First Report of Tobacco Ringspot Virus Naturally Infecting Cotton (Gossypium hirsutum) in the United States

Abstract

Cotton (Gossypium hirsutum L.) is one of the major cash crops grown in the United States (U.S.) with a total acreage of over 11.5 million acres in 2021 (NASS, 2021). In Oklahoma, cotton represents an important economic crop and was grown on 490,000 acres during the 2021 growing season (NASS, 2021). In 2021, during a survey of a cotton field in Beckham County of Oklahoma, cotton plants showed typical virus-like symptoms including mosaic, yellow ring spots, discoloration and short internodes (Supplementary Fig. 1). Thirteen symptomatic and five asymptomatic samples were collected from cotton plants and brought to the University of Tulsa for further processing. Total RNA was extracted from all samples using the Spectrum Plant Total RNA Kit (Sigma-Aldrich). Total RNA from two symptomatic samples (named EC3 and EC4) were subjected to high-throughput sequencing (HTS) on the NextSeq 500/550 High-Output kit v2.5 (Illumina, USA) at the genomic facility, Oklahoma State University (Stillwater, OK, USA). A total of 17,542,322 and 22,572,118 trimmed pair-ends reads for both samples were assembled using CLC Genomics Workbench (v12.0.3) (Qiagen, Inc) and subjected to BLASTn analysis. Two contigs of 556 bp and 1062 bp (average coverage 2,799X) for sample EC3 showed 99% and 91% nucleotide (nt) identities with 3’-UTR, 5’-UTR and P1A gene respectively of the Tobacco ringspot virus (TRSV) RNA1 of isolates WA-AM1 (MW495243.1), and IA-1-2017 (MT563078.1) respectively. The other two contigs, 221 bp and 561 bp (average coverage 23,070X) for sample EC4 showed, 100% and 96% nt identities with 3’-UTR, protease, and RdRp genes of TRSV RNA1, isolates WA-AM1 and YW (MT042825.1) respectively. The HTS data did not reveal any other viral sequence in these two cotton samples. To further confirm the presence of TRSV in these samples, previously designed specific primers to TRSV (Forward: 5’-GGAAATTAACTGGGATGATTT-3’ and Reverse: 5’-GAGCTCCAACCTTAAAACCA-3’) for RNA1, targeting the P1A and helicase genes, and another primer pair (Forward: 5’-GCATCCTCCCATGTTTTCT-3’ and Reverse: 5’-GGGACAAACACGACACTA-3’) for RNA2, targeting the coat protein and 3’-untranslated region, of TRSV were tested by RT-PCR assay. The sizes of amplified PCR products obtained from both isolates (EC3 and EC4) on 1% agarose gel were approximately 1,000 bp for RNA1 and 1,100 bp for RNA2. The amplified PCR products were cloned and three independent recombinant clones for each primer set were analyzed by Sanger sequencing. The resulting consensus sequences were used in a BLASTn search against the Genbank and matched with TRSV sequences. Consensus nt sequences analysis specific to RNA1 of EC3 isolate (Accession no. OM563300) and EC4 isolate (Accession no OM563301) showed 97% nt identities with TRSV isolate IA-1-2017. Consensus nt sequences specific to RNA 2 of EC3 isolate (Accession no. OM630605) and EC4 isolate (Accession no OM5630606) showed 92% and 90% nt identities with the corresponding sequences of WA-AM1 and IA-1-2017 isolates respectively. Further screening of the remaining 11 symptomatic samples resulted in two more positive TRSV samples that were co-infected with Cotton leafroll dwarf virus (CLRDV), six were positive to only CLRDV, and three were negative to both viruses by RT-PCR assay using the above TRSV specific primers and CLRDV specific primers AL674F/1407R (Avelar et al. 2019). None of the asymptomatic cotton samples were positive by RT-PCR to TRSV or CLRDV. Our results confirmed the presence of TRSV infection in these symptomatic cotton plants. The presence of TRSV could pose a new threat to cotton crops in Oklahoma and the U.S. due to its wide host range (Adam and Antoniw, 2005), and transmission through many vectors including nematodes, (Keinath et al. 2017), and seed (Hill and Whitman, 2014). To the best of our knowledge, this is the first report of TRSV infecting cotton naturally in the U.S. and in the world.