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

被引:17
|
作者
Tomasechova, Jana [1 ,2 ]
Hancinsky, Richard [2 ]
Predajna, Lukas [1 ]
Kraic, Jan [2 ,3 ]
Mihalik, Daniel [2 ,4 ]
Soltys, Katarina [5 ,6 ]
Vavrova, Silvia [7 ]
Boehmer, Miroslav [7 ]
Sabanadzovic, Sead [8 ]
Glasa, Miroslav [1 ,2 ]
机构
[1] Slovak Acad Sci, Inst Virol, Biomed Res Ctr, Dubravska Cesta 9, Bratislava 84505, Slovakia
[2] Univ Ss Cyril & Methodius, Fac Nat Sci, Nam J Herdu 2, Trnava 91701, Slovakia
[3] Res Inst Plant Prod, Natl Agr & Food Ctr, Bratislavska Cesta 122, Piestany 92168, Slovakia
[4] Univ Zilina, Inst High Mt Biol, Univ 8215-1, Zilina 01026, Slovakia
[5] Comenius Univ, Comenius Univ Sci Pk, Ilkovicova 8, Bratislava 84104, Slovakia
[6] Comenius Univ, Dept Microbiol & Virol, Ilkovicova 6, Bratislava 84104, Slovakia
[7] Comenius Univ, Dept Mol Biol, Ilkovicova 6, Bratislava 84104, Slovakia
[8] Mississippi State Univ, Dept Biochem Mol Biol Entomol & Plant Pathol, Mississippi State, MS 39762 USA
来源
PLANTS-BASEL | 2020年 / 9卷 / 01期
基金
美国食品与农业研究所;
关键词
high-throughput sequencing; HTS; endornavirus; pepper; genome; genetic diversity; IDENTIFICATION; VIRUSES;
D O I
10.3390/plants9010041
中图分类号
Q94 [植物学];
学科分类号
071001 ;
摘要
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.
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页数:9
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