High-throughput RNA sequencing analysis of Mallotus japonicus revealed novel polerovirus and amalgavirus.

High-throughput RNA sequencing (RNA-seq) analysis of samples from Mallotus japonicus, a traditional medicinal plant, yielded two novel RNA viruses tentatively named Mallotus japonicus virus A (MjVA) and Mallotus japonicus virus B (MjVB). The MjVA and MjVB genomes encode proteins showing amino acid sequence similarities to those of poleroviruses (the genus Polerovirus, the family Solemoviridae) and amalgaviruses (the genus Amalgavirus, the family Amalgaviridae), respectively. The MjVA genome contains seven highly overlapping open reading frames, which are translated to seven proteins through various translational mechanisms, including -1 programmed ribosomal frameshifting (PRF) at the slippery motif GGGAAAC, non-AUG translational initiation, and stop codon readthrough. The MjVB genome encodes two proteins; one of which is translated by +1 PRF mechanism at the slippery motif UUUCGN. The abundance analysis of virus-derived RNA fragments revealed that MjVA is highly concentrated in plant parts with well-developed phloem tissues as previously demonstrated in other poleroviruses, which are transmitted by phloem feeders, such as aphids. MjVB, an amalgavirus generally transmitted by seeds, is distributed in all samples at low concentrations. Thus, this study demonstrates the effectiveness and usefulness of RNA-seq analysis of plant samples for the identification of novel RNA viruses and analysis of their tissue distribution. Keywords: Polerovirus; Amalgavirus; Mallotus japonicus; RNA virus; viral genome; programmed ribosomal frameshifting.

Artemisia capillaris nucleorhabdovirus 1, a novel member of the genus Alphanucleorhabdovirus, identified in the Artemisia capillaris transcriptome.

A novel, negative-sense, single-stranded RNA virus, Artemisia capillaris nucleorhabdovirus 1 (AcNRV1), was identified in the transcriptome data of Artemisia capillaris (commonly known as capillary wormwood) root tissue. The AcNRV1 genome contains six open reading frames encoding a nucleocapsid (N), phosphoprotein, movement protein P3, matrix protein, glycoprotein, and polymerase (L). Sequence comparison and phylogenetic analysis using L and N protein sequences revealed that AcNRV1 is a novel member of the genus Alphanucleorhabdovirus, one of the six plant-infecting rhabdovirus genera of the family Rhabdoviridae. Wheat yellow striate virus and rice yellow stunt virus were identified as the closest known rhabdoviruses of AcNRV1. The conserved regulatory sequences involved in transcription termination/polyadenylation (TTP) and transcription initiation (TI) of individual genes were identified in the AcNRV1 genome with the consensus sequence 3'-(A/U)UUAUUUUU-GGG-UUG-5' (in the negative-sense genome), whereby dashes separate the TTP, untranscribed intergenic spacer, and TI elements. The AcNRV1 genome sequence will contribute to further understanding the genome structural evolution of plant rhabdoviruses. Keywords: Artemisia capillaris nucleorhabdovirus 1; plant virus; Alphanucleorhabdovirus; Rhabdoviridae.