High-throughput metagenomics analysis exposes the presence of gladiolus mosaic virus and a novel Potyvirus from Iris versicolor showing mosaic symptoms

Potyviruses can cause substantial economic damage by reducing the yield and market value of infected plants. Here, we present the first annotated genome sequences of a gladiolus mosaic virus (GdMV) isolate and a new putative Potyvirus from iris by transcriptome sequencing. The genomic RNA of GdMV-IR consists of 9548 nt, excluding the 3’-terminal poly(A) tail, and encodes a large polyprotein of 3014 aa and a small fusion protein of 72 aa. GdMV-IR shared 83–99/91–99% nt/aa polyprotein identities with extant GdMV isolates, with the highest identity to Australian isolates (BC32/MH886516, Bate9/JN127345). GdMV isolates were classified into two phylogroups. Six distinct haplotypes were identified, indicating that GdMV exhibits high genetic diversity and dynamic evolution. The GdMV genome undergoes purifying selection but is not uniformly distributed across genomic RNAs. Most codons in coding regions experience negative selection or neutrality, while some exhibit positive selection. The sequence of the unknown potyvirus shared polyprotein identity levels below the species threshold with the most closely related known potyviruses, indicating that it belongs to a novel species. The genome of the new potyvirus, provisionally named iris potyvirus C (IrPVC), was 9415 nt long (excluding poly(A) tail) and contained conserved motifs typical of potyviruses. It featured two ORFs: one encoding a polyprotein of 3014 aa, and the other encoding a PIPO protein of 72 aa. Phylogenetic analysis of ORF sequences positioned IrPVC-IR close to members of the genus Potyvirus and confirmed that IrPVC-IR is a distinct potyvirus, most closely related to GdMV and ornithogalum mosaic virus isolates, with 71.6–72.5% nt and 79.4–80.5% aa polyprotein identities. GdMV and IrPVC are newly reported in Iran and globally, respectively, providing basic information for virus disease management.