Genetic variability in the coat protein gene of Potato virus X and the current relationship between phylogenetic placement and resistance groupings

Limited potexvirus diversity in eastern Gulf of Mexico seagrass meadows

Turtlegrass virus X, which infects the seagrass Thalassia testudinum, is the only potexvirus known to infect marine flowering plants. We investigated potexvirus distribution in seagrasses using a degenerate reverse transcription polymerase chain reaction (RT-PCR) assay originally designed to capture potexvirus diversity in terrestrial plants. The assay, which implements Potex-5 and Potex-2RC primers, successfully amplified a 584 nt RNA-dependent RNA polymerase (RdRp) fragment from TVX-infected seagrasses. Following validation, we screened 74 opportunistically collected, apparently healthy seagrass samples for potexviruses using this RT-PCR assay. The survey examined the host species T. testudinum, Halodule wrightii, Halophila stipulacea, Syringodium filiforme, Ruppia maritima, and Zostera marina. Potexvirus PCR products were successfully generated only from T. testudinum samples and phylogenetic analysis of sequenced PCR products revealed five distinct TVX sequence variants. Although the RT-PCR assay revealed limited potexvirus diversity in seagrasses, the expanded geographic distribution of TVX shown here emphasizes the importance of future studies to investigate T. testudinum populations across its native range and understand how the observed fine-scale genetic diversity affects host-virus interactions.

Genetic Diversity among Rose Rosette Virus Isolates: A Roadmap towards Studies of Gene Function and Pathogenicity

The phylogenetic relationships of ninety-five rose rosette virus (RRV) isolates with full-length genomic sequences were analyzed. These isolates were recovered mostly from commercial roses that are vegetatively propagated rather than grown from seed. First, the genome segments were concatenated, and the maximum likelihood (ML) tree shows that the branches arrange independent of their geographic origination. There were six major groups of isolates, with 54 isolates in group 6 and distributed in two subgroups. An analysis of nucleotide diversity across the concatenated isolates showed lower genetic differences among RNAs encoding the core proteins required for encapsidation than the latter genome segments. Recombination breakpoints were identified near the junctions of several genome segments, suggesting that the genetic exchange of segments contributes to differences among isolates. The ML analysis of individual RNA segments revealed different relationship patterns among isolates, which supports the notion of genome reassortment. We tracked the branch positions of two newly sequenced isolates to highlight how genome segments relate to segments of other isolates. RNA6 has an interesting pattern of single-nucleotide mutations that appear to influence amino acid changes in the protein products derived from ORF6a and ORF6b. The P6a proteins were typically 61 residues, although three isolates encoded P6a proteins truncated to 29 residues, and four proteins extended 76-94 residues. Homologous P5 and P7 proteins appear to be evolving independently. These results suggest greater diversity among RRV isolates than previously recognized.

Detection of Ancient Viruses and Long-Term Viral Evolution

The COVID-19 outbreak has reminded us of the importance of viral evolutionary studies as regards comprehending complex viral evolution and preventing future pandemics. A unique approach to understanding viral evolution is the use of ancient viral genomes. Ancient viruses are detectable in various archaeological remains, including ancient people's skeletons and mummified tissues. Those specimens have preserved ancient viral DNA and RNA, which have been vigorously analyzed in the last few decades thanks to the development of sequencing technologies. Reconstructed ancient pathogenic viral genomes have been utilized to estimate the past pandemics of pathogenic viruses within the ancient human population and long-term evolutionary events. Recent studies revealed the existence of non-pathogenic viral genomes in ancient people's bodies. These ancient non-pathogenic viruses might be informative for inferring their relationships with ancient people's diets and lifestyles. Here, we reviewed the past and ongoing studies on ancient pathogenic and non-pathogenic viruses and the usage of ancient viral genomes to understand their long-term viral evolution.

Advances in RNA-Silencing-Related Resistance against Viruses in Potato

Potato is a major food crop that has the potential to feed the increasing global population. Potato is the fourth most important crop and a staple food for many people worldwide. The traditional breeding of potato poses many challenges because of its autotetraploid nature and its tendency toward inbreeding depression. Moreover, potato crops suffer considerable production losses because of infections caused by plant viruses. In this context, RNA silencing technology has been successfully applied in model and crop species. In this review, we describe the RNA interference (RNAi) mechanisms, including small-interfering RNA, microRNA, and artificial microRNA, which may be used to engineer resistance against potato viruses. We also explore the latest advances in the development of antiviral strategies to enhance resistance against potato virus X, potato virus Y, potato virus A, potato leafroll virus, and potato spindle tuber viroid. Furthermore, the challenges in RNAi that need to be overcome are described in this review. Altogether, this report would be insightful for the researchers attempting to understand the RNAi-mediated resistance against viruses in potato.

Evolution of Potato virus X

Potato virus X (PVX) is the type potexvirus of economic significance. The pathogen is distributed worldwide, threatening solanaceous plants in particular. Based on the coat protein (CP) gene, PVX isolates are classified into two major genotypes (I and II). To gain more insights into the molecular epidemiology and evolution of PVX, recombination analyses were conducted and significant signals were detected. Bayesian coalescent method was then applied to the time-stamped entire CP sequences. According to the estimates, the global subtype I-1 went into expansion in the 20th century and was evolving at a moderate rate. Based on the CP phylogenies, a divergence scenario was proposed for PVX. Surveys of codon usage variation showed that PVX genes had additional bias independent of compositional constraint. In codon preference, PVX was both similar to and different from the three major hosts, potato (Solanum tuberosum), tobacco (Nicotiana tabacum), and tomato (S. lycopersicum). Moreover, the suppression of CpG and UpA dinucleotide frequencies was observed in PVX.

The Phylogeography of Potato Virus X Shows the Fingerprints of Its Human Vector

Potato virus X (PVX) occurs worldwide and causes an important potato disease. Complete PVX genomes were obtained from 326 new isolates from Peru, which is within the potato crop's main domestication center, 10 from historical PVX isolates from the Andes (Bolivia, Peru) or Europe (UK), and three from Africa (Burundi). Concatenated open reading frames (ORFs) from these genomes plus 49 published genomic sequences were analyzed. Only 18 of them were recombinants, 17 of them Peruvian. A phylogeny of the non-recombinant sequences found two major (I, II) and five minor (I-1, I-2, II-1, II-2, II-3) phylogroups, which included 12 statistically supported clusters. Analysis of 488 coat protein (CP) gene sequences, including 128 published previously, gave a completely congruent phylogeny. Among the minor phylogroups, I-2 and II-3 only contained Andean isolates, I-1 and II-2 were of both Andean and other isolates, but all of the three II-1 isolates were European. I-1, I-2, II-1 and II-2 all contained biologically typed isolates. Population genetic and dating analyses indicated that PVX emerged after potato's domestication 9000 years ago and was transported to Europe after the 15th century. Major clusters A-D probably resulted from expansions that occurred soon after the potato late-blight pandemic of the mid-19th century. Genetic comparisons of the PVX populations of different Peruvian Departments found similarities between those linked by local transport of seed potato tubers for summer rain-watered highland crops, and those linked to winter-irrigated crops in nearby coastal Departments. Comparisons also showed that, although the Andean PVX population was diverse and evolving neutrally, its spread to Europe and then elsewhere involved population expansion. PVX forms a basal Potexvirus genus lineage but its immediate progenitor is unknown. Establishing whether PVX's entirely Andean phylogroups I-2 and II-3 and its Andean recombinants threaten potato production elsewhere requires future biological studies.

Pest categorisation of potato virus X (non-EU isolates)

Following a request from the EU Commission, the Panel on Plant Health has addressed the pest categorisation of non‐EU isolates of potato virus X (PVX). The information currently available on geographical distribution, biology, epidemiology, potential entry pathways, potential additional impact and availability of control measures of non‐EU isolates of PVX has been evaluated with regard to the criteria to qualify as a potential Union quarantine pest. Because non‐EU isolates of PVX are absent from the EU, they do not meet one of the requirements to be regulated as a regulated non‐quarantine pest (RNQP) (presence in the EU); as a consequence, the Panel decided not to evaluate the other RNQP criteria for these isolates. On the basis of their ability to overcome potato resistance genes, PVX isolates can be divided into several pathotypes. PVX isolates that are not able to overcome resistance genes and PVX isolates that are able to overcome the Nb and/or Nx resistance genes are already present in the EU. Isolates able to overcome the Rx resistance gene have only been reported from South America. These Rx breaking isolates could potentially have an additional impact over the current situation in the EU and therefore meet all the criteria to qualify as a potential Union quarantine pest. All other non‐EU isolates, should they be introduced, are not expected to have additional impact and therefore do not meet this criterion to qualify as a potential Union quarantine pest.

An isolate of Potato Virus X capsid protein from N. benthamiana: Insights from homology modeling and molecular dynamics simulation

Since Potato Virus X (PVX) is easily transmitted mechanically between their hosts, its control is difficult. We have previously reported new isolate of this virus (PVX-Iran, GenBank Accession number FJ461343). However, the molecular basis of resistance breaking activity and its relation to capsid protein structure are still not well-understood. SDS-PAGE, ELISA, Western blot and RT-PCR molecular examinations were performed on the inoculated plants Nicotiana benthamiana. The pathological symptoms were related to the PVX isolate. The capsid protein (CP) structure were modeled based on homology and subjected to three independent 80 ns molecular dynamics minimization (GROMACS, OPLS force field) in the SPC water box. The RMSD, RMSF, SASA, and electrostatic properties were retrieved from the trajectories. Flexibility and hydrophilic nature of the N-terminal residues (1-34) of solvated CP could be observed in conformational changes upon minimization. The obtained structure was then docked with NbPCIP1 using ClusPro 2.0. The strong binding affinity of these two proteins (≈-16.0 Kcal mol-1) represents the formation of inclusion body and hence appearance of the symptoms.

Population genetic analysis of potato virus X based on the CP gene sequence

To investigate the genetic variation and molecular evolution of potato virus X (PVX), 87 coat protein (CP) gene sequences were retrieved from GenBank and analyzed. Of the PVX isolates studied, one recombinant isolate (X3) was detected from South America population of the virus. The other isolates belonged to two lineages, Eurasia and America, with the significant FST value (0.60). Non-synonymous nucleotide diversity to synonymous nucleotide diversity (ω = dN/dS) was less than 1 indicating that the CP gene has been under negative selection or neutral evolution. Further analysis showed that all of the codons in both lineages were under negative selection pressure. No significant genetic differentiation was found between Chinese, Indian, Iranian, Japanese, and the UK populations whereas South America population was distinctly differentiated from other populations. Different evolutionary constraints found for the two lineages suggest that possible mutations and genetic drift were important evolutionary forces driving the genetic diversification of PVX population.

Detección serológica y molecular del Potato virus X (PVX) en tubérculos-semilla de papa (Solanum tuberosum L. y Solanum phureja Juz. Bukasov) en Antioquia, Colombia

<p>El Potato virus (PVX) es uno de los virus más limitantes del cultivo de la papa en el mundo. Es transmitido solamente por contacto y por tubérculo-semilla. Su control se fundamenta en la siembra de tubérculos certificados por su sanidad viral y en la disponibilidad de metodologías de diagnóstico altamente sensibles. En este trabajo se evaluó la prevalencia del PVX en cuatro diferentes tejidos de tubérculos de Solanum tuberosum subsp. andigena var. Diacol-Capiro y S. phureja var. Criolla Colombia utilizando pruebas de DAS-ELISA para 128 submuestras y de RT-qPCR para 32 grupos de submuestras (4 submuestras/grupo). Los resultados de las pruebas serológicas  indicaron la presencia de PVX en el 6,25 y 50% de las submuestras analizadas para la variedad Diacol-Capiro y Criolla Colombia, respectivamente; mientras que los niveles de prevalencia del PVX utilizando la detección por RT-qPCR fueron del 93,75%, independientemente de la variedad de papa y del tejido evaluado. Los valores promedio del ciclo umbral (Ct) en las RT-qPCR fueron de 25,6 (Ct=18,02 a 34,49) y el análisis de las curvas de desnaturalización permitió identificar dos variantes del virus con valores de Tm de 79,5±1°C y 83,7±1°C. La secuenciación de los amplicones obtenidos por RT-qPCR para los controles positivos y para dos de las muestras, confirmó su naturaleza viral. Estos resultados señalan unos muy altos niveles de prevalencia de PVX en el material de siembra de papa en Antioquia y la necesidad de fortalecer los programas de certificación de semilla con pruebas de detección como RT-qPCR.</p>

Complete genome sequences of new divergent potato virus X isolates and discrimination between strains in a mixed infection using small RNAs sequencing approach

Potato virus X (PVX; genus Potexvirus, family Alphaflexiviridae, order Tymovirales) is one of the most widespread and intensively studied viruses of potato. However, little is known about its diversity in its likely center of radiation, the Andean region of South America. To fill this gap, the strategy of Illumina deep sequencing of small RNAs was used to obtain complete or near complete genome sequence of PVX from 5 symptomatically infected greenhouse and 3 field samples (Solanum tuberosum) from Peru. PVX sequences determined in this study were assigned into three different phylogenetic groups of isolates. Notably, a complete genome sequence of a representative of a new PVX phylogenetic lineage was obtained, which shows a high level of sequence dissimilarity to other completely sequenced isolates (∼17%). The new PVX genotype was detected in greenhouse and field samples. One of the field samples was infected with the mixture of two PVX strains, which were efficiently discriminated using small RNA sequencing approach. The study confirms the utility of small RNAs deep sequencing for successful viral strain differentiation and discovery of new viral strains and indicates a high diversity of PVX in the Andean region of South America, a pattern which may be expected also for other potato pathogens.

Molecular characterization and field survey of Iranian potato virus X isolates

Six hundred and one symptomatic potato samples were collected from nine provinces in Iran. Screening by double-antibody sandwich enzyme linked immunosorbent assay using a potato virus X (PVX) together with a few potyviruses polyclonal antibodies, produced positive reactions in 4.3 % of samples against PVX. Based on symptoms on different test plant, the isolates were divided into two groups: the first groups causing blistering and malformation of leaves and the second showed mild mosaic and vein clearing in Nicotiana glutinosa. The almost complete nucleotide sequence of two isolates as a representative of severe and a mild isolates were determined. Genomes of two PVX Iranian isolates are identical to that of the most PVX isolates comprise 6435 nucleotides in length excluding 101 nucleotide in the 5' end of the genome and shares 94.8-96.7 % identities with European and Asian, and 77-96.1 % with American isolates. Furthermore, the 3'-terminal sequences, including the coat protein coding region of other 13 Iranian isolates were determined and compared with the GenBank sequences. Phylogenetic analysis of the cp gene of 13 Iranian isolates together all those available in public databases indicated that the 13 Iranian isolates all belong to low diversity clade I.

Evolution and variability of Solanum RanGAP2, a cofactor in the incompatible interaction between the resistance protein GPA2 and the Globodera pallida effector Gp-RBP-1

Background

The Ran GTPase Activating Protein 2 (RanGAP2) was first described as a regulator of mitosis and nucleocytoplasmic trafficking. It was then found to interact with the Coiled-Coil domain of the Rx and GPA2 resistance proteins, which confer resistance to Potato Virus X (PVX) and potato cyst nematode Globodera pallida, respectively. RanGAP2 is thought to mediate recognition of the avirulence protein GP-RBP-1 by GPA2. However, the Gpa2-induced hypersensitive response appears to be relatively weak and Gpa2 is limited in terms of spectrum of efficiency as it is effective against only two nematode populations. While functional and evolutionary analyses of Gp-Rbp-1 and Gpa2 identified key residues in both the resistance and avirulence proteins that are involved in recognition determination, whether variation in RanGAP2 also plays a role in pathogen recognition has not been investigated.

Results

We amplified a total of 147 RanGAP2 sequences from 55 accessions belonging to 18 different di-and tetraploid Solanum species from the section Petota. Among the newly identified sequences, 133 haplotypes were obtained and 19.1% of the nucleotide sites were found to be polymorphic. The observed intra-specific nucleotide diversity ranges from 0.1 to 1.3%. Analysis of the selection pressures acting on RanGAP2 suggests that this gene evolved mainly under purifying selection. Nonetheless, we identified polymorphic positions in the protein sequence at the intra-specific level, which could modulate the activity of RanGAP2. Two polymorphic sites and a three amino-acid deletion in RanGAP2 were found to affect the timing and intensity of the Gpa2-induced hypersensitive response to avirulent GP-RBP-1 variants even though they did not confer any gain of recognition of virulent GP-RBP-1 variants.

Conclusions

Our results highlight how a resistance gene co-factor can manage in terms of evolution both an established role as a cell housekeeping gene and an implication in plant parasite interactions. StRanGAP2 gene appears to evolve under purifying selection. Its variability does not seem to influence the specificity of GPA2 recognition but is able to modulate this activity by enhancing the defence response. It seems therefore that the interaction with the plant resistance protein GPA2 (and/or Rx) rather than with the nematode effector was the major force in the evolution of the RanGAP2 locus in potato. From a mechanistic point of view these results are in accordance with a physical interaction of RanGAP2 with GPA2 and suggest that RBP-1 would rather bind the RanGAP2-GPA2 complex than the RanGAP2 protein alone.

Biological Properties of Potato virus X in Potato: Effects of Mixed Infection with Potato virus S and Resistance Phenotypes in Cultivars from Three Continents

Interactions between Potato virus X (PVX) and Potato virus S (PVS) were studied in potato plants, and isolates of PVX were inoculated to potato cultivars from four continents to identify occurrence of PVX resistance genes. Mixed infection with PVX and PVS increased the titer of PVS and enhanced expression of foliar symptoms in primarily and secondarily infected plants of 'Royal Blue'. PVX isolates belonging to strain groups 1 and 3 (WA1+3) or 3 (XK3 and TAS3) were sap and graft inoculated (1 to 3 isolates each) to 38 cultivars and one breeding line. Presence of extreme PVX resistance gene Rx was identified in four Australian ('Auski', 'Billabong', 'Flame', and 'Ruby Lou') and two European ('Mondial' and 'Rodeo') cultivars, and in a clone of North American 'Atlantic'. PVX hypersensitivity gene Nx was identified for the first time in two Australian ('Bliss' and 'MacRusset'), four European ('Almera', 'Harmony', 'Maxine', and 'Nadine'), and one North American ('Ranger Russet') cultivars, and in Australian breeding line 98-10713. PVX hypersensitivity gene Nb was identified for the first time in one Australian ('White Star'), five European ('Innovator', 'Kestrel', 'Kipfler', 'Laurine', and 'Royal Blue'), and one North American ('Shepody') cultivars. Probable ancestral sources of the resistance genes found in different cultivars were identified. Thus, although PVX resistance genes often occur in parents used in crosses, knowledge of their occurrence in parents and cultivars is often lacking. On sap inoculation, systemic hypersensitive phenotypes that caused shoot death often developed in cultivars with Nx but not necessarily in all shoots. This phenotype caused severe necrotic symptoms in infected tubers. In some instances, passage through cultivars with Nb separated strain group 3 from mixed isolate WA1+3.

Genetic variability in the coat protein genes of Cymbidium mosaic virus isolates from orchids

The variability in the nucleotide (nt) and amino acid (aa) sequences of the coat protein (CP) of Cymbidium mosaic virus (CymMV), which naturally infects orchids worldwide, was investigated. The CP genes of 55 CymMV isolates originating from different locations in Korea were amplified using RT-PCR and sequenced. The encoded CP consists of 223 aa. The CP sequences of the Korean isolates were compared with those of previously published CymMV isolates originating from different countries at both nt and aa levels. The Korean isolates shared 74.9-98.3 and 52.7-100% CP homology with CymMV isolates from other countries at the nt and aa levels, respectively. No particular region of variability could be found in either grouping of viruses. In the deduced CymMV CP aa sequence, the C-terminal region was more divergent than the N-terminal. The phylogenetic tree analysis based on nt sequence diversity of CP genes of CymMV isolates supported the hypothesis that CymMV isolates were divided into two subgroups. However, these subgroups were not formed by phylogenetic tree analysis of CP aa sequences. There was no distinct correlation between geographical locations and specific sequence identity, while recombination analysis revealed that there were no intra-specific recombination events among CymMV isolates.

Identification of the molecular make-up of the Potato virus Y strain PVY(Z): genetic typing of PVY(Z)-NTN

Potato virus Y (PVY) strains were originally defined by interactions with different resistance genes in standard potato cultivars. Five distinct strain groups are defined that cause local or systemic hypersensitive responses (HRs) in genetic background with a corresponding N gene: PVY(O), PVY(N), PVY(C), PVY(Z), and PVY(E). The nucleotide sequences of multiple isolates of PVY(O) and PVY(N) differ from each other by ≈8% along their genomes. Additionally, complete genome sequences of multiple recombinant isolates are composed of segments of parental PVY(O) and PVY(N) sequences. Here, we report that recombinant isolate PVY-L26 induces an HR in potato 'Maris Bard' carrying the putative Nz gene, and is not recognized by two other resistance genes, Nc and Ny(tbr). These genetic responses in potato, combined with the inability of PVY-L26 to induce vein necrosis in tobacco, clearly define it as an isolate from the PVY(Z) strain group and provide the first information on genome structure and sequence of PVY(Z). The genome of PVY-L26 displays typical features of European NTN-type isolates with three recombinant junctions (PVY(EU-NTN)), and the PVY-L26 is named PVY(Z)-NTN. Three typical PVY(NTN) isolates and two PVY(N) isolates, all inducing vein necrosis in tobacco, were compared with PVY-L26. One PVY(NTN) isolate elicited HR reactions in Maris Bard, similar to PVY-L26, while two induced a severe systemic HR-like reaction quite different from the quasi-symptomless reaction induced by two PVY(N) isolates. 'Yukon Gold' potato from North America produced HR against several PVY(NTN) isolates, including PVY-L26, but only late and limited systemic necrosis against one PVY(N) isolate. Consequently, according to symptoms in potato indicators, both PVY(Z) and PVY(NTN) isolates appeared biologically very close and clearly distinct from PVY(O) and PVY(N) strain groups.