Identification of a novel potyvirus from the nickel-hyperaccumulating plant Senecio coronatus in South Africa

• Identified SenCoV1 , a novel potyvirus from Senecio coronatus in South Africa. • SenCoV1 genome encodes a large polyprotein with nine conserved cleavage sites. • The virus has a unique GAAAAAAA sequence enabling P3N-PIPO transframe protein expression. • Phylogenetic analysis confirms SenCoV1 as a distinct Potyvirus species. • Study highlights transcriptome datasets’ utility for discovering cryptic plant viruses. Senecio coronatus , commonly known as the woolly grassland senecio, is a perennial plant endemic to southern Africa. It is widely distributed across grassland biomes including the ultramafic outcrops of the Barberton Greenstone Belt in South Africa where some populations have evolved the ability to hyperaccumulate the toxic element nickel in their shoot tissues. In this study, we performed high-throughput RNA sequencing of healthy S. coronatus plants collected from this region. Analysis of the transcriptome data revealed the coding-complete sequence of a latently infected RNA virus genome, tentatively named Senecio coronatus virus 1 (SenCoV1). The SenCoV1 genome is 9632 nucleotides long and encodes a large polyprotein of 3132 amino acids. Sequence analysis revealed that the polyprotein shares 56.9 % amino acid identity with that of plum pox virus, a well-characterized member of the genus Potyvirus (family Potyviridae ), suggesting that SenCoV1 is a novel member of this genus. The genome contains nine conserved putative proteolytic cleavage sites, yielding ten mature potyviral peptides, and includes the RNA polymerase slippage sequence GAAAAAAA, with seven adenine residues, facilitating the translation of the transframe fusion protein P3N-PIPO. Phylogenetic analysis further confirmed that SenCoV1 is a distinct and highly divergent member of the genus Potyvirus . This study highlights the utility of transcriptome datasets for uncovering cryptic viral diversity and provides new insights into the evolutionary complexity of plant RNA viruses.