Analysis of Virome by High-Throughput Sequencing Revealed Multiple Infection and Intra-Virus Diversity in a Single Grapevine Plant

PDF

Authors: Miroslav Glasa, Lukáš Predajňa, Nina Sihelská, Katarína Šoltys and Ana-Belén Ruiz-García

Volume/Issue: Volume 23: Issue 1

Published online: 26 May 2020

Pages:

DOI: https://doi.org/10.2478/ahr-2020-0009


Abstract

The ribosomal-depleted total RNA from white-berry grapevine (Vitis vinifera, SK933) plant showing severe chlorosis and downrolling of leaves was used for the high-throughput sequencing (HTS) analysis in order to unravel the potential contribution of the viral pathogens to the symptomatology observed. The combination of de novo assembly and mapping of ca. 1.1 millions of HTS reads enabled to identify and characterise a complex viral/viroid infection involving Grapevine leafroll-associated virus-2 (GLRaV-2), Grapevine leafroll-associated virus-3 (GLRaV-3), Grapevine rupestris stem pitting-associated virus (GRSPaV), Grapevine rupestris vein feathering virus (GRVFV), Grapevine Syrah virus-1 (GSyV-1) and Hop stunt viroid (HSVd). The determined nearly complete genomes of GLRaV-2 SK933 showed its high genetic divergence from previously characterised isolates. In case of GRSPaV, two variants representing different evolutionary lineages have been identified in the plant. The results further pinpoint the complexity of grapevine viral diseases and show that mixed virus infection of grapevine is rather a rule than an exception.


Keywords: Vitis vinifera, virus, diversity, next generation sequencing

PDF

References

ALMEIDA, R.P. – DAANE, K.M. – BELL, V.A. – BLAISDELL, G.K. – COOPER, M.L. – HERRBACH, E. – PIETERSEN, G. 2013. Ecology and management of grapevine leafroll disease. In Frontiers in Microbiology, vol. 4, 2013, pp. 94, doi:10.3389/fmicb.2013.00094.


BASSO, M.S. – FAJARDO, T.V.M., – SALDARELLI, P. 2017. Grapevine virus diseases: economic impact and current advances in viral prospection and management. In Revista Brasileira de Fruticultura, vol. 39, 2017, e-411, doi: 10.1590/0100-29452017411


BRISTER, J.R. – AKO-ADJEI, D. – BAO, Y. – BLINKOVA, O. 2015. NCBI Viral Genomes Resource. In Nucleic Acids Research, vol. 43, 2015, pp. 571–577. doi: 10.1093/nar/gku1207


GLASA, M. – PREDAJŇA, L. 2012. Partial sequence analysis of a grapevine leafroll-associated virus 3 isolate from Slovakia. In Journal of Plant Pathology, vol. 94, 2012, pp. 675–679.


GLASA, M. – PREDAJŇA, L. – KOMÍNEK, P. – NAGYOVÁ, A. – CANDRESSE, T. – OLMOS, A. 2014. Molecular characterization of divergent grapevine Pinot gris virus isolates and their detection in Slovak and Czech grapevines. In Archives of Virology, vol. 159, 2014, pp. 2103–2107.


GLASA, M. – PREDAJŇA, L. – KOMÍNEK, P. 2011. Grapevine fleck virus isolates split into two distinct molecular groups. In Journal of Phytopathology, vol. 159, 2011, pp. 805–807.


GLASA, M. – PREDAJŇA, L. – SIHELSKÁ, N. – ŠOLTYS, K. – RUIZGARCÍA, A.B. – OLMOS, A. – WETZEL, T. – SABANADZOVIC, S. 2018. Grapevine virus T is relatively widespread in Slovakia and Czech Republic and genetically diverse. In Virus Genes, vol. 54, 2018, pp. 737–741.


GLASA, M. – PREDAJŇA, L. – ŠOLTYS, K. – SABANADZOVIC, S. – OLMOS, A. 2015. Detection and molecular characterisation of Grapevine Syrah virus-1 isolates from Central Europe. In Virus Genes, vol. 51, 2015, pp. 112–121.


GLASA, M. – PREDAJŇA, L. – ŠOLTYS, K. – SIHELSKÁ, N. – NAGYOVÁ, A. – WETZEL, T. – SABANADZOVIC, S. 2017. Analysis of Grapevine rupestris stem pitting-associated virus in Slovakia reveals differences in intra-host population diversity and naturally occurring recombination events. In The Plant Pathology Journal, vol. 33, 2017, pp. 34–42.


GLASA, M. – PREDAJŇA, L. – WETZEL, T. – ŠOLTYS, K. – SABANADZOVIC, S. 2019. First report of Grapevine rupestris vein feathering virus in grapevine in Slovakia. In Plant Disease, vol. 103, 2019, pp. 170.


KOMÍNEK, P. – GLASA, M. – KOMÍNKOVÁ, M. 2009. Analysis of multiple virus-infected grapevine plant reveals persistence but uneven virus distribution. In Acta Virologica, vol. 53, 2009, pp. 281–285.


KUMAR, S. – STECHER, G. – TAMURA, K. 2016. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. In Molecular Biology and Evolution, vol. 33, 2016, pp. 1870–1874.


MALIOGKA, V.I. – MARTELLI, G.P. – FUCHS, M. – KATIS, N.I. 2015. Control of viruses infecting grapevine. In Advances in Virus Research, vol. 91, 2015, pp. 175–227.


MALIOGKA, V.I. – MINAFRA, A. – SALDARELLI, P. – RUIZ-GARCÍA, A.B. – GLASA, M. – KATIS, N. – OLMOS, A. 2018. Recent advances on detection and characterization of fruit tree viruses using high-throughput sequencing technologies. In Viruses, vol. 10, pii: E436, doi: 10.3390/v10080436


MARTELLI, G.P. 2017. An overview on grapevine viruses, viroids, and the diseases they cause. In Grapevine Viruses: Molecular Biology, Diagnostics and Management (Meng, B. – Martelli, G.P. – Golino, D.A. – Fuchs, M. eds.)- Springer International Publishing, 2017, pp. 31–46. doi: 10.1007/978-3-319-57706-7_2


PREDAJŇA, L. – GAŽIOVÁ, A. – HOLOVIČOVÁ, E. – GLASA, M. 2013. Analysis of a short genomic region of Grapevine leafroll-associated virus 1 (GLRaV-1) reveals the presence of two different molecular groups of isolates in Slovakia. In Acta Virologica, vol. 57, 2013, pp. 353–356.


PREDAJŇA, L. – GLASA, M. 2016. Partial sequence analysis of geographically close Grapevine virus A isolates reveals their high regional variability and an intra-isolate heterogeneity. In Journal of Phytopathology, vol. 164, 2016, pp. 427–431.


ROZAS, J. – FERRER-MATA, A. – SÁNCHEZ-DELBARRIO, J.C. – GUIRAO-RICO, S. – LIBRADO, P. – RAMOS-ONSINS, S.E. – SÁNCHEZGRACIA, A. 2017. DnaSP 6: DNA Sequence Polymorphism Analysis of large data sets. In Molecular Biology and Evolution, vol. 34, 2017, pp. 3299–3302.


SALDARELLI, P. – GIAMPETRUZZI, A – MAREE, H – AL RWAHNIH, M. 2017. High-Throughput Sequencing: Advantages beyond virus identification. In Grapevine Viruses: Molecular Biology, Diagnostics and Management (Meng, B. – Martelli, G.P. – Golino, D.A. – Fuchs, M. eds.), Springer International Publishing, 2017, pp. 625–642, doi: 10.1007/978-3-319-57706-7_30


VELASCO, R. – ZHARKIKH, A. – TROGGIO, M. – CARTWRIGHT, D.A. – CESTARO, A. et al. 2007. A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. In PLoS One, vol. 2, 2007, E1326. doi: 10.1371/journal.pone.0001326


ZHERDEV, A.V. – VINOGRADOVA, S.V. – BYZOVA, N.A. – POROTIKOVA, E.V. – KAMIONSKAYA, A.M. – DZANTIEV, B.B. 2018. Methods for the diagnosis of grapevine viral infections: A review. In Agriculture, vol. 8, 2018, pp. 195; doi: 10.3390/agriculture8120195.