Beet curly top virus strain specific interactions with sugar beet genotypes reveal potential role of viral small non-coding RNAs (sncRNAs) and small peptides during early infection.
Sugar beet is an economically important crop in the United States (U.S.) and Europe and is highly susceptible to the Beet curly top virus (BCTV) which negatively affects sugar beet yield and sugar production. In the western U.S., the predominant strains of BCTV in sugar beet include CA/Logan, Colorado, Severe, and Worland. Severity of disease symptoms depend upon different factors, including virus strain/s, plant genotype, age at infection. The regulatory role of BCTV strain specific small non-coding RNAs (sncRNAs) and their interaction with the host is unclear. Using BCTV susceptible and resistant genotypes, natural infection, and global RNAseq, we demonstrate differential regulation of sugar beet genes by BCTV strain specific sncRNAs. Among detected sncRNAs, sncRNA_36 as an example was common to all four strains and showed moderate negative correlation with EL10Ac9g22982 (transmembrane protein 53) gene expression in the susceptible line. Whereas CA/Logan specific sncRNAs namely sncRNA_4, 20, 21 showed higher negative correlation with EL10Ac1g01206 (LRR protein), EL10Ac5g12605 (7-deoxyloganetic acid glucosyltransferase), and EL10Ac6g14074 (transmembrane emp24) expression in the susceptible line respectively. Peptidomics analysis identified putative small open reading frame (sORF) derived peptides from BCTV strains. The data presented here suggest that genome divergence among BCTV strains differentially affects the production of sncRNAs and small peptides which could potentially affect pathogenicity and disease symptom development.