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High-Throughput Sequencing Reveals Bell Pepper Endornavirus Infection in Pepper (Capsicum annum) in Slovakia and Enables Its Further Molecular Characterization

1
Biomedical Research Center of the Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 84505 Bratislava, Slovak Republic
2
Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Nám. J. Herdu 2, 91701 Trnava, Slovak Republic
3
National Agricultural and Food Centre, Research Institute of Plant Production, Bratislavská cesta 122, 92168 Piešťany, Slovak Republic
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Institute of High Mountain Biology, University of Žilina, Univerzitná 8215/1, 010 26 Žilina, Slovak Republic
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Comenius University Science Park, Comenius University in Bratislava, Ilkovičova 8, 841 04 Bratislava, Slovak Republic
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Department of Microbiology and Virology, Comenius University in Bratislava, Ilkovičova 6, 841 04 Bratislava, Slovak Republic
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Department of Molecular Biology, Comenius University in Bratislava, Ilkovičova 6, 841 04 Bratislava, Slovak Republic
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Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
*
Author to whom correspondence should be addressed.
Plants 2020, 9(1), 41; https://doi.org/10.3390/plants9010041
Received: 28 November 2019 / Revised: 21 December 2019 / Accepted: 24 December 2019 / Published: 26 December 2019
(This article belongs to the Special Issue Diagnosis and Control of Plant Viral Diseases)
Ribosomal RNA-depleted total RNAs from a sweet pepper plant (Capsicum annuum, labelled as N65) grown in western Slovakia and showing severe virus-like symptoms (chlorosis, mottling and deformation of leaf lamina) were subjected to high-throughput sequencing (HTS) on an Illumina MiSeq platform. The de novo assembly of ca. 5.5 million reads, followed by mapping to the reference sequences, revealed the coinfection of pepper by several viruses; i.e., cucumber mosaic virus (CMV), watermelon mosaic virus (WMV), pepper cryptic virus 2 (PCV2) and bell pepper endornavirus (BPEV). A complete polyprotein-coding genomic sequence (14.6 kb) of BPEV isolate N65 was determined. A comparison of BPEV-N65 sequences with BPEV genomes available in GenBank showed 86.1% to 98.6% identity at the nucleotide level. The close phylogenetic relationship with isolates from India and China resulted in their distinct grouping compared to the other BPEV isolates. Further analysis has revealed the presence of BPEV in sweet or chili peppers obtained from various sources and locations in Slovakia (plants grown in gardens, greenhouse or retail shop). Additionally, the partial sequencing of two genomic portions from 15 BPEV isolates revealed that the Slovak isolates segregated into two molecular clusters, indicating a genetically distinct population (mean inter-group nucleotide divergence reaching 12.7% and 14.5%, respectively, based on the genomic region targeted). Due to the mix infections of BPEV-positive peppers by potato virus Y (PVY) and/or CMV, the potential role of individual viruses in the observed symptomatology could not be determined. This is the first evidence and characterization of BPEV from the central European region. View Full-Text
Keywords: high-throughput sequencing; HTS; endornavirus; pepper; genome; genetic diversity high-throughput sequencing; HTS; endornavirus; pepper; genome; genetic diversity
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Tomašechová, J.; Hančinský, R.; Predajňa, L.; Kraic, J.; Mihálik, D.; Šoltys, K.; Vávrová, S.; Böhmer, M.; Sabanadzovic, S.; Glasa, M. High-Throughput Sequencing Reveals Bell Pepper Endornavirus Infection in Pepper (Capsicum annum) in Slovakia and Enables Its Further Molecular Characterization. Plants 2020, 9, 41.

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