 | Cite as

Molecular characterization and complete genome of alstroemeria mosaic virus (AlMV)

  • Francisco Mosquera-YuquiEmail author
  • Patricia Garrido
  • Francisco J. Flores
Original Paper
  • 13 Downloads

Abstract

Even though alstroemeria mosaic virus (AlMV) is one of the most important viruses affecting alstroemeria plants, its genome is only partially available in public sequence databases. High throughput sequencing (HTS) of RNA from alstroemeria plants with symptoms of mosaic and streaking, collected in Lasso-Ecuador, indicated the presence of AlMV and lily symptomless virus. In this study, we aimed to assemble and characterize the complete genome sequence of AlMV. Reads from Illumina sequencing of ribosomal RNA-depleted total RNA were assembled into contigs that were mapped to the sunflower chlorotic mottle virus genome, revealing the 9974 bp complete genome sequence of AlMV. Multiple sequence alignment of the AlMV polyprotein with close homologs allowed the identification of ten mature proteins P1, HC-Pro, P3, 6K1, CI, 6K2, NIa-VPg, NIa-Pro, NIb and CP. Furthermore, several potyvirus motifs were identified in the AlMV polyprotein including those related to potyvirus aphid transmission 334KMTC337, 592PTK594 and 2800DAG2802. Phylogenetic analysis based in the polyprotein showed that AlMV belongs to the potato virus Y clade and its closest relative is sunflower ring blotch virus. This study describes the first complete genome of AlMV and its placement within the genus Potyvirus, providing valuable information for future studies on this economically important virus.

Keywords

AlMV Alstroemeria Genome Polyprotein Potyvirus 

Notes

Acknowledgements

The authors thank Dr. Nathan Richard Walker for revising and improving our manuscript. All bioinformatics analyses were performed in the Rumiñahui high performance cluster of Universidad de las Fuerzas Armadas-ESPE. Biological samples were collected and sequenced under framework contract MAE–DNB–CM–2017–0071.

Author contributions

Conceived the study: FJF. Designed and performed the research: FMY, PG, and FJF. Analyzed data: FMY, and FJF. Curated data: FMY. Wrote the manuscript: FMY, PG. Reviewed the manuscript and supervised the research: FJF. All authors read and approved the final manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.

Research involving human and animal rights

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

References

  1. 1.
    Hans G (2018) Alstroemerias (Alstroemeria hybrids) as a tunnel-grown cut flower crop. National Cut Flower Centre-AHDB Horticulture Information Sheet 10Google Scholar
  2. 2.
    Bellardi MG, Vibio M, Bertaccini A (1992) Natural occurrence of freesia mosaic virus in Alstroemeria sp. Plant Dis 76:643CrossRefGoogle Scholar
  3. 3.
    Brunt AA, Phillips S (1981) Alstroemeria. Ann. Rep. Glasshouse Crops Research Institute for 1979, LittlehamptonGoogle Scholar
  4. 4.
    Hassani-Mehraban A, Botermans M, Verhoeven JT, Meekes E, Saaijer J, Peters D, Goldbach R, Kormelink R (2010) A distinct tospovirus causing necrotic streak on Alstroemeria sp. in Colombia. Arch Virol 155:423–428CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Hassani-Mehraban A, Dullemans AM, Verhoeven JTJ, Roenhorst JW, Peters P, van der Vlugt RAA, Kormelink R (2019) Alstroemeria yellow spot virus (AYSV): a new orthotospovirus species within a growing Eurasian clade. Arch Virol 164:117–126CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Spence NJ, Mills PR, Barbara DJ (2000) A survey of viruses of Alstroemeria in the UK and the characterisation of carlaviruses infecting Alstroemeria. Eur J Plant Pathol 106:843–847CrossRefGoogle Scholar
  7. 7.
    Van der Vlugt RAA, Bouwen I (1997) Identification of potyviruses infecting Alstroemeria. In: Dehne H-WAG, Diekmann M, Frahm F, Mauler-Machnik A, Halteren P (eds) Diagnosis and identification of plant pathogens. Kluwer Academic Publishers, Dordrecht, pp 469–471Google Scholar
  8. 8.
    Van der Vlugt RAA, Bouwen I (2002) Alstroemeria streak virus is an isolate of Alstroemeria mosaic potyvirus. Phytomed Dtsch Phytomed Ges Sonderh 1:31Google Scholar
  9. 9.
    Fuji S-I, Mochizuki N, Fujinaga M, Ikeda M, Shinoda K, Uematsu S, Furuya H, Naito H, Fukumoto F (2007) Incidence of viruses in Alstroemeria plants cultivated in Japan and characterization of Broad bean wilt virus-2, Cucumber mosaic virus and Youcai mosaic virus. J Gen Plant Pathol 73:216–221CrossRefGoogle Scholar
  10. 10.
    De Blank CM, Van Zaayen A, Bouwen I (1994) Towards a reliable detection of Alstroemeria mosaic virus. Acta Hortic 377:199–208CrossRefGoogle Scholar
  11. 11.
    Phillips S, Brunt AA (1986) Four viruses of alstroemeria in Britain. Acta Hortic 177:227–234CrossRefGoogle Scholar
  12. 12.
    Yasuda S, Saka K, Natsuaki KT (1998) Characterization and serodiagnosis of alstroemeria mosaic potyvirus. Jpn J Trop Agric 42:85–93Google Scholar
  13. 13.
    Hakkaart FA, Versluijs JMA (1988) Virus elimination by meristem-tip culture from a range of Alstroemeria cultivars. Neth J Plant Pathol 94:49–56CrossRefGoogle Scholar
  14. 14.
    Fuji S, Terami F, Furuya H, Naito H, Fukumoto F (2004) Nucleotide sequence of the coat protein genes of Alstroemeria mosaic virus and Amazon lily mosaic virus, a tentative species of genus Potyvirus. Arch Virol 149:1843–1849CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Wang CY, Chang YC (2006) First identification of Alstroemeria mosaic virus in Taiwan. Plant Pathol 55:566CrossRefGoogle Scholar
  16. 16.
    Pearson MN, Cohen D, Cowell S et al (2009) A survey of viruses of flower bulbs in New Zealand. 38:305–309Google Scholar
  17. 17.
    Gutiérrez-Estrada A, Zavaleta-Mejía E, Gaytán-Acuña EA, Herrera-Guadarrama AJ (2000) Virus associated with Alstroemeria in México. Rev Mex Fitopatol 17:97–103Google Scholar
  18. 18.
    Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Bushnell B (2014) BBMap: a fast, accurate, splice-aware aligner. Report number: LBNL-7065E, Lawrence Berkeley National Laboratory Berkeley, CAGoogle Scholar
  20. 20.
    Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    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 28:1647–1649CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30:3059–3066CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    Castresana J (2002) GBLOCLKS: selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Version 0.91b. Copyrighted by J. Castresana, EMBL.Google Scholar
  24. 24.
    Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874CrossRefGoogle Scholar
  25. 25.
    Suchard M, Lemey P, Baele G, Ayres D, Drummond AJ, Rambaut A (2018) Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol 4:vey016Google Scholar
  26. 26.
    Chung BY, Miller WA, Atkins JF, Firth AE (2008) An overlapping essential gene in the Potyviridae. Proc Natl Acad Sci USA 105:5897–5902CrossRefPubMedPubMedCentralGoogle Scholar
  27. 27.
    Dujovny G, Sasaya T, Koganesawa H, Usugi T, Shohara K, Lenardon SL (2000) Molecular characterization of a new potyvirus infecting sunflower. Arch Virol 145:2249–2258CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Hong Y, Hunt AG (1996) RNA polymerase activity catalyzed by a potyvirus-encoded RNA-dependent RNA polymerase. Virology 226:146–151CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Langeveldt SA, Dore J-M, Memelink J, Derks AFLM, van der Vlugt CIM, Asjes CJ, Bol JF (1991) Identification of potyviruses using the polymerase chain reaction with degenerate primers. J Gen Virol 72:1531–1541CrossRefGoogle Scholar
  30. 30.
    Peng YH, Kadoury D, Gal-On A, Huet H, Wang Y, Raccah B (1998) Mutations in the HC-Pro gene of zucchini yellow mosaic potyvirus: effects on aphid transmission and binding to purified virions. J Gen Virol 79:897–904CrossRefPubMedPubMedCentralGoogle Scholar
  31. 31.
    Riechmann JL, Laín S, García JA (1992) Highlights and prospects of potyvirus molecular biology. J Gen Virol 73:1–16CrossRefPubMedPubMedCentralGoogle Scholar
  32. 32.
    Rohožková J, Navrátil M (2011) P1 peptidase: a mysterious protein of family Potyviridae. J Biosci 36:189–200CrossRefPubMedPubMedCentralGoogle Scholar
  33. 33.
    Shiboleth YM, Haronsky E, Leibman D, Arazi T, Wassenegger M, Whitham SA, Gaba V, Gal-On A (2007) The conserved FRNK box in HC-Pro, a plant viral suppressor of gene silencing, is required for small RNA binding and mediates symptom development. J Virol 81:13135–13148CrossRefPubMedPubMedCentralGoogle Scholar
  34. 34.
    Urcuqui-Inchima S, Haenni AL, Bernardi F (2001) Potyvirus proteins: a wealth of functions. Virus Res 74:157–175CrossRefPubMedPubMedCentralGoogle Scholar
  35. 35.
    Valli A, López-Moya JJ, García JA (2007) Recombination and gene duplication in the evolutionary diversification of P1 proteins in the family Potyviridae. J Gen Virol 88:1016–1028CrossRefGoogle Scholar
  36. 36.
    Xiang H, Han Y-H, Han C, Li D, Yu J (2007) Molecular characterization of two Chinese isolates of Beet mosaic virus. Virus Genes 35:795–799CrossRefPubMedPubMedCentralGoogle Scholar
  37. 37.
    Cabrera-Mederos D, Bejerman N, Trucco V, de Breuil S, Lenardon S, Giolitti F (2017) Complete genome sequence of sunflower ring blotch virus, a new potyvirus infecting sunflower in Argentina. Arch Virol 162:1787–1790CrossRefPubMedPubMedCentralGoogle Scholar
  38. 38.
    Bellardi MG, Bertaccini A, Betti L (1994) Survey of viruses infecting Alstroemeria in Italy. Acta Hortic 377:73–80CrossRefGoogle Scholar
  39. 39.
    Wylie SJ, Adams M, Chalam C, Kreuze J, López-Moya JJ, Ohshima K, Praveen S, Rabenstein F, Stenger D, Wang A, Zerbini FM, Consortium IR (2017) ICTV virus taxonomy profile: Potyviridae. J Gen Virol 98:352–354CrossRefPubMedPubMedCentralGoogle Scholar
  40. 40.
    Atreya PL, Atreya CD, Pirone TP (1991) Amino acid substitutions in the coat protein result in loss of insect transmissibility of a plant virus. Proc Natl Acad Sci USA 88:7887–7891CrossRefPubMedPubMedCentralGoogle Scholar
  41. 41.
    Atreya PL, Lopez-Moya JJ, Chu M, Atreya CD, Pirone TP (1995) Mutational analysis of the coat protein N-terminal amino acids involved in potyvirus transmission by aphids. J Gen Virol 76:265–270CrossRefPubMedPubMedCentralGoogle Scholar
  42. 42.
    Huet H, Gal-On A, Meir E, Lecoq H, Raccah B (1994) Mutations in the helper component protease gene of zucchini yellow mosaic virus affect its ability to mediate aphid transmissibility. J Gen Virol 75:1407–1414CrossRefPubMedPubMedCentralGoogle Scholar
  43. 43.
    Anindya R, Joseph J, Gowri TDS, Savithri HS (2004) Complete genomic sequence of pepper vein banding virus (PVBV): a distinct member of the genus Potyvirus. Arch Virol 149:625–632CrossRefPubMedPubMedCentralGoogle Scholar
  44. 44.
    Chen J, Chen JP, Chen JS, Adams MJ (2001) Molecular characterisation of an isolate of Dasheen mosaic virus from Zantedeschia aethiopica in China and comparisons in the genus Potyvirus. Arch Virol 146:1821–1829CrossRefPubMedPubMedCentralGoogle Scholar
  45. 45.
    Mlotshwa S, Verver J, Sithole-Niang I, Van Kampen T, Van Kammen A, Wellink J (2002) The genomic sequence of cowpea aphid-borne mosaic virus and its similarities with other potyviruses. Arch Virol 147:1043–1052CrossRefPubMedPubMedCentralGoogle Scholar
  46. 46.
    Domier LL, Latorre IJ, Steinlage TA, McCoppin N, Hartman GL (2003) Variability and transmission by Aphis glycines of North American and Asian Soybean mosaic virus isolates. Arch Virol 148:1925–1941CrossRefPubMedPubMedCentralGoogle Scholar
  47. 47.
    Ali A, Natsuaki T, Okuda S (2006) The complete nucleotide sequence of a Pakistani isolate of watermelon mosaic virus provides further insights into the taxonomic status in the bean common mosaic virus subgroup. Virus Genes 32:307–311CrossRefPubMedPubMedCentralGoogle Scholar
  48. 48.
    Bravo E, Calvert LA, Morales FJ (2008) The complete nucleotide sequence of the genomic RNA of bean common mosaic virus strain NL4. Rev Acad Colomb Cienc Exactas Fis Nat 32:37–46Google Scholar
  49. 49.
    Fukumoto T, Nakamura M, Rikitake M, Iwai H (2012) Molecular characterization and specific detection of two genetically distinguishable strains of East Asian Passiflora virus (EAPV) and their distribution in southern Japan. Virus Genes 44:141–148CrossRefPubMedPubMedCentralGoogle Scholar
  50. 50.
    Fukumoto T, Nakamura M, Wylie SJ, Chiaki Y, Iwai H (2013) Complete nucleotide sequence of a new isolate of passion fruit woodiness virus from Western Australia. Arch Virol 158:1821–1824CrossRefPubMedPubMedCentralGoogle Scholar
  51. 51.
    Riska SY, Inudo K, Nakamura M, Fukumoto T, Takushi T, Fuji S-I, Iwai H (2019) East Asian Passiflora distortion virus: a novel potyvirus species causing deformation of passionfruits in Japan. J Gen Plant Pathol 85:221–231CrossRefGoogle Scholar
  52. 52.
    Kraus J, Cleveland S, Putnam ML (2010) A new Potyvirus sp. infects verbena exhibiting leaf mottling symptoms. Plant Dis 94:1132–1136CrossRefPubMedPubMedCentralGoogle Scholar
  53. 53.
    Moodley V, Ibaba JD, Naidoo R, Gubba A (2014) Full-genome analyses of a Potato Virus Y (PVY) isolate infecting pepper (Capsicum annuum L.) in the Republic of South Africa. Virus Genes 49:466–476CrossRefPubMedPubMedCentralGoogle Scholar
  54. 54.
    Oruetxebarria I, Kekarainen T, Spetz C, Valkonen J (2000) Molecular characterization of Potato virus V genomes from Europe indicates limited spatiotemporal strain differentiation. Phytopathology 90:437–444CrossRefPubMedPubMedCentralGoogle Scholar
  55. 55.
    Atreya CD, Pirone TP (1993) Mutational analysis of the helper component-proteinase gene of a potyvirus: effects of amino acid substitutions, deletions, and gene replacement on virulence and aphid transmissibility. Proc Natl Acad Sci USA 90:11919–11923CrossRefPubMedPubMedCentralGoogle Scholar
  56. 56.
    Li R, Gao S, Hernandez AG, Wechter WP, Fei Z, Ling KS (2012) Deep sequencing of small RNAs in tomato for virus and viroid identification and strain differentiation. PLoS ONE 7:e37127CrossRefPubMedPubMedCentralGoogle Scholar
  57. 57.
    Orílio AF, Dusi AN, Madeira NR, Inoue-Nagata AK (2009) Characterization of a member of a new Potyvirus species infecting arracacha in Brazil. Arch Virol 154:181–185CrossRefPubMedPubMedCentralGoogle Scholar
  58. 58.
    Spetz C, Valkonen JPT (2003) Genomic sequence of Wild potato mosaic virus as compared to the genomes of other potyviruses. Arch Virol 148:373–380CrossRefPubMedPubMedCentralGoogle Scholar
  59. 59.
    Lucinda N, da Rocha WB, Inoue-Nagata AK, Nagata T (2012) Complete genome sequence of pepper yellow mosaic virus, a potyvirus, occurring in Brazil. Arch Virol 157:1397–1401CrossRefPubMedPubMedCentralGoogle Scholar
  60. 60.
    Seifers DL, Salomon R, Marie-Jeanne V, Alliot B, Signoret P, Haber S, Loboda A, Ens W, Standing KG (2000) Characterization of a novel potyvirus isolated from maize in Israel. Phytopathology 90:505–513CrossRefPubMedPubMedCentralGoogle Scholar
  61. 61.
    Yu XQ, Lan YF, Wang HY, Liu JL, Zhu XP, Valkonen JPT, Li XD (2007) The complete genomic sequence of Tobacco vein banding mosaic virus and its similarities with other potyviruses. Virus Genes 35:801–806CrossRefPubMedPubMedCentralGoogle Scholar
  62. 62.
    Hasiów-Jaroszewska B, Fares MA, Elena SF (2014) Molecular evolution of viral multifunctional proteins: the case of Potyvirus HC-pro. J Mol Evol 78:75–86CrossRefPubMedPubMedCentralGoogle Scholar
  63. 63.
    Revers F, García JA (2015) Molecular biology of potyviruses. Adv Virus Res 92:101–199CrossRefPubMedPubMedCentralGoogle Scholar
  64. 64.
    Adams MJ, Antoniw JF, Beaudoin F (2005) Overview and analysis of the polyprotein cleavage sites in the family Potyviridae. Mol Plant Pathol 6:471–487CrossRefPubMedPubMedCentralGoogle Scholar
  65. 65.
    Schechter I, Berger A (1968) On the active site of proteases. III. Mapping the active site of papain; specific peptide inhibitors of papain. Biochem Biophys Res Commun 32:898–902CrossRefPubMedPubMedCentralGoogle Scholar
  66. 66.
    Moury B, Verdin E (2012) Viruses of pepper crops in the Mediterranean basin: a remarkable stasis. Adv Virus Res 84:127–162CrossRefPubMedPubMedCentralGoogle Scholar
  67. 67.
    Orilio AF, Lucinda N, Dusi AN, Nagata T, Inoue-Nagata AK (2013) Complete genome sequence of arracacha mottle virus. Arch Virol 158:291–295CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Departamento de Ciencias de La Vida y La AgriculturaUniversidad de Las Fuerzas Armadas-ESPESangolquíEcuador
  2. 2.Centro de Investigación de Alimentos, CIAL, Facultad de Ciencias de La Ingeniería e IndustriasUniversidad Tecnológica EquinoccialQuitoEcuador

Personalised recommendations