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Emerging and population analysis of Grapevine Pinot gris virus isolates from Iran

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Abstract

Grapevine Pinot gris virus (GPGV) is a novel member of Trichovirus genus in Betaflexiviridae family. During 2018–2019, 114 leaf and green shoot samples were collected from the main vineyards in Iran Zanjan, Hamedan and East Azerbaijan provinces. After total RNA extraction and cDNA synthesis, the samples were tested by PCR assay using two pairs of specific primers corresponding to the coat protein (CP) and movement protein (MP) regions of GPGV, in which 6 out of 114 samples were found to be infected by GPGV. Population genetics analysis and molecular evolution of GPGV were done based on the CP and MP gene sequences of six new Iranian isolates and 53 additional isolates from several different countries in three continents: Asia, Europe, and America. The phylogenetic tree of GPGV isolates was clustered into two independent clades with significant FST values (> 0.44). The ω values were calculated < 1 for the GPGV isolates for both genes. These findings demonstrated that the GPGV evolutionary selection pressure is under negative selection. To our knowledge, this is the first detailed study on the molecular characterization, phylogenetic analysis, and provide a better understanding of the population evolution of GPGV isolates from vineyards in Iran. The new Iranian isolates were lied in a new cluster near to European isolates.

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References

  • Abadkhah M, Koolivand D, Eini O (2018) A new distinct clade for Iranian Tomato spotted wilt virus isolates based on the polymerase, nucleocapsid, and non-structural genes. Plant Pathol J 34(6):514–531

    Article  CAS  Google Scholar 

  • Abadkhah M, Hajizadeh M, Koolivand D (2020) Global population genetic structure of Bean common mosaic virus. Arch Phytopathol Pflanzenschutz 53(5–6):266–281. https://doi.org/10.1080/03235408.2020.1743525

    Article  CAS  Google Scholar 

  • Abou Kubaa R, Choueiri E, Jreijiri F, Khoury YE, Saldarelli P (2019) First report of Grapevine Pinot gris virus in Lebanon and the Middle East. J Plant Pathol. https://doi.org/10.1007/s42161-019-00453-w

    Article  Google Scholar 

  • Bertazzon N, Filippin L, Forte V, Angelini E (2015) Grapevine Pinot gris virus seems to have recently been introduced to vineyards in Veneto, Italy. Arch Virol. https://doi.org/10.1007/s00705-015-2718-2

    Article  PubMed  Google Scholar 

  • Chung CT, Niemela SL, Miller RH (1989) One-step preparation of competent Escherichia coli: transformation and storage of bacterial cells in the same solution. Proc Natl Acad Sci 86(7):2172–2175

    Article  CAS  Google Scholar 

  • Cieniewicz EJ, Qiu W, Saldarelli P, Fuchs M (2020) Believing is seeing: lessons from emerging viruses in grapevine. J Plant Pathol. https://doi.org/10.1007/s42161-019-00484-3

    Article  Google Scholar 

  • Dolan PT, Whitfield ZJ, Andino R (2018) Mechanisms and concepts in RNA virus population dynamics and evolution. Annu Rev Virol 5:15.1-15.24

    Article  Google Scholar 

  • Eichmeier A, Peňázová E, Muljukina N (2018) Survey of Grapevine Pinot gris virus in certified grapevine stocks in Ukraine. Eur J Plant Pathol 152:555–560

    Article  Google Scholar 

  • Elçi E, Gazel M, Roumi V, Çag˘layan K (2018) Incidence, distribution and limited genetic variability among Turkish isolates of Grapevine Pinot gris virus from different grapevine cultivars. J Plant Dis Protect. https://doi.org/10.1007/s41348-018-0175-3

    Article  Google Scholar 

  • Fajardo TVM, Eiras M, Nickel O (2017) First report of Grapevine Pinot gris virus infecting grapevine in Brazil. Australas Plant Dis Notes 12(1):45

    Article  Google Scholar 

  • Fan XD, Dong YF, Zhang ZP, Ren F, Hu GJ, Li ZN, Zhou JP (2015) First report of Grapevine Pinot gris virus in grapevines in China. Plant Dis 100:2

    Google Scholar 

  • Fan XD, Zhang ZP, Ren F, Hu GJ, Zhou J, Li ZN, Wang G, Dong Y (2017) Occurrence and genetic diversity of Grapevine berry inner necrosis virus from grapevines in China. Plant Dis 101:144–149

    Article  CAS  Google Scholar 

  • Fu YX, Li WH (1993) Statistical tests of neutrality of mutations. Genetics 133:693–709

    Article  CAS  Google Scholar 

  • Giampetruzzi A, Roumi V, Roberto R, Malossini U, Yoshikawa N, La Notte P, Terlizzi F, Credi R, Saldarelli P (2012) A new grapevine virus discovered by deep sequencing of virus- and viroid-derived small RNAs in cv Pinot gris. Virus Res 163:262–268

    Article  CAS  Google Scholar 

  • Gentili A, Prota V, Moro G, Schianchi N, Di Lucca E, Luigi M, Faggioli F (2017) Identification of Grapevine Pinot gris virus in Sardinia and Lazio (South and Central Italy). J Plant Pathol 99:527–530

    Google Scholar 

  • Glasa M, Predajna L, Kominek P, Nagyova A, Candresse T, Olmos A (2014) Molecular characterization of divergent grapevine Pinot gris virus isolates and their detection in Slovak and Czech grapevines. Arch Virol 159:2103–2107

    Article  CAS  Google Scholar 

  • Gorbalenya AE, Lauber C (2017) Phylogeny of viruses. Ref Module Biomed Sci. https://doi.org/10.1016/B978-0-12-801238-3.95723-4

    Article  Google Scholar 

  • Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22(2):160–174

    Article  CAS  Google Scholar 

  • Hily JM, Poulicard N, Candresse T, Vigne E, Beuve M, Renault L, Velt A, Spilmont AS, Lemaire O (2020) Datamining, genetic diversity analyses, and phylogeographic reconstructions redefine the worldwide evolutionary history of Grapevine Pinot gris virus and Grapevine berry inner necrosis virus. Phytobiomes J 4(2):165–177

    Article  Google Scholar 

  • Hudson RR, Boos DD, Kaplan NL (1992a) A statistical test for detecting population subdivision. Mol Biol Evol 9:138–151

    CAS  PubMed  Google Scholar 

  • Hudson R, Slatkin RM, Maddison WP (1992b) Estimation of levels of gene flow from DNA sequence data. Genetics 132:583–589

    Article  CAS  Google Scholar 

  • Hudson RR (2000) A new statistic for detecting genetic differentiation. Genetics 155:2011–2014

    Article  CAS  Google Scholar 

  • Kosakovsky Pond SL, Frost SDW (2005) Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol 22:1208–1222

    Article  Google Scholar 

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33(7):1870–1874

    Article  CAS  Google Scholar 

  • Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms Mol. Biol Evol 35(6):1547–1549

    Article  CAS  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(21):2947–2948

    Article  CAS  Google Scholar 

  • Malagnini V, Lillo ED, Saldarelli P, Beber R, Duso C, Raiola A, Zanotelli L, Valenzano D, Giampetruzzi A, Morelli M, Ratti C, Causin R, Gualandri V (2016) Transmission of Grapevine Pinot gris virus by Colomerus vitis (Acari: Eriophyidae) to grapevine. Arch Virol 161(9):2595–2599

    Article  CAS  Google Scholar 

  • Mello B (2018) Estimating TimeTrees with MEGA and the TimeTree resource. Mol Biol Evol 35(9):2334–2342

    Article  CAS  Google Scholar 

  • Moradi R, Koolivand D, Eini O, Hajizadeh M (2017) Phylogenetic analysis of two Iranian Grapevine virus A isolates using coat protein gene sequence. Indian J Genet Plant Breed 6(1):48–57

    Google Scholar 

  • Muhire BM, Varsani A, Martin DP (2014) SDT: a virus classification tool based on pairwise sequence alignment and identity calculation. PLoS ONE 9:e108277

    Article  Google Scholar 

  • Nei M, Tajima F (1981) DNA polymorphism detectable by restriction endonucleases. Genetics 97:145–163

    Article  CAS  Google Scholar 

  • Rozas J, Sanchez-De I, Barrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496–2497

    Article  CAS  Google Scholar 

  • Rozas J, Ferrer-Mata A, Sanchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sánchez-Gracia A (2017) DnaSP 6: DNA sequence polymorphism analysis of large datasets. Mol Biol Evol 34(12):3299–3302

    Article  CAS  Google Scholar 

  • Rubio L, Guerri J, Moreno P (2013) Genetic variability and evolutionary dynamics of viruses of the family Closteroviridae. Front Microbiol 4:151. https://doi.org/10.3389/fmicb.2013.00151

    Article  PubMed  PubMed Central  Google Scholar 

  • Saldarelli P, Gualandri V, Malossini U, Glasa M (2017) Grapevine Pinot gris virus. In: Meng B, Martelli GP, Golino DA, Fuchs M (eds) Grapevine viruses: molecular biology, diagnostics and management. Springer International Publishing, New York, pp 351–363

    Chapter  Google Scholar 

  • Sokhandan-Bashir N, Melcher U (2012) Population genetic analysis of Grapevine fanleaf virus. Arch Virol 157:1919–1929

    Article  CAS  Google Scholar 

  • Su L, Bhagwat B, Bernardy M, Wiersma PA, Cheng Z, Xiang Y (2016) Molecular analysis of three new Cherry mottle leaf virus isolates reveals intra-species genetic diversity and inter-species gene transfer. Phytoparasitica 44:571–574

    Article  CAS  Google Scholar 

  • Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595

    Article  CAS  Google Scholar 

  • Tarquini G, Ermacora P, Bianchi GL, De Amicis F, Pagliari L, Martini M, Loschi A, Saldarelli P, Loi N, Musetti R (2018) Localization and subcellular association of Grapevine Pinot gris virus in grapevine leaf tissues. Protoplasma 255:923–935

    Article  CAS  Google Scholar 

  • Tarquini G, Amicis FD, Martini M, Ermacora P, Loi N, Musetti R, Bianchi GL, Firrao G (2019) Analysis of new Grapevine Pinot gris virus (GPGV) isolates from Northeast Italy provides clues to track the evolution of a newly emerging clade. Arch Virol 164(6):1655–1660

    Article  CAS  Google Scholar 

  • Tokhmechi K, Koolivand D (2019) First report of Grapevine Pinot gris virus infection in grapevine in Iran. J Plant Pathol. 102:549

    Article  Google Scholar 

  • Tsompana M, Abad J, Purugganan M, Moyer JW (2005) The molecular population genetics of the Tomato spotted wilt virus (TSWV) genome. Mol Ecol 14:53–66

    Article  CAS  Google Scholar 

  • Wu Q, Habili N (2017) The recent importation of Grapevine Pinot gris virus into Australia. Virus Genes 53(6):935–938

    Article  CAS  Google Scholar 

  • Xiao H, Shabanian M, Moore C, Li C, Meng B (2018) Survey for major viruses in commercial Vitis vinifera wine grapes in Ontario. Virol J 15:127

    Article  Google Scholar 

  • Yoshikawa N, Iida H, Goto S, Magome H, Takahashi T, Terai Y (1997) Grapevine berry inner necrosis, a new trichovirus: comparative studies with several known Trichoviruses. Arch Virol 142:1351–1363

    Article  CAS  Google Scholar 

  • Zamorano A, Medina G, Fernández C, Cui W, Quiroga N, Fiore N (2019) First report of Grapevine Pinot gris virus infecting grapevine in Chile. Plant Dis 103:6

    Article  Google Scholar 

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Authors and Affiliations

  1. Department of Plant Protection, Faculty of Agriculture, University of Zanjan, Zanjan, Iran

    Kimia Tokhmechi, Mahsa Abadkhah & Davoud Koolivand

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  1. Kimia Tokhmechi
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  2. Mahsa Abadkhah
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  3. Davoud Koolivand
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Correspondence to Davoud Koolivand.

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Tokhmechi, K., Abadkhah, M. & Koolivand, D. Emerging and population analysis of Grapevine Pinot gris virus isolates from Iran. 3 Biotech 11, 368 (2021). https://doi.org/10.1007/s13205-021-02914-5

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