Detection and characterization of a second carlavirus in Rosa sp.
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ANNOTATED SEQUENCE RECORD
Detection and characterization of a second carlavirus in Rosa sp. Alfredo Diaz‑Lara1 · Dimitre Mollov2 · Deborah Golino1 · Maher Al Rwahnih1 Received: 5 June 2020 / Accepted: 18 September 2020 © Springer-Verlag GmbH Austria, part of Springer Nature 2020
Abstract A new virus resembling members in the genus Carlavirus was identified in an Out of Yesteryear rose (Rosa sp.) by highthroughput sequencing. The virus was discovered during the screening of a rose virus collection belonging to Foundation Plant Services (UC-Davis). The full genome of the virus is 8825 nt long, excluding a poly(A) tail, and includes six predicted genes coding for replicase, triple gene block, coat protein (CP), and nucleic acid binding protein. The closest relative of the putative virus is rose virus A (RVA; genus Carlavirus), with 75% and 78% aa sequence identity in the replicase and CP, respectively. The relationship with RVA and other carlaviruses was supported by phylogenetic analyses using replicase and CP sequences. Based on genome organization, sequence identity, and phylogenetic analysis, the virus found in the Out of Yesteryear plant represents a new member of the genus Carlavirus and is provisionally named “rose virus B” (RVB). Further testing by reverse transcription PCR confirmed the presence of RVB in the original source and seven additional rose selections from the same collection. Recently, rose virus A (RVA) was discovered in a symptomatic memorial rose (Rosa wichuraiana Crép.) located in a private rosarium in Maryland, USA [1]. RVA represented the first member of the genus Carlavirus (family Betaflexiviridae) identified and characterized in rose plants. The typical genome organization of carlaviruses comprises six open reading frames (ORFs) encoding replicase, coat protein (CP), nucleic acid binding protein, and triple gene block (TGB). In 2019, during the high-throughput sequencing (HTS) analysis of an asymptomatic Out of Yesteryear rose located in a rose virus collection at Foundation Plant Services (FPS, UC-Davis), a partial sequence with homology to members of the genus Carlavirus was identified and further investigated. In this report, we describe a new carlavirus infecting rose and provide primer sequences for its detection by reverse transcription PCR (RT-PCR).
Handling Editor: Sead Sabanadzovic. * Maher Al Rwahnih [email protected] 1
Department of Plant Pathology, University of CaliforniaDavis, Davis, CA 95616, USA
USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD 20705, USA
2
Following the methodology described by Diaz-Lara et al. [2], total nucleic acid (TNA) was extracted from the Out of Yesteryear rose. TNA extracts were used as template for cDNA library construction, employing a TruSeq Stranded Total RNA with Ribo-Zero Plant Kit (Illumina) as per the manufacturer’s protocol. The cDNA library was sequenced using the Illumina NextSeq 500 platform and yielded approximately 19 million data reads. Subsequently, de novo contigs were generated from these reads
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