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Identification of a new virus from the family Luteoviridae in Miscanthus sinensis

Dimitre Mollov: USDA-ARS, BARC, National Germplasm Recourses Laboratory

<div><em>Sugarcane Yellow Leaf Virus</em> (SCYLV) is a widespread and economically important virus infecting sugarcane. <em>Miscanthus,</em> a sugarcane relative, is considered resistant to SCYLV and is used in sugarcane breeding. We detected a new virus in a quarantined <em>Miscanthus</em> <em>sinensis </em>accession using high throughput sequencing (HTS). Leaves exhibiting yellowing symptoms were selected for total RNA extraction and used as templates for ribosomal-depleted RNA library preparation. The resulting libraries were sequenced on an Illumina NextSeq 500 platform. Sequence reads were assembled into contigs that revealed a single virus infection. To complete the genome assembly the 5’ and 3’ ends were cloned, Sanger sequenced, and combined with the HTS data. The complete genome is 5,859 nt and comprises six open reading frames with an organization like SCYLV and phylogenetic relatedness to <em>Luteoviridae</em>. At the whole genome level, the highest nucleotide sequence identity (79%) was to SCYLV. A BLASTp analysis of the CP amino acid sequences showed highest identity to SCYLV (79-86%) and wheat leaf yellowing-associated virus (WLYaV) (81%). The RdRp amino acid sequences had highest identity to SCYLV (79-86%) and to WLYaV (81%). These percent identities for both CP and RdRp are below the species demarcation criteria. Identifying and characterizing this new virus is important for developing improved diagnostic methods and will contribute to quarantine and disease management efforts.</div>