Complete genome sequence of shamrock chlorotic ringspot virus, a novel potyvirus infecting ornamental Oxalis triangularis in the United States and the Netherlands

Authors: Jordan, Ramon; Mollov, Dimitre; GUARAGNA, MARY ANN - Retired ARS Employee; LOCKHART, BENHAM - University Of Minnesota

Submitted to: Acta Horticulturae
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/4/2023
Publication Date: 3/31/2024
Citation: Jordan, R.L., Mollov, D.S., Guaragna, M., Lockhart, B. 2024. Complete genome sequence of shamrock chlorotic ringspot virus, a novel potyvirus infecting ornamental Oxalis triangularis in the United States and the Netherlands. Acta Horticulturae. https://doi.org/10.17660/ActaHortic.2024.1392.6.
DOI: https://doi.org/10.17660/ActaHortic.2024.1392.6

Interpretive Summary: Plants in the genus Oxalis are morphologically diverse and are naturally distributed in North and South America and South Africa. Ornamental Oxalis triangularis, commonly known as false shamrock because of its triangular leaves, is grown as a potted plant in the United States, especially for marketing in the spring around St. Patrick’s Day. A virus causing chlorotic ringspot in ornamental Oxalis triangularis was first described in the state of Washington in 1981 and was named shamrock chlorotic ringspot virus (SCRV). In 2013, ARS scientists in Beltsville, MD received a symptomatic shamrock plant for analysis and confirmed that it was infected with SCRV. Analysis of the genome nucleotide sequence of the infecting virus indicates that SCRV is a unique species belonging to the genus Potyvirus in the family Potyviridae. The information and tools developed in this work will be useful to state and federal regulatory officials to make timely and appropriate recommendations in safeguarding the movement of horticultural products into and throughout the U.S.

Technical Abstract: Ornamental Oxalis, commonly known as the Shamrock plant, is grown as a potted plant in the United States especially for marketing in the spring around St. Patrick’s Day. A potyvirus causing chlorotic ringspot in ornamental Oxalis regnellii was first described in WA in 1981. Plants showing similar symptoms and having potyvirus particles were reported in NY in 2009 and in FL in 2012. The name Shamrock chlorotic ringspot virus (SCRV) was coined. Potyvirus-like filamentous virus particles were observed by TEM in symptomatic leaf samples from Oxalis triangularis plants from WI (2012-2013) showing similar symptoms. Total RNA extracted from a symptomatic plant tested positive for the presence of potyvirus in RT-PCR using universal primers. RNA extracted from partially purified virion preparations from symptomatic tissue was used as template for a random PCR to produce a cDNA library. The complete nucleotide sequence of SCRV was obtained from multiple overlapping cDNA clones, coupled with 5’ and 3’ RACE cloning, and determined to be 10,120 nucleotides, excluding the 3'-terminal poly(A) tail. It contains two open reading frames (ORFs), with the large one encoding a polyprotein of 3,276 amino acids (aa) and the small overlapping ORF encoding a PIPO protein of 70 aa. SCRV shared the highest sequence identities with members of the genus Potyvirus, with less than 53% and 47% identities for the genome and polyprotein, respectively. Based on the predicted polyprotein cleavage sites, the number and size of the predicted processed mature peptides, and phylogenetic relatedness to known members of the family Potyviridae, SCRV appears to be a new species in the genus Potyvirus.