Whole Genome Characterization of Prunus Necrotic Ringspot Virus and Prune Dwarf Virus Infecting Stone Fruits in Russia

被引:1
作者
Chirkov, Sergei [1 ]
Sheveleva, Anna [1 ]
Tsygankova, Svetlana [2 ]
Slobodova, Natalia [2 ,3 ]
Sharko, Fedor [2 ,4 ]
Petrova, Kristina [2 ,5 ]
Mitrofanova, Irina [6 ]
机构
[1] Lomonosov Moscow State Univ, Fac Biol, Dept Virol, Moscow 119234, Russia
[2] Kurchatov Inst, Natl Res Ctr, Moscow 123182, Russia
[3] HSE Univ, Fac Biol & Biotechnol, Moscow 101000, Russia
[4] Russian Acad Sci, Fed Res Ctr Fundamentals Biotechnol, Moscow 119071, Russia
[5] Res Ctr Med Genet, Moscow 115522, Russia
[6] Russian Acad Sci, Tsitsin Main Bot Garden, Moscow 127276, Russia
关键词
Prunus spp; virome; high-throughput sequencing; prunus necrotic ringspot virus; prune dwarf virus; full-length genomes; ourmia-like virus; MOLECULAR CHARACTERIZATION; VARIABILITY; PROTEIN;
D O I
10.3390/horticulturae9080941
中图分类号
S6 [园艺];
学科分类号
0902 ;
摘要
We conducted a survey of the phytosanitary status of the Prunus germplasm collection in the Nikita Botanical Gardens, Yalta, Russia. The virome of plants displaying virus-like symptoms was studied using Illumina MiSeq high-throughput sequencing. Reads related to prunus necrotic ringspot virus (PNRSV), prune dwarf virus (PDV), and ourmia-like virus 1 (OuLV1) were generated in a number of samples. Near complete genomes of two divergent PNRSV isolates, PDV isolate, and a contig partly covered OuLV1 genome were assembled de novo using the metaSPAdes program. The structure of the genomic RNA1, RNA2, and RNA3 of the new ilarvirus isolates was shown to be typical of PNRSV and PDV. This is the first report and characterization of the PNRSV and PDV full-length genomes from Russia, expanding the information on their geographical distribution and genetic diversity. An open reading frames (ORF)-based phylogeny of all full-length PNRSV and PDV genomes available in GenBank divided each ORF into two or three main clusters. A number of isolates migrated from one cluster to another cluster, depending on the analyzed genome segment. The different branching order may indicate reassortment in the evolutionary history of some PDV and PNRSV isolates.
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页数:17
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