Molecular and Biological Characterization of <i>Potato virus Y</i> Isolates from Vietnam

Schubert, Jörg; Thieme, Thomas; Thieme, Ramona; Ha, Cuong Viet; Hoang, Giang

doi:10.1111/jph.12362

Cited by 13 publications

(2 citation statements)

References 31 publications

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“…Furthermore, intra-strain genetic variability and 'rare' or previously unclassified recombinant genetic structures have been described [14,16], which adds to the complexity. Currently, in addition to five non-recombinant genotypes (PVY O , -Eu-N , -Na-N , -O5 , -C ), thirty-six unique recombinants structures between two or more parental lineages have been reported [14,16,[19][20][21][22][23][24][25][26][27][28][29][30][31]. Certain PVY recombinants are often associated with the induction of potato tuber necrotic ringspot disease (PTNRD) in susceptible potato cultivars [13,32,33], which can make tubers unmarketable.…”

Section: Introductionmentioning

confidence: 99%

“…Certain PVY recombinants are often associated with the induction of potato tuber necrotic ringspot disease (PTNRD) in susceptible potato cultivars [13,32,33], which can make tubers unmarketable. Among them, PVY NTN genotypes have been reported from many areas of the world [24,30,31,[33][34][35][36][37][38][39] and represent a relevant concern for potato production. PVY O used to be the predominant strain infecting potatoes, but recently the recombinant genotypes, once a minor part of the PVY complex, became prevalent in many regions of the world [19,33,34,36,37,[39][40][41][42][43][44][45][46][47][48].…”

Section: Introductionmentioning

confidence: 99%

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

Bartola

Byrne

Mullins

2020

Viruses

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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.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Bartola

Byrne

Mullins

2020

Viruses

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Genetic diversity of potato virus Y (PVY): sequence analyses reveal ten novel PVY recombinant structures

2017

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The potato virus Y (PVY) complex includes five non-recombinant strains and a growing number of recombinants. Up to now, the bulk of these PVY recombinants were found to be composed of genome segments coming from only two "parental" genomes, PVY and PVY, with a small minority including segments from other parents, e.g. PVY, PVY, and a segment of the recombinant strain PVY-NE11. Here, comprehensive analyses of 396 whole genomes of PVY isolates from 34 countries and a variety of hosts revealed 28 isolates to be rare or novel recombinants. When subjected to a thorough recombination analysis, these 28 PVY isolates were found to represent 25 poorly sampled PVY recombinant structures, ten of which had not been recognized previously. Nine of the ten novel structures carried parental sequences from PVY or PVY-NE11 strains recombined with PVY and PVY sequences, while seven of the new structures contained sequences from three different parents. The number of known PVY recombinant patterns now stands at thirty six. These recombinant structures present a challenge for PVY strain typing, but may shed light on interactions between PVY and host resistance genes.

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Investigation into the strain typing of Potato Virus Y isolates in Egypt

et al. 2020

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Molecular and Biological Characterization of Potato virus Y Isolates from Vietnam

Cited by 13 publications

References 31 publications

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

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

Genetic diversity of potato virus Y (PVY): sequence analyses reveal ten novel PVY recombinant structures

Investigation into the strain typing of Potato Virus Y isolates in Egypt

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