Characterization of Potato Virus Y Isolates and Assessment of Nanopore Sequencing to Detect and Genotype Potato Viruses

Abstract

Potato virus Y (PVY) is the most economically important virus infecting cultivated potato (Solanum tuberosum L.). Accurate diagnosis is crucial to regulate the trade of tubers and for the sanitary selection of plant material for propagation. However, high genetic diversity of PVY represents a challenge for the detection and classification of isolates. Here, the diversity of Irish PVY isolates from a germplasm collection and commercial sites was investigated using conventional molecular and serological techniques. Recombinant PVY isolates were prevalent, with PVYNTNa being the predominant genotype. In addition, we evaluated Nanopore sequencing to detect and reconstruct the whole genome sequence of four viruses (PVY, PVX, PVS, PLRV) and five PVY genotypes in a subset of eight potato plants. De novo assembly of Nanopore sequencing reads produced single contigs covering greater than 90% of the viral genome and sharing greater than 99.5% identity to the consensus sequences obtained with Illumina sequencing. Interestingly, single near full genome contigs were obtained for different isolates of PVY co-infecting the same plant. Mapping reads to available reference viral genomes enabled us to generate near complete genome sequences sharing greater than 99.90% identity to the Illumina-derived consensus. This is the first report describing the use of Oxford Nanopore’s MinION to detect and genotype potato viruses. We reconstructed the genome of PVY and other RNA viruses; indicating the technologies potential for virus detection in potato production systems, and for the study of genetic diversity of highly heterogeneous viruses such as PVY.

Molecular Characterization of Potato Virus Y (PVY) Using High-Throughput Sequencing: Constraints on Full Genome Reconstructions Imposed by Mixed Infection Involving Recombinant PVY Strains

“…Mixed infections by different PVY isolates are reported to be quite common [44,45]. In the work reported here, 3 of the 10 tested samples (T1, T40, and T62) were identified as bearing a mix of different PVY variants.…”

Current Developments and Challenges in Plant Viral Diagnostics: A Systematic Review

“…Potato virus Y (PVY) is the most economically important virus infecting cultivated potato ( Solanum tuberosum L.), and high genetic diversity of this virus represents a challenge for its detection and classification. Della Bartola and colleagues [ 178 ] investigated Irish PVY isolates using conventional molecular and serological techniques. Additionally, nanopore sequencing was used to detect and reconstruct the whole genome sequence of four viruses (PVY, PVX, PVS, and PLRV) and five PVY genotypes in a subset of eight potato plants.…”

“…Additionally, nanopore sequencing was used to detect and reconstruct the whole genome sequence of four viruses (PVY, PVX, PVS, and PLRV) and five PVY genotypes in a subset of eight potato plants. Reconstruction of the genomes of PVY and other RNA viruses showed that nanopore technologies have enormous potential for virus detection in potato production systems and for the study of the genetic diversity of highly heterogeneous viruses like PVY [ 178 ]. This study demonstrated the identification of RNA viruses in potato plants using portable nanopore technology.…”

“…Potato virus Y (PVY) Potato plant Potato virus Y genetic diversity analyzed [178] Arabis mosaic virus (ArMV) Potato plant First report of ArMV in potato plants [179] Sri Lankan cassava mosaic virus (SLCMV) Cassava plant Complete genome sequencing of SLCMV [180] Sowthistle yellow vein virus (SYVV) Sowthistle plant Historically important plant rhabdovirus [181] Tomato severe rugose virus (ToSRV) Tomato weed (Physalis angulata L.)…”

Special Issue: “Plant Virus Pathogenesis and Disease Control”

“…Della Bartola and colleagues [ 3 ], and de Nazare Almeida Dos Reis and colleagues [ 4 ] used contemporary sequence and bioinformatics approaches to look at etiology and diversity of viruses in potatoes and tomatoes, respectively. Nanopore sequencing was used to identify complete genomes for four different viruses infecting potatoes, and even proved to be an effective approach for identification of potato virus Y variants and recombinants in mixed infections [ 3 ]. This practical application of this relatively inexpensive and portable technology provides a new platform for rapid, accurate identification of specific virus genotypes.…”