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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » National Germplasm Resources Laboratory » Research » Publications at this Location » Publication #360928

Research Project: Characterizing and Detecting Pathogens to Ensure Safe Exchange of Plant Germplasm

Location: National Germplasm Resources Laboratory

Title: New Emaravirus identified in spicebush (Lindera benzoin)

item Mollov, Dimitre
item Grinstead, Sam
item Fuentes-Bueno, Irazema
item CRESWELL, TOM - Purdue University
item RUHL, GAIL - Purdue University
item BUSH, ELIZABETH - Virginia Polytechnic Institution & State University
item HANSEN, MARY ANN - Virginia Polytechnic Institution & State University
item BEALE, JULIE - University Of Kentucky
item JOHNSON, DAVID - Missouri Department Of Agriculture

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 4/15/2019
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Common spicebush, Lindera benzoin, is a deciduous shrub native to North America and planted as a landscape ornamental throughout the Eastern and Southern U.S. In 2017 common spicebush with chlorotic leaves and distorted growth was submitted to the Plant and Pest Diagnostic Laboratory (PPDL) at Purdue University, Indiana. Total RNA from symptomatic leaves was subjected to cDNA library preparation and high throughput sequencing (HTS). More than 20 million HTS reads (75 nucleotides long) were generated and assembled into over 35 thousand contigs. BLASTX analysis revealed four contigs (7,034 nt, 2,189 nt, 1,499 nt, and 1,575 nt) similar to plant virus sequences. These contigs were related to RNAs 1-4 of a virus most likely belonging to the genus Emaravirus, a taxon currently with nine viruses, all having multi-segmented genomes. RNA 1 had 46% similarity to the RNA-dependent RNA-polymerase and RNA 4 had 49% identity to the movement protein of High Plains wheat mosaic emaravirus. RNA 2 had 41% identity to the glycoprotein and RNA 3 had 41% identity to the nucleocapsid protein of Raspberry leaf blotch emaravirus. Based on HTS genomic sequences, primers were designed and an RT-PCR detection assay was developed and validated. In 2018, similarly symptomatic samples were sent to USDA-ARS from Virginia and Kentucky, and to Purdue PPDL from Ohio and Missouri. These samples represented landscape settings, as well as nursery stock. All samples tested positive using the validated RT-PCR assay. Amplicons were cloned and sequenced. All Sanger sequences showed high identity (96-100%) to the newly discovered emaravirus. These results confirm that the virus is widespread and highlight the importance of applying HTS in plant virus diagnostics.