Potato virus Y biological strain group YD: hypersensitive resistance genes elicited and phylogenetic placement

Potato virus Y (PVY) disrupts healthy seed potato production and causes tuber yield and quality losses globally. Its subdivisions consist of strain groups defined by potato hypersensitive resistance (HR) genes and phylogroups defined by sequencing. When PVY isolate PP was inoculated to potato cultivar differentials with HR genes, the HR phenotype pattern obtained resembled that caused by strain group PVYD isolate KIP1. A complete genome of isolate PP was obtained by high throughput sequencing. After removal of its short terminal recombinant segment, it was subjected to phylogenetic analysis together with 30 complete non-recombinant PVY genomes. It fitted within the same minor phylogroup PVYO3 sub-clade as KIP1. Putative HR gene Nd was proposed previously to explain the unique HR phenotype pattern that developed when differentials were inoculated with PVYD. However, an alternative explanation was that PVYD elicits HR, with HR genes Nc and Ny instead. To establish which gene(s) it elicits, isolates KIP1 and PP were inoculated to F1 potato seedlings from: (i) crossing Kipfler and White Rose with Ruby Lou, and (ii) self-pollinated Desiree and Ruby Lou; where Kipfler is susceptible (S) but White Rose, Desiree and Ruby Lou develop HR. With both isolates, the HR:S segregation ratios obtained fitted 5:1 for Kipfler x Ruby Lou, 11:1 for White Rose x Ruby Lou, and 3:1 for Desiree. Those for Ruby Lou were 68:1 (isolate PP) and 52:0 (isolate KIP1). Since potato is tetraploid, these ratios suggest PVYD elicits HR with Ny from Ruby Lou (duplex condition) and Desiree (simplex condition), and Nc from White Rose (simplex condition), but provide no evidence that Nd exists. Therefore, our differential cultivar inoculations and inheritance studies highlight that PVYD isolates elicit an HR phenotype in potato cultivars with either of two HR genes, Nc or Ny, so putative gene Nd can be discounted. Moreover, phylogenetic analysis placed the complete genome of isolate PP within the same minor phylogroup PVYO3 sub-clade as KIP1 which constitutes the most basal divergence within overall major phylogroup PVYO.

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Molecular characterization of potato virus y inducing potato tuber necrotic ringspot disease in Serbia

Genetika ◽

10.2298/gensr1602487r ◽

2016 ◽

Vol 48 (2) ◽

pp. 487-496 ◽

Cited By ~ 1

Author(s):

Danijela Ristic ◽

Ivan Vucurovic ◽

Slobodan Kuzmanovic ◽

Drago Milosevic ◽

Katarina Gasic ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Potato Tuber ◽

Molecular Characterization ◽

Potato Virus ◽

Complete Genome ◽

Potato Virus Y ◽

Bootstrap Support ◽

Limiting Factor ◽

Potato Seed ◽

Tuber Necrosis

The Potato virus Y (PVY) is the most important limiting factor for potato seed production in Serbia. Currently, PVY is a major concern for the potato seed growers. Initially, serological (ELISA) tests were carried out on 100 potato seed tubers from each of the seven potato cv. during 2013. The infection rates with the PVYN was between 5 and 36%. A complete genome sequencing of the most common Serbian isolate of PVY (3D), followed by molecular characterization and phylogenetic analysis has been performed to show what group it belongs to. Our isolate?s complete genome sequence (KJ946936) showed that the Serbian PVY isolate (3D) is 99.7% identical at nt level, with other tuber necrosis strain group (PVYNTN) from Europe. Phylogenetic analysis revealed three consistent lineages of isolates, showing that our isolate was clustered with the isolates from Europe and North America in the PVYN lineage which induces potato tuber necrotic ringspot disease (PTNRD). The Serbian isolate of PVYNTN together with the isolates from Europe was clustered in the branch of European sublineage, with a high bootstrap support and no genetic diversity. This is the first study in Serbia demonstrating phylogenetic distinction between our isolate and other isolates of PVY.

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Genetic Diversity of Potato virus Y in Potato Production Areas in Northeast China

Plant Disease ◽

10.1094/pdis-04-18-0687-re ◽

2019 ◽

Vol 103 (2) ◽

pp. 289-297 ◽

Cited By ~ 6

Author(s):

Yanju Bai ◽

Shuxin Han ◽

Yanling Gao ◽

Wei Zhang ◽

Guoquan Fan ◽

...

Keyword(s):

Potato Virus ◽

Inner Mongolia ◽

Potato Virus Y ◽

Potato Cultivar ◽

Potato Production ◽

Potato Spindle Tuber Viroid ◽

Single Strain ◽

Strain Group ◽

Common Potato ◽

Genome Level

In 2011–2014, ELISA or nucleic acid spot hybridization (NASH) testing for common potato viruses or Potato spindle tuber viroid (PSTVd) was performed on 500 leaf samples collected in potato fields in the northeast provinces Heilongjiang and Inner Mongolia, China. The results revealed that 38.4% (Heilongjiang) and 27.7% (Inner Mongolia) were positive for Potato virus Y (PVY). To unveil the strain composition and population structure of PVY in the region, the multiplex RT-PCR described by Chikh-Ali et al. was performed on all of the ELISA-PVY-positive samples. Of the 158 samples whose PVY strain scenarios could be determined, PVYNTN-NW-SYR-II and PVYN-Wi were the most abundant strains, occurring in 58.9 and 47.5% samples, followed by PVYNTN-NW-SYR-I (31.0%), PVYN:O (19.6%), Eu-PVYNTN (7.6%), NA-PVYN (1.3%), and PVYO (0.6%). In the 84 single-strain-infected samples, PVYN-Wi accounted for 41.7%, PVYNTN-NW-SYR-II for 40.5%, PVYNTN-NW-SYR-I for 14.3%, and PVYN:O and Eu-PVYNTN for 3.6% each. Seven isolates representing PVYNTN-NW-SYR-I (HLJ-6-1 and HLJ-9-4), PVYNTN-NW-SYR-II (INM-W-369-12 and SC-1-1-2), PVYN:O (HLJ-30-2), and PVYN-Wi (HLJ-BDH-2 and HLJ-C-429) were sequenced and analyzed molecularly. Whereas the sequence identities for isolates belonging to the same strain group were >98.5%, they fell for isolates belonging to different strain groups to 92.7–98.1% at the genome level and 96.1–98.4% at the polyprotein level. Interestingly, the exact location of the recombination events varied among isolates within a strain group. Phylogenetic analysis of all 42 full length PVY sequences from China indicated that most clustered to various recombinant groups, despite the fact that the PVY isolates were isolated from at least five host species. Pathological analysis of four isolates representing PVYN:O, PVYN-Wi, PVYNTN-NW-SYR-I, and PVYNTN-NW-SYR-II revealed that the PVYNTN-NW-SYR-II isolate incited the most severe symptoms on potato cultivar Kexin 13, followed by PVYNTN-NW-SYR-I, PVYN:O and PVYN-Wi. The PVYNTN-NW-SYR-I and PVYNTN-NW-SYR-II isolates also caused necrotic ringspots on the tubers of Kexin 13, indicating their ability to induce the potato tuber necrotic ringspot disease in potato.

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Genetic Determinants of Potato virus Y Required to Overcome or Trigger Hypersensitive Resistance to PVY Strain Group O Controlled by the Gene Ny in Potato

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-09-12-0219-r ◽

2013 ◽

Vol 26 (3) ◽

pp. 297-305 ◽

Cited By ~ 35

Author(s):

Yan-Ping Tian ◽

Jari P. T. Valkonen

Keyword(s):

Potato Virus ◽

Potato Virus Y ◽

Three Dimensional ◽

Genetic Determinants ◽

Hypersensitive Resistance ◽

Strain Group ◽

Function Relationship ◽

Α Helix ◽

Viral Determinants ◽

Necessary And Sufficient

Potato virus Y (PVY) (genus Potyvirus) is the most economically damaging and widely distributed virus in potato. Spread of PVY in the field is controlled by growing resistant cultivars. The dominant potato gene Nytbr for hypersensitive resistance (HR) controls ordinary PVY strains (PVYO) but is overcome by PVYN strains. Studies with infectious PVY chimeras and mutants indicated that the viral determinants necessary and sufficient to overcome Nytbr reside within the helper component proteinase (HC-Pro) (residues 227 to 327). Specifically, eight residues and the modeled three-dimensional conformation of this HC-Pro region distinguish PVYN from PVYO strains. According to the model, the conserved IGN and CCCT motifs implicated in potyvirus replication and movement, respectively, are situated in a coiled structure and an α-helix, respectively, within this region in PVYO; however, their locations are reversed in PVYN. Two residues (R269 and K270) are crucial for the predicted PVYO-specific HC-Pro conformation. Two viral chimeras triggered Nytbr and induced veinal necrosis in tobacco, which is novel for PVY. One chimera belonged to strain group PVYE. Our results suggest a structure–function relationship in recognition of PVYO HC-Pro by Nytbr, reveal HC-Pro amino acid signatures specific to PVYO and PVYN, and facilitate identification of PVY strains overcoming Nytbr.

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

Plants ◽

10.3390/plants10040753 ◽

2021 ◽

Vol 10 (4) ◽

pp. 753

Author(s):

Miroslav Glasa ◽

Richard Hančinský ◽

Katarína Šoltys ◽

Lukáš Predajňa ◽

Jana Tomašechová ◽

...

Keyword(s):

High Throughput ◽

Potato Virus ◽

Mixed Infection ◽

High Throughput Sequencing ◽

Potato Virus Y ◽

De Novo ◽

Sweet Pepper ◽

Complete Sequence ◽

Genome Region ◽

Mapping Parameters

In recent years, high throughput sequencing (HTS) has brought new possibilities to the study of the diversity and complexity of plant viromes. Mixed infection of a single plant with several viruses is frequently observed in such studies. We analyzed the virome of 10 tomato and sweet pepper samples from Slovakia, all showing the presence of potato virus Y (PVY) infection. Most datasets allow the determination of the nearly complete sequence of a single-variant PVY genome, belonging to one of the PVY recombinant strains (N-Wi, NTNa, or NTNb). However, in three to-mato samples (T1, T40, and T62) the presence of N-type and O-type sequences spanning the same genome region was documented, indicative of mixed infections involving different PVY strains variants, hampering the automated assembly of PVY genomes present in the sample. The N- and O-type in silico data were further confirmed by specific RT-PCR assays targeting UTR-P1 and NIa genomic parts. Although full genomes could not be de novo assembled directly in this situation, their deep coverage by relatively long paired reads allowed their manual re-assembly using very stringent mapping parameters. These results highlight the complexity of PVY infection of some host plants and the challenges that can be met when trying to precisely identify the PVY isolates involved in mixed infection.

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Occurrence and Molecular Characterization of Recombinant Potato virus YNTN Isolates from Sulawesi, Indonesia

Plant Disease ◽

10.1094/pdis-07-15-0817-re ◽

2016 ◽

Vol 100 (2) ◽

pp. 269-275 ◽

Cited By ~ 11

Author(s):

Mohamad Chikh-Ali ◽

Nilsa A. Bosque-Pérez ◽

Dalton Vander Pol ◽

Dantje Sembel ◽

Alexander V. Karasev

Keyword(s):

Potato Virus ◽

Potato Virus Y ◽

Potato Cultivar ◽

Whole Genome ◽

Chain Reaction ◽

Recombinant Type ◽

Whole Genomes ◽

Polymerase Chain ◽

First Time

The importance of potato has increased dramatically in Indonesia over the last three decades. During this period, ‘Granola’, a potato cultivar originally from Germany, has become the most common cultivar for fresh consumption in Indonesia. In August 2014, a survey was conducted in Sulawesi, where potato fields cultivated with Granola and its selection, ‘Super John’, were sampled for Potato virus Y (PVY) presence. PVY was found in Sulawesi for the first time. Samples determined to be positive for PVY were subsequently typed to strain using reverse-transcription polymerase chain reaction assays. All PVY isolates sampled were identified as PVYNTN recombinants, with three recombination junctions in P3, VPg, and CP regions of the genome. Three local PVY isolates were subjected to whole-genome sequencing and subsequent sequence analysis. The whole genomes of the Indonesian PVYNTN isolates I-6, I-16, and I-17 were found to be closely related to the European PVYNTN-A. This recombinant type was shown previously to cause potato tuber necrotic ringspot disease (PTNRD) in susceptible potato cultivars. The dependence of potato farmers on mostly a single cultivar, Granola, may have given a competitive advantage to PVYNTN over other PVY strains, resulting in the predominance of the PVYNTN recombinant. The dominance of PVYNTN in Sulawesi, and possibly in Indonesia as a whole, represents a potential risk to any newly introduced potato cultivar to the country, especially cultivars susceptible to PTNRD.

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