Contribution of Next-Generation Sequencing to Complex Virome Analyses of Plants: A Case Study of Viruses Infecting Dandelion (Taraxacum officinale)

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ISBN: 978-80-972360-8-3

Contribution of Next-Generation Sequencing to Complex Virome Analyses of Plants: A Case Study of Viruses Infecting Dandelion (Taraxacum officinale)

Adam Achs1,2 , Peter Alaxin3 , Lukáš Predajňa , Zdeno Šubr , Miroslav Glasa4 ,
1 Slovak Academy of Sciences, Biomedical Research Center, Institute of Virology, Department of Virus Ecology
2 Comenius University in Bratislava, Faculty of Natural Sciences, Department of Molecular Biology
3 University of Ss. Cyril and Methodius in Trnava, Faculty of Natural Sciences, Department of Biotechnology
4 University of Ss. Cyril and Methodius in Trnava, Faculty of Natural Sciences, Department of Biology
adam.achs1@gmail.com

Next-Generation Sequencing (NGS) offers a faster, more complex, and precise tool for whole-genome analysis of viral pathogens in designated hosts. For the last couple of years, that NGS has been implemented into the field of plant virology, it has been helping tremendously with the research of host-virus interactions, viral host range, and geographical distribution. Virologists can now study these environmental interactions in more detail with the promise of the expansion of our existing current knowledge [1, 2]. As a part of the effort to understand the role of plant/virus interactions in the agroecological interface, we have studied a complex virome (genomic information of all viruses present in the host) of dandelion (Taraxacum officinale L.) because of its overall abundance and also its presence near the agriculturally important areas and fields. This plant species thus has the potential to function as a reservoir for viruses crossing the boundaries between crops and uncultured plants.

Analysis of a symptomatic dandelion plant found in an urban setting area in Bratislava revealed an infection including three plant viral species, all belonging to the same Secoviridae family [3]. The most abundant among all of them was the representative of the genus SequivirusDandelion Yellow Mosaic Virus (DaYMV), generating most of the bioinformatic data. We were even able to distinguish between two distinct isolates (GenBank accession numbers MT559283.1 and MT559284.1). The other two species – Lettuce Secovirus 1 (LS1) and Lettuce Waikavirus 1 (LW1) – have their genomic RNA represented by a smaller number of copies, thus only partial genomes were obtained. In addition, the fourth viral species – Lettuce Chordovirus 1 (LCh1) from a different family of Betaflexiviridae, was also present in the sample, but only in a very small number of RNA copies. Almost all of the viral species discussed above are known pathogens of lettuce including newly identified ones (LW1 and LCh1) [4, 5, 6], widening the knowledge of their natural host range. Our work further underlines the usefulness of the NGS approach to study virus occurrence in the environmental samples.

Poďakovanie: 

This research was supported by grants APVV-18-0005 from the Slovak Research and Development Agency and VEGA 2/0030/20 from the Scientific Grant Agency of the Ministry of Education and Slovak Academy of Sciences.

Zdroje: 

[1] Datta, S., Budhauliya, R., Das, B., Chatterjee, S., Vanlalhmuaka, Veer, V. (2015) Next-generation sequencing in clinical virology: Discovery of new viruses. World. J. Virol., 4: 265-276. 

[2] Goodwin, S., McPherson, J.D., McCombie, W.R. (2016). Coming of age: ten years of next-generation sequencing technologies. Nat. Rev., 17: 333-351.

[3] Jadao, A. S., Krause-Sakate, R., Liberti, D., Pavan, M. A., Echer, M. M., Svanella-Dumas, L., Zerbini, F. M., Candresse, T., Le Gall, O. (2007). Further characterization of two sequiviruses infecting lettuce and development of specific RT-PCR primers. Arch. Virol., 152(5): 999-1007.

[4] Micali, G., Fox, A., Hany, U., Skelton, A., Jackson, L., Buxton-Kirk, A., Burns, C., Wright, K., Adams, I. P. (2017). A novel virus of the family Secoviridae detected in UK lettuce. (Unpublished: https://www.ncbi.nlm.nih.gov/nuccore/KX925437)

[5] Svanella-Dumas, L., Tsarmpopoulos, I., Marais, A., Faure, C., Theil, S., Glasa, M., Predajna, L., Gaudin, J., De Oliveira, M. L., Krause-Sakate, R., Candresse, T. (2021). Molecular and biological characterization of novel and known Sequiviridae members infecting lettuce (Unpublished: https://www.ncbi.nlm.nih.gov/nuccore/MT348710https://www.ncbi.nlm.nih.gov/nuccore/MT559284)

[6] Svanella-Dumas, L., Tsarmpopoulos, I., Marais, A., Theil, S., Faure, C., Gaudin, J., Candresse, T. (2018). Complete genome sequence of lettuce chordovirus 1 isolated from cultivated lettuce in France. Arch. Virol., 163: 2543-2545.