The Expanding Menagerie of Prunus-Infecting Luteoviruses

Members of the genus Luteovirus are responsible for economically destructive plant diseases worldwide. Over the past few years, three luteoviruses infecting Prunus trees have been characterized. However, the biological properties, prevalence, and genetic diversity of those viruses have not yet been studied. High-throughput sequencing of samples of various wild, cultivated, and ornamental Prunus species enabled the identification of four novel species in the genus Luteovirus for which we obtained complete or nearly complete genomes. Additionally, we identified another new putative species recovered from Sequence Read Archive data. Furthermore, we conducted a survey on peach-infecting luteoviruses in eight European countries. Analyses of 350 leaf samples collected from germplasm, production orchards, and private gardens showed that peach-associated luteovirus (PaLV), nectarine stem pitting-associated virus (NSPaV), and a novel luteovirus, peach-associated luteovirus 2 (PaLV2), are present in all countries; the most prevalent virus was NSPaV, followed by PaLV. The genetic diversity of these viruses was also analyzed. Moreover, the biological indexing on GF305 peach indicator plants demonstrated that PaLV and PaLV2, like NSPaV, are transmitted by graft at relatively low rates. No clear viral symptoms have been observed in either graft-inoculated GF305 indicators or different peach tree varieties observed in an orchard. The data generated during this study provide a broader overview of the genetic diversity, geographical distribution, and prevalence of peach-infecting luteoviruses and suggest that these viruses are likely asymptomatic in peach under most circumstances.This study was funded by the European Union through the Horizon 2020 Marie Skłodowska-Curie Actions Innovative Training Network (H2020 MSCA-60 ITN) project “INEXTVIR” (grant agreement number 813542). The ChLVA research part was financed by the Academy of Sciences of the Czech Republic (RVO60077344). The plant indexing biological tests conducted by CTIFL were funded by INTERFEL (fresh fruit and vegetable interprofessional association). D. Safarova and M. Navratil received support from the Ministry of Agriculture of the Czech Republic, National Agency for Agricultural Research (project QK1920124). M. Glasa and D. Mihálik received support from the Slovak Research & Development Agency (project APVV-18-0005)Peer reviewe

Further investigation of a genetically divergent group of plum pox virus-M strain in Turkey

In the past several years, a limited number of isolates of a diverse group of Plum pox virus (PPV) strain -M were discovered in the European part of Istanbul, Turkey. In this study, stone fruit samples were collected from the European part of Istanbul and investigated by PCR typing and sequence analyses for determining prevalence and genetic diversity of this divergent PPV-M isolates. Out of the 230 sampled trees, 97 were determined to be infected with PPV. Strains of 88 isolates were identified and 67 of them (76%) were divergent PPV-M isolates, detected in apricot, peach and plum trees revealing that they could be evolutionarily successful divergent PPV-M isolates prevalent in Istanbul. The divergent Istanbul M isolates formed a monophyletic clade thereby named as PPV-MIs. Additionally, recombination analysis suggested that PPV-MIs isolates could be the donor of the PPV-M-type recombinant fragment of the PPV-Rec strain

Software Repository Analysis for Investigating Design-Code Compliance

Compliance check between code and design is a labor-intensive job to do, since it requires the code to be reverse engineered and checked versus design manually. On the other hand, investigation of the design-code compliance would give some valuable information to software development and maintenance managers. In this study, an approach for employing software repository analysis and text mining techniques to extract and analyze compliance levels of design and code efficiently is presented

Detection and partial characterization of grapevine leafroll-associated virus 1 in pomegranate trees in Turkey

WOS: 000373994100018Foliar virus-like symptoms consisting of yellowing, chlorotic spots, oak-leaf and vein clearing were observed on pomegranate cultivar Hicaz in Hatay province of Turkey in 2013. Three symptomatic out of 23 pomegranate samples reacted to Grapevine leafroll-associated virus 1 (GLRaV-1) antibodies in DAS-ELISA. In order to confirm the presence of GLRaV-1 in pomegranate, total RNA extracted from petiole samples was used in RT-PCR using specific primers designed on sequences of the heat-shock protein 70 homolog (HSP70h), coat protein (CP), coat protein duplicate 2 (CPd2) and open reading frame 9 (p24) genes of GLRaV-1. Amplicons were only obtained from symptomatic pomegranate samples for the CP, CPd2, and p24 genes but, unlike for GLRaV-1 isolates from grapevine, no amplicon was obtained for the HSP70h gene of GLRaV-1 isolates from pomegranate. The CP, CPd2 and p24 genes of GLRaV-1 from pomegranate (accession no. KP411914-KP411922) had 91-94 % nucleotide sequence identity with GLRaV-1 isolates from grapevine. Phylogenetic analyses reconstructed using the neighbor joining method showed a clustering of GLRaV-1 isolates from pomegranate and grapevine. These results suggest that pomegranate could be an alternate host for GLRaV-1

Genetic Variation and Possible Mechanisms Driving the Evolution of Worldwide \u3ci\u3eFig mosaic virus\u3c/i\u3e Isolates

Fig mosaic virus (FMV) is a multipartite negative-sense RNA virus infecting fig trees worldwide. FMV is transmitted by vegetative propagation and grafting of plant materials, and by the eriophyid mite Aceria ficus. In this work, the genetic variation and evolutionary mechanisms shaping FMV populations were characterized. Nucleotide sequences from four genomic regions (each within the genomic RNAs 1, 2, 3, and 4) from FMV isolates from different countries were determined and analyzed. FMV genetic variation was low, as is seen for many other plant viruses. Phylogenetic analysis showed some geographically distant FMV isolates which clustered together, suggesting long-distance migration. The extent of migration was limited, although varied, between countries, such that FMV populations of different countries were genetically differentiated. Analysis using several recombination algorithms suggests that genomes of some FMV isolates originated by reassortment of genomic RNAs from different genetically similar isolates. Comparison between nonsynonymous and synonymous substitutions showed selection acting on some amino acids; however, most evolved neutrally. This and neutrality tests together with the limited gene flow suggest that genetic drift plays an important role in shaping FMV populations

Susceptibility of different prunus rootstocks to natural infection of plum pox virus-Turkey (PPV-T) in Central Anatolia

Sharka is the most damaging viral disease of Prunus spp. and the causative agent is plum pox virus (PPV). PPV is widespread and poses a serious problem in stone fruit crops in Turkey. A unique strain of PPV has so far been identified in Turkey and called as PPV-Turkey (PPV-T). The aims of the present study were to describe the efficiency of PPV-T transmission via aphids and to identify the susceptibility of different Prunus rootstocks against PPV-T strain under natural inoculum in Kayseri province located Central Anatolia Region of Turkey. This experiment was established in a small residential orchard where PPV-T infected apricot and plum trees were detected. Five different Prunus rootstocks from which 200 individuals were planted in PPV-T infected orchard and experiment was designed in a randomized complete block desing with 10 replications per block. All rootstocks were regularly tested by DAS-ELISA and RT-PCR during 2015–2017. The results showed that the most susceptible rootstocks in terms of PPV-T infection were Nemaguard, Myrobalan 29B and Myrobalan 29C with the infection rate of 3.61%, 2.74% and 1.04%, respectively. On the other hand, GF677 and Garnem were never found infected with PPV-T. Aphis gossypii, A. craccivora, A. spiraecola, Brachycaudus helichrysi, Hyalopterus pruni, Myzus persicae, Macrosiphum euphorbiae were detected as most abundant aphid species in experimental plot. In 2015, the highest percentage of viruliferous aphids was found as A. gossypii (100%), followed by B. helichrysi (77.8%), A. spiraecola (55.72%), M. persicae (46.05%) and H. pruni (30.76%) whereas it was 100% for A. gossypii and M. euphorbiae followed by A. spiraecola (76.32%), M. persicae (73.1%), H. pruni (62.06%) and B. helichrysi (61.53%) in 2016 by squash real time RT-PCR. The present study showed that PPV-T was effectively transmitted by different aphid species in natural conditions in Kayseri district. It was concluded that Nemaguard and Myrobalan which were found to be the most sensitive rootstocks to PPV-T should not be preferred by growers as Prunus rootstock where PPV poses a high risk

Potential psyllid vectors of 'Candidatus Phytoplasma mali and Candidatus Phytoplasma pyri in Turkey

BGPI : équipe 6International audiencePsyllids are vectors of phytoplasma, which cause important diseases of pome fruit trees. Psyllid species reported as phytoplasma vectors were captured during 2010–2011 in several pome fruit growing regions in Turkey. Potential psyllid vectors of ‘Candidatus Phytoplasma mali’ were collected from Malus spp. (apple), Cydonia oblonga (quince), Crataegus spp. (hawthorn) and also from the overwintering hosts, whereas those of ‘Candidatus Phytoplasma pyri’ were collected from wild and cultured forms of Pyrus spp. (pear) trees. The psyllids were identified morphologically as Cacopsylla picta, C. melanoneura-C. affinis complex, C. crataegi, C. pyrisuga, C. pyri, C. pyricola and other Cacopsylla species. The highestnatural phytoplasma infection rate was found in C. picta followed by C. pyri, C. melanoneura-C. affinis complex and C. crataegi with rates of 4.36, 3.84, 2.77 and 1.67%, respectively. No phytoplasma were detected in C. pyrisuga, C. pyricola, or the other Cacopsylla spp. ‘Ca. P. mali’ was detected in C. picta, C. melanoneura-C. affinis complex and C. pyri; ‘Ca. P. pyri’ was detected in C. picta, C. crataegi, C. melanoneura-C. affinis complex and C. pyri individuals. To our knowledge, this is the first report on the possible psyllid vectors of ‘Ca. P. mali’ in Turkey

Identification and molecular characterization of a novel foveavirus from Rubus spp. in Turkey

A novel plant virus was identified by high-throughput sequencing analysis from a raspberry plant showing slight mottling symptom. The complete genome sequence of this virus is 8645 nucleotides long, including the 5′ and 3′ UTRs. Its genome contains five ORFs and is very close to members of the genus Foveavirus (Quinvirinae, Betaflexiviridae) in terms of genome organization, TGB presence and the sizes of the RdRp and CP proteins. The novel virus shares 33.5–51.3 % and 23.3–41.3 % nucleotide identity to other genera of the Betaflexifiviridae family based on polymerase (RdRp) and CP genes, respectively. Compared to other foveavirus species, the RdRp protein showed the highest sequence identity (45.3 %) to the RdRp of peach chlorotic mottle virus (PCMV) while the maximal sequence identity for the CP protein was 33.9 % with grapevine rupestris stem pitting-associated virus (GRSPaV). The low nucleotide and amino acid sequence identity with known foveaviruses indicated that it was a novel virus, for which the provisional name “rubus virus 1 (RuV1)” is proposed. The phylogenetic analysis supports the assignment of this virus as a new species of the genus Foveavirus. A survey of 537 Rubus spp. samples grown in six provinces of Turkey, including some symptomatic samples, showed a RuV1 prevalence of 2.2 %, confirming its presence in both raspberry and blackberry plants in a single province, although no obvious association between virus infection and specific symptoms was found

Acta Horticulturae

Turkey is the most important producer and exporter country of apricot, Prunus armeniaca. Production of apricots for fresh market relies on foreign cultivars grown on Mediterranean and Aegean regions while Malatya is the most important region for production of dry apricots based on local cultivars. Plum pox virus (PPV) in Turkey has been known since 1968, but it was not widespread until recent years. Malatya region has been free of sharka disease so far, but the disease has already been reported from many different provinces since 2006. Because of that, introgression of resistance to PPV in the local cultivars with good pomological characteristics became an important objective for the apricot crop. In the current breeding program, obtaining new cultivars resistant to PPV, selection of resistant seedlings by using molecular markers linked to PPV resistance was aimed at. Nineteen local apricot genitors and progenies obtained from the crosses between the PPV resistant cultivar ‘Stark Early Orange’ (SEO), ‘Harcot’ and local cultivars such as ‘Hacıhaliloğlu’, ‘Kabaaşı’, ‘Hasanbey’, ‘Çöloğlu’, ‘Adilcevaz5’, ‘Şekerpare’, ‘MahmudunEriği’, ‘Soğancı’ and ‘Çataloğlu’ were screened with markers. The markers PGS1.21 and PGS2.23 co-segregating with resistance to PPV were used to screen a total of 189 apricot progenies. None of the local genitors had alleles linked to PPV resistance. Among the progenies screened, 15 seedlings from ‘Şekerpare’ by SEO, 12 from ‘Adilcevaz5’ by SEO, 7 from ‘Hacıhaliloğlu’ by SEO, 9 from ‘Kabaaşı’ by SEO, 5 from ‘Çöloğlu’ by SEO, 9 from ‘Çataloğlu’ by SEO, 4 from ‘Hasanbey’ by SEO, and 1 from ‘MahmudunEriği’ by SEO and none of the ‘Harcot’ by ‘Soğancı’ presented resistant alleles and were selected for further studies