Genomic Analysis of a Novel Torradovirus “Rehmannia Torradovirus Virus”: Two Distinct Variants Infecting Rehmannia glutinosa

TL;DR

A new virus called Rehmannia torradovirus virus was discovered infecting a medicinal plant, with two distinct variants identified through genomic analysis.

Contribution

Discovery and classification of a novel Torradovirus species infecting Rehmannia glutinosa with two distinct genomic variants.

Findings

ReTV strains were classified into two distinct variants based on genomic and sequence analysis.

ReTV detection rate was 100% in all tested Rehmannia glutinosa samples.

Phylogenetic analysis showed ReTV is closely related to squash chlorotic leaf spot virus.

Abstract

Rehmannia glutinosa, a crucial medicinal plant native to China, is extensively cultivated across East Asia. We used high-throughput sequencing to identify viruses infecting R. glutinosa with mosaic, leaf yellowing, and necrotic symptoms. A novel Torradovirus, which we tentatively named “Rehmannia torradovirus virus” (ReTV), was identified. The complete sequences were obtained through reverse-transcription polymerase chain reaction (RT-PCR), 5′ and 3′ rapid amplification of cDNA ends, and Sanger sequencing. The amino acid sequence alignment between the ReTV-52 isolate and known Torradovirus species in the Pro-Pol and coat protein regions were 51.3–73.3% and 37.1–68.1%, respectively. Meanwhile, the amino acid sequence alignment between the ReTV-8 isolate and known Torradovirus species in the Pro-Pol and coat protein regions were 52.7–72.8% and 36.8–67.5%, respectively. The sequence analysis classified ten ReTV strains into two variants. The ReTV-52 genome has two RNA segments of 6939 and 4569 nucleotides, while that of ReTV-8 consists of two RNA segments containing 6889 and 4662 nucleotides. Sequence comparisons and phylogenetic analysis showed ReTV strains clustered within the Torradovirus, exhibiting the closet relation to the squash chlorotic leaf spot virus. The RT-PCR results showed a 100% ReTV detection rate in all 60 R. glutinosa samples. Therefore, ReTV should be classified as a novel Torradovirus species. ReTV is potentially dangerous to R. glutinosa, and necessitating monitoring this virus in the field.

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