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12 pages, 3583 KiB

Open AccessArticle

Identification and Characterization of a Novel Umbra-like Virus, Strawberry Virus A, Infecting Strawberry Plants

by Igor Koloniuk, Jaroslava Přibylová, Radek Čmejla, Lucie Valentová and Jana Fránová

Plants 2022, 11(5), 643; https://doi.org/10.3390/plants11050643 - 26 Feb 2022

Cited by 8 | Viewed by 2200

Abstract

A novel RNA virus infecting strawberry plants was discovered using high-throughput sequencing. The analyzed plant was simultaneously infected with three different genetic variants of the virus, provisionally named strawberry virus A (StrVA). Although StrVA is phylogenetically clustered with several recently discovered, unclassified plant [...] Read more.

A novel RNA virus infecting strawberry plants was discovered using high-throughput sequencing. The analyzed plant was simultaneously infected with three different genetic variants of the virus, provisionally named strawberry virus A (StrVA). Although StrVA is phylogenetically clustered with several recently discovered, unclassified plant viruses, it has a smaller genome and several unique features in its genomic organization. A specific and sensitive qPCR system for the detection of identified StrVA genetic variants was designed. A survey conducted in the Czech Republic revealed that StrVA was present in 28.3% of strawberry samples (n = 651) from various origins (plantations, gardens, and propagation material). Sequencing of 48 randomly selected StrVA-positive strawberry samples showed that two or all three StrVA genetic variants were present in 62.5% of the samples in various proportions. StrVA was found in mixed infections with other viruses (strawberry mild yellow edge virus, strawberry crinkle virus, strawberry mottle virus, strawberry polerovirus 1, or strawberry virus 1) in 57.1% of the samples, which complicated the estimation of its biological relevance and impact on the health status of the plants. Full article

(This article belongs to the Special Issue Identification and Molecular Characterization of Plant Virus)

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16 pages, 3720 KiB

Open AccessArticle

Identification of Viruses Infecting Oats in Korea by Metatranscriptomics

by Na-Kyeong Kim, Hyo-Jeong Lee, Sang-Min Kim and Rae-Dong Jeong

Plants 2022, 11(3), 256; https://doi.org/10.3390/plants11030256 - 19 Jan 2022

Cited by 7 | Viewed by 2164

Abstract

Controlling infectious plant viruses presents a constant challenge in agriculture. As a source of valuable nutrients for human health, the cultivation of oats (Avena sativa L.) has recently been increased in Korea. To date, however, few studies have been undertaken to identify [...] Read more.

Controlling infectious plant viruses presents a constant challenge in agriculture. As a source of valuable nutrients for human health, the cultivation of oats (Avena sativa L.) has recently been increased in Korea. To date, however, few studies have been undertaken to identify the viruses infecting oats in this country. In this study, we carried out RNA-sequencing followed by bioinformatics analyses to understand the virosphere in six different geographical locations in Korea where oats are cultivated. We identified three different virus species, namely, barley yellow dwarf virus (BYDV) (BYDV-PAV and BYDV-PAS), cereal yellow dwarf virus (CYDV) (CYDV-RPS and CYDV-RPV), and rice black-streaked dwarf virus (RBSDV). Based on the number of virus-associated reads and contigs, BYDV-PAV was a dominant virus infecting winter oats in Korea. Interestingly, RBSDV was identified in only a single region, and this is the first report of this virus infecting oats in Korea. Single nucleotide polymorphisms analyses indicated that most BYDV, CYDV, and RBSDV isolates show considerable genetic variations. Phylogenetic analyses indicated that BYDVs and CYDVs were largely grouped in isolates from Asia and USA, whereas RBSDV was genetically similar to isolates from China. Overall, the findings of this study provide a preliminary characterization of the types of plant viruses infecting oats in six geographical regions of Korea. Full article

(This article belongs to the Special Issue Identification and Molecular Characterization of Plant Virus)

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8 pages, 2061 KiB

Open AccessBrief Report

Complete Genome Sequence of an Isolate of Passiflora chlorosis virus from Passion Fruit (Passiflora edulis Sims)

by Patricia Fresnillo, Sara Jover-Gil, Alon Samach and Héctor Candela

Plants 2022, 11(14), 1838; https://doi.org/10.3390/plants11141838 - 13 Jul 2022

Cited by 1 | Viewed by 2021

Abstract

We report the first complete genome sequence of an isolate of Passiflora chlorosis virus (PaCV), a member of the Potyviridae family, identified in passion fruit (Passiflora edulis Sims) plants grown in Israel. The assembled genome is 9672 nucleotides long and encodes a [...] Read more.

We report the first complete genome sequence of an isolate of Passiflora chlorosis virus (PaCV), a member of the Potyviridae family, identified in passion fruit (Passiflora edulis Sims) plants grown in Israel. The assembled genome is 9672 nucleotides long and encodes a 3084 amino acids polyprotein that is predicted to be proteolytically cleaved into 10 mature peptides. Our analysis of the genome sequence shows that PaCV is a distinct species, sharing 68.5% nucleotide sequence identity and 71.5% amino acid sequence identity with isolates of the bean common mosaic necrosis virus (BCMNV), the most closely related virus classified within the genus Potyvirus. Using quantitative PCR, we detected the virus in RNA samples from leaves exhibiting symptoms of infection, with higher levels in clearly chlorotic leaves, but not in those from healthy leaves. Full article

(This article belongs to the Special Issue Identification and Molecular Characterization of Plant Virus)

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