Discovery of two novel potyvirus genome sequences by high-throughput RNA sequencing in Aconitum carmichaelii tissue samples

The genus Potyvirus (the family Potyviridae) is the largest group of plant-infecting viruses transmitted by aphids. Through high-throughput RNA sequencing analysis of asymptomatic samples of Aconitum carmichaelii, a significant medicinal herb in Asia, we identified the genome sequences of two RNA viruses, tentatively named Aconitum potyvirus 1 (AcoPV1) and Aconitum potyvirus 2 (AcoPV2). The genomes of AcoPV1 and AcoPV2 encode polyproteins composed of 3,069 and 3,054 amino acids, respectively. Sequence comparisons and phylogenetic analyses established that AcoPV1 and AcoPV2 represent unique, novel members within the genus Potyvirus. The estimated RNA polymerase slippage rates at the GAAAAAA motif, responsible for the production of P3N-PIPO or P3N-ALT trans-frame fusion proteins, were 0.79% in AcoPV1 and 1.38% in AcoPV2. The RNA reads of AcoPV1 and AcoPV2 were predominantly found in the leaf and flower tissues, indicating potential feeding preferences of vectors for these viruses. These findings demonstrate the effectiveness of high-throughput RNA sequencing in not only uncovering novel potyviruses, but also in elucidating their genomic dynamics within host plants.