Leaves of hollyhock (Alcea rosea) exhibiting vein chlorosis and yellow mosaic symptoms were collected at public sites in Lausanne and Nyon, two cities of western Switzerland. Diagnostic methods ...untangled in samples from both sites the mixed infections of a novel isometric virus, tentatively named "Alcea yellow mosaic virus" (AYMV) with the carlavirus Gaillardia latent virus. A new potyvirus was also identified in samples from Nyon. A combination of Illumina, Nanopore and Sanger sequencing was necessary to assemble the full-length genome of AYMV, revealing an exceptionally high cytidine content and other features typically associated with members of the genus Tymovirus. The host range of AYMV was found to be restricted to mallows, including ornamentals as well as economically important plants. Phylogenetic analyses further showed that AYMV belongs to a Tymovirus subclade that also gathers the other mallow-infecting members. The virus was readily transmitted by sap inoculation, and the weevil species Aspidapion radiolus was evidenced as a vector. Transmission assays using another weevil or other insect species did not succeed, and seed transmission was not observed.
Pectobacterium and Dickeya species are the causal agents of blackleg and soft rot diseases in potatoes. The main pathogenic species identified so far on potatoes are Dickeya dianthicola, Dickeya ...solani, Pectobacterium atrosepticum, Pectobacterium brasiliense, Pectobacterium carotovorum, and Pectobacterium parmentieri. Ten years ago, the most prevalent Soft Rot Pectobacteriaceae in Europe were the Dickeya species, P. atrosepticum and P. carotovorum, with some variations among countries. Since then, a drastic increase in the abundance of P. brasiliense has been observed in most European countries. This shift is difficult to explain without comparing the pathogenicity of all Dickeya and Pectobacterium species. The pathogenicity of all the above-mentioned bacterial species was assessed in field trials and in vitro tuber slice trials in Switzerland. Two isolates of each species were inoculated by soaking tubers of cv. Desiree in a suspension of 105 CFU/mL, before planting in the field. For all trials, the Dickeya species were the most virulent ones, but long-term strain surveys performed in Switzerland indicate that P. brasiliense is currently the most frequent species detected. Our results show that the pathogenicity of the species is not the main factor explaining the high prevalence of P. brasiliense and P. parmentieri in the Swiss potato fields.
Blackleg and soft rot in potato caused by Pectobacterium and Dickeya enterobacteral genera are among the most destructive bacterial diseases in this crop worldwide. In Europe, over the last century, ...Pectobacterium spp. were the predominant causal agents of these diseases. As for Dickeya, before the large outbreak caused by D. solani in the 2000s, only D. dianthicola was isolated in Europe. The population dynamics of potato blackleg causing soft rot Pectobacteriaceae was, however, different in Switzerland as compared to that in other European countries with a high incidence (60 up to 90%) of Dickeya species (at the time called Erwinia chrysanthemi) already in the 1980s. To pinpoint what may underlie this Swiss peculiarity, we analysed the diversity present in the E. chrysanthemi Agroscope collection gathering potato isolates from 1985 to 2000s. Like elsewhere in Europe during this period, the majority of Swiss isolates belonged to D. dianthicola. However, we also identified a few isolates, such as D. chrysanthemi and D. oryzeae, two species that have not yet been reported in potatoes in Europe. Interestingly, this study allowed the characterisation of two “early” D. solani isolated in the 1990s. Genomic comparison between these early D. solani strains and strains isolated later during the large outbreak in the 2000s in Europe revealed only a few SNP and gene content differences, none of them affecting genes known to be important for virulence.
Wild plants serve as a large reservoir of known and yet-unknown viruses and as a source of viral pathogens of cultivated plants. Yellow mosaic disease of forest shrub
Ligustrum vulgare
(privet) was ...recurrently observed in Europe for more than 100 years. Using a universal virus identification approach based on deep sequencing and
de novo
assembly of viral small interfering (si)RNAs we identified a causative agent of this disease in Switzerland and reconstructed its complete 3-segmented RNA genome. Notably, a short 3′-terminal common region (CR) attached to each segment via a ∼53–71 nucleotide poly(A) tract, as determined by RT-PCR sequencing, was initially identified as an orphan siRNA contig with conserved tRNA-like secondary structure. Phylogenomic analysis classified this virus as a novel member in the genus
Hordeivirus
of family
Virgaviridae
, which we named ligustrum mosaic virus (LigMV). Similar to other hordeiviruses, LigMV formed rod-shape virions (visualized by electron microscopy), was transmitted through seeds and could also be mechanically transmitted to herbaceous hosts
Chenopodium quinoa
and
Nicotiana benthamiana
. Blot hybridization analysis identified genomic and subgenomic RNAs, sharing the 3′-CR and likely serving as monocistronic mRNAs for seven evolutionarily-conserved viral proteins including two subunits of viral RNA-dependent RNA polymerase, coat protein, triple gene block proteins mediating viral movement and cysteine-rich suppressor of RNA silencing. Analysis of size, polarity, and hotspot profiles of viral siRNAs suggested that they are produced by the plant antiviral Dicer-like (DCL) proteins DCL2 and DCL4 processing double-stranded intermediates of genomic RNA replication. Whole genome sequencing of French and Austrian isolates of LigMV revealed its genetic stability over a wide geographic range (>99% nucleotide identity to Swiss isolates and each other), suggesting its persistence and spread in Europe via seed dispersal.
Massive outbreaks of virus yellows (VY) and syndrome “basses richesses” (SBR) are thought to be responsible for the major loss of sugar beet yields in 2020 in western cantons of Switzerland. Typical ...yellowing symptoms were visible during field inspections, and control measures were reportedly ineffective or even absent. Both diseases induce yellowing but have distinct etiologies; while VY is caused by aphid-transmitted RNA viruses, SBR is caused by the cixiid-transmitted γ-proteobacterium Candidatus Arsenophonus phytopathogenicus. To clarify the situation, samples from diseased plants across the country were screened for the causal agents of VY and SBR at the end of the season. Beet yellows virus (BYV) and Beet chlorosis virus (BChV) showed high incidence nationwide, and were frequently found together in SBR-infected fields in the West. Beet mild yellowing virus (BMYV) was detected in two sites in the West, while there was no detection of Beet western yellows virus or Beet mosaic virus. The nucleotide diversity of the detected viruses was then investigated using classic and high-throughput sequencing. For both diseases, outbreaks were analyzed in light of monitoring of the respective vectors, and symptoms were reproduced in greenhouse conditions by means of insect-mediated inoculations. Novel quantification tools were designed for BYV, BChV and Ca. A. phytopathogenicus, leading to the identification of specific tissues tropism for these pathogens.
and
species are the causal agents of blackleg and soft rot diseases. This article explores the possibility of using the glycoalkaloids (GAs) naturally produced by the potato tuber after the greening ...process as a blackleg control method. We first tested the effect of GAs extracted from four potato cultivars on the growth and viability of one
and one
strain in growth media. Then, four years of field experiments were performed in which the incidence of blackleg was assessed in plants grown from the seed tubers of cv. Agria that were subjected to various greening treatments. In the growth media, all GAs isolated from the four cultivars appeared to be bacteriostatic and bactericidal against both bacteria strains. The inhibitory effect varied among GAs from different cultivars. Except for a one-year field trial, the blackleg incidence was lower in plants grown from green seed tubers without the yield being affected. The blackleg control was marginal, probably due to the low production of GAs by the tubers of cv. Agria after greening. Based on our findings, seed tuber greening has a good potential for blackleg control after the identification of varieties that present optimal GA composition after greening.
Five isolates of a new member of the family
, tentatively named blackcurrant leafroll-associated virus 1 (BcLRaV-1), were identified in the currant. The 17-kb-long genome codes for 10 putative ...proteins. The replication-associated polyprotein has several functional domains, including papain-like proteases, methyltransferase, Zemlya, helicase, and RNA-dependent RNA polymerase. Additional open reading frames code for a small protein predicted to integrate into the host cell wall, a heat-shock protein 70 homolog, a heat-shock protein 90 homolog, two coat proteins, and three proteins of unknown functions. Phylogenetic analysis showed that BcLRaV-1 is related to members of the genus
, whereas recombination analysis provided evidence of intraspecies recombination.
Despite the fact that
sp. are ubiquitous fungi, their viromes have been little studied. By analysing a collection of
fungi, two new partitiviruses named Cladosporium cladosporioides partitivirus 1 ...(CcPV1) and Cladosporium cladosporioides partitivirus 2 (CcPV2) co-infecting a strain of
were identified. Their complete genome consists of two monocistronic dsRNA segments (RNA1 and RNA2) with a high percentage of pairwise identity on 5' and 3' end. The RNA directed RNA polymerase (RdRp) of both viruses and the capsid protein (CP) of CcPV1 display the classic characteristics required for their assignment to the
genus. In contrast, CcPV2 RNA2 encodes for a 41 KDa CP that is unusually smaller when aligned to CPs of other viruses classified in this genus. The structural role of this protein is confirmed by electrophoresis on acrylamide gel of purified viral particles. Despite the low percentage of identity between the capsid proteins of CcPV1 and CcPV2, their three-dimensional structures predicted by AlphaFold2 show strong similarities and confirm functional proximity. Fifteen similar viral sequences of unknown function were annotated using the CcPV2 CP sequence. The phylogeny of the CP was highly consistent with the phylogeny of their corresponding RdRp, supporting the organization of
into three distinct clades despite stretching the current demarcation criteria. It is proposed that a new subgenus be created within the genus Gammapartitivirus for this new group.
Pectinolytic bacteria such as Dickeya spp. and Pectobacterium spp. represent a significant threat for seed potato production in Europe. Dickeya spp. induces various symptoms such as plant wilting, ...stem rot (usually referred to as blackleg) and tuber soft rot. Expression of wilting and blackleg symptoms depends on a range of factors: the susceptibility of the cultivar, the aggressiveness of the Dickeya strain and environmental factors such as soil moisture, temperature and plant evapotranspiration. Using the flow of sap driven by plant transpiration, these bacteria can colonize the entire plant vascular system. However, it is not known whether this vascular colonization differs according to the nature of the inoculum (soil-carried or tuber-borne) and whether this has an impact on the expression of symptoms. To better characterize the consequences of colonization of the xylem vessels by Dickeya, greenhouse and field trials were carried out with plants infected via mother tuber inoculation or root inoculation. The development of symptoms was tracked, as were changes in plants’ transpiration rate, and plant transpiration was used as an index of the early stages of symptom expression. Our trials revealed that seed- and soil- carried inocula can both induce wilting and blackleg symptoms in potato plants. It was also found that blackleg symptoms appearing during the first three weeks after plant emergence are caused mainly by a tuber-borne inoculum. Finally, it was established that the presence of a latent inoculum in the xylem vessels does not alter the plant transpiration process, as long as there are no wilting symptoms on rotting lesions.
Dickeya and Pectobacterium species are the causal agents of blackleg and soft rot diseases. This article explores the possibility of using the glycoalkaloids (GAs) naturally produced by the potato ...tuber after the greening process as a blackleg control method. We first tested the effect of GAs extracted from four potato cultivars on the growth and viability of one Dickeya and one Pectobacterium strain in growth media. Then, four years of field experiments were performed in which the incidence of blackleg was assessed in plants grown from the seed tubers of cv. Agria that were subjected to various greening treatments. In the growth media, all GAs isolated from the four cultivars appeared to be bacteriostatic and bactericidal against both bacteria strains. The inhibitory effect varied among GAs from different cultivars. Except for a one-year field trial, the blackleg incidence was lower in plants grown from green seed tubers without the yield being affected. The blackleg control was marginal, probably due to the low production of GAs by the tubers of cv. Agria after greening. Based on our findings, seed tuber greening has a good potential for blackleg control after the identification of varieties that present optimal GA composition after greening.
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