Illuminating the Plant Rhabdovirus Landscape through Metatranscriptomics Data

Abstract

Rhabdoviruses infect a large number of plant species and cause significant crop diseases. They have a negative-sense, single-stranded unsegmented or bisegmented RNA genome. The number of plant-associated rhabdovirid sequences has grown in the last few years in concert with the extensive use of high-throughput sequencing platforms. Here, we report the discovery of 27 novel rhabdovirus genomes associated with 25 different host plant species and one insect, which were hidden in public databases. These viral sequences were identified through homology searches in more than 3000 plant and insect transcriptomes from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) using known plant rhabdovirus sequences as the query. The identification, assembly and curation of raw SRA reads resulted in sixteen viral genome sequences with full-length coding regions and ten partial genomes. Highlights of the obtained sequences include viruses with unique and novel genome organizations among known plant rhabdoviruses. Phylogenetic analysis showed that thirteen of the novel viruses were related to cytorhabdoviruses, one to alphanucleorhabdoviruses, five to betanucleorhabdoviruses, one to dichorhaviruses and seven to varicosaviruses. These findings resulted in the most complete phylogeny of plant rhabdoviruses to date and shed new light on the phylogenetic relationships and evolutionary landscape of this group of plant viruses. Furthermore, this study provided additional evidence for the complexity and diversity of plant rhabdovirus genomes and demonstrated that analyzing SRA public data provides an invaluable tool to accelerate virus discovery, gain evolutionary insights and refine virus taxonomy.

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

“…In rhabdovirus genomes, the gene junction regions have a conserved regulatory sequence involved in the transcription termination and polyadenylation of the preceding gene transcript (the TTP element) as well as the transcriptional initiation and capping of the following gene transcript (the TI element) (Jackson et al, 2005;Ogino and Green, 2019;Bejerman et al, 2021;Shin et al, 2021). The gene junction regions of the AcNRV1 genome, together with those of the WYSV and RYSV genomes, were analyzed to predict conserved sequences.…”

“…Rhabdoviruses (the family Rhabdoviridae) infect animals and plants and have negative-sense, singlestranded RNA genomes (Dietzgen et al, 2017;Walker et al, 2018;Bejerman et al, 2021). The family Rhabdoviridae comprises three subfamilies, 40 genera, and more than ocapsid (N), phosphoprotein (P), movement protein 3 (P3), matrix protein (M), surface glycoprotein (G), and large multi-functional protein (L), in the order of 3'-N-P-P3-M-G-L-5' (Walker et al, 2018).…”

“…Rhabdovirus genes are transcribed into separate mRNAs from the negative-sense RNA genome through a transcriptase complex composed of the L and P proteins (Jackson et al, 2005;Walker et al, 2011). The gene junction regions of rhabdoviruses contain conserved regulatory sequences called transcription termination/polyadenylation (TTP) and transcription initiation (TI) elements that mediate polyadenylation of the preceding gene transcript and transcriptional initiation of the next gene, respectively (Jackson et al, 2005;Goh et al, 2020;Bejerman et al, 2021;Shin et al, 2021). One or several nucleotides located between the TTP and TI elements are not transcribed; this region is called the untranscribed intergenic spacer (UIS).…”

“…One or several nucleotides located between the TTP and TI elements are not transcribed; this region is called the untranscribed intergenic spacer (UIS). For example, the consensus sequences of the WYSV and RYSV conserved regulatory sequences are presented as 3'-UAAAUUUUU-GGGG-UUG-5' and 3'-AUUAUUUUU -GGG-UUG-5', respectively, whereby dashes (-) separate the TTP, UIS, and TI elements (Huang et al, 2003;Liu et al, 2018;Bejerman et al, 2021).…”

“…When plant tissues are latently infected with RNA viruses, full-length virus genome sequences can be obtained by assembling transcriptome reads and identifying virus genome contigs (Bejerman et al, 2020;Choi et al, 2021;Goh et al, 2021;. Many novel rhabdovirus genome sequences, including those of Trichosanthes associated rhabdovirus 1, Agave tequilana virus 1, and Zostera as-sociated varicosavirus 1, have previously been identified in plant transcriptome data (Goh et al, 2020;Bejerman et al, 2021;Shin et al, 2021). In the present study, the genome sequence of a novel rhabdovirus belonging to the genus Alphanucleorhabdovirus (the family Rhabdoviridae) was identified in Artemisia capillaris (commonly known as capillary wormwood) root transcriptome data (Ichihashi et al, 2018).…”