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Poster: Diseases of Plants: New & Emerging Diseases


Genome sequence analysis of a legume-infecting Tomato chlorotic spot virus isolate
R. ADEGBOLA (1), R. Kemerait (2), S. Adkins (3), R. Naidu (1) (1) Washington State University, U.S.A.; (2) Department of Plant Pathology, The University of Georgia, U.S.A.; (3) USDA ARS USHRL, U.S.A.

Tomato chlorotic spot virus (TCSV, genus Tospovirus, family Bunyaviridae) has emerged as a significant constraint to economically important horticultural crops in Florida and the Caribbean region. In this study, we have determined the full genome sequence of a TCSV isolate from peanut (Arachis hypogea) collected in Haiti. Total RNA isolated from virus-infected leaves was used to generate sequences of the S-, M-, and L-RNA genomic segments by a combination of conventional Sanger sequencing and next-generation sequencing (NGS). The consensus sequences generated from Sanger sequencing were compared against those derived from de novo assembly of the filtered NGS reads to confirm the quality and accuracy of the complete genome sequences of the three RNA segments. The 8,873 nucleotide (nt) L-RNA shared 98% nt identity with the L-RNA sequence of a TCSV isolate from Brazil. The 4,847 nt M-RNA shared 99% nt identity with the M-RNA sequence of a Groundnut ringspot virus and TCSV reassortant from Florida. The 3,310 nt S-RNA shared 32.5 to 73.8% nt identity with S-RNA sequences of other tospoviruses. Phylogenetic analysis of proteins encoded by individual TCSV genomic RNA segments with corresponding proteins encoded by other tospoviruses is in progress. This study demonstrates advantages of NGS methods for high throughput, insightful analysis of genome segment sequences of a multi-partite negative-stranded RNA virus directly from field infected tissue with no viral enrichment.