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Updated: Sep 27, 2026

Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes
Published on: July 27, 2018
The complete nucleotide sequence of Pepper mottle virus-Florida RNA
1Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama 36849, USA.
Abstract:
The Pepper mottle virus-Florida (PepMoV-FL) RNA genome was cloned and sequenced, and shown to consist of 9,717 nucleotides (nt) excluding the poly (A) tail. A single open reading frame was identified beginning at nucleotide position 169 encoding a polyprotein of 3068 amino acids. Phylogenetic sequence analysis revealed that of 44 full-length viral RNA genomes analyzed within the family Potyviridae, PepMoV-FL was most closely related to PepMoV-California (PepMoV-CA), Potato virus Y-H (PVY-H), PVY-N, PVY(o) and Potato virus V-DV42 (PVV-DV42). Using the PepMoV-FL sequence as a basis for comparison, the overall nucleotide sequence identity was highest between PepMoV-FL and PepMoV-CA at 93%, while the relationship was more distant with PVV-DV42 at 64% and for the PVY strains at 61%. A unique direct repeat sequence of 76 nucleotides was identified in the PepMoV-FL 3'-untranslated region (UTR), and this repeat sequence was confirmed not to occur in the PepMoV-CA sequence. Since the Florida isolate was among the first of the PepMoV isolates described, extensive biological and serological data on this isolate are available, and it has now been cloned and sequenced, we recommend that PepMoV-FL be recognized as the PepMoV type strain.
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