Complete Genome Sequencing of Three Clade-1 Xanthomonads Reveals Genetic Determinants for a Lateral Flagellin and the Biosynthesis of Coronatine-Like Molecules in Xanthomonas.

Evolutionarily, early-branching xanthomonads, also referred to as clade-1 xanthomonads, include major plant pathogens, most of which colonize monocotyledonous plants. Seven species have been validly described, among them the two sugarcane pathogens Xanthomonas albilineans and Xanthomonas sacchari, as well as Xanthomonas translucens, which infects small-grain cereals and diverse grasses but also asparagus and pistachio trees. Single-gene sequencing and genomic approaches have indicated that this clade likely contains more, yet-undescribed species. In this study, we sequenced representative strains of three novel species using long-read sequencing technology. Xanthomonas campestris pv. phormiicola strain CFBP 8444 causes bacterial streak on New Zealand flax, another monocotyledonous plant. Xanthomonas sp. strain CFBP 8443 has been isolated from common bean, and Xanthomonas sp. strain CFBP 8445 originated from banana. Complete assemblies of the chromosomes confirmed their unique phylogenetic position within clade 1 of Xanthomonas. Genome mining revealed novel genetic features, hitherto undescribed in other members of the Xanthomonas genus. In strain CFBP 8444, we identified genes related to the synthesis of coronatine-like compounds, a phytotoxin produced by several pseudomonads, which raises interesting questions about the evolution and pathogenicity of this pathogen. Furthermore, strain CFBP 8444 was found to contain a second, atypical flagellar gene cluster in addition to the canonical flagellar gene cluster. Overall, this research represents an important step toward better understanding the evolutionary history and biology of early-branching xanthomonads.

Metagenomics approach for Polymyxa betae genome assembly enables comparative analysis towards deciphering the intracellular parasitic lifestyle of the plasmodiophorids.

Genomic knowledge of the tree of life is biased to specific groups of organisms. For example, only six full genomes are currently available in the rhizaria clade. Here, we have applied metagenomic techniques enabling the assembly of the genome of Polymyxa betae (Rhizaria, Plasmodiophorida) RES F41 isolate from unpurified zoospore holobiont and comparison with the A26-41 isolate. Furthermore, the first P. betae mitochondrial genome was assembled. The two P. betae nuclear genomes were highly similar, each with just ~10.2 k predicted protein coding genes, ~3% of which were unique to each isolate. Extending genomic comparisons revealed a greater overlap with Spongospora subterranea than with Plasmodiophora brassicae, including orthologs of the mammalian cation channel sperm-associated proteins, raising some intriguing questions about zoospore physiology. This work validates our metagenomics pipeline for eukaryote genome assembly from unpurified samples and enriches plasmodiophorid genomics; providing the first full annotation of the P. betae genome.

Rhizomania: Hide and Seek of Polymyxa betae and the Beet Necrotic Yellow Vein Virus with Beta vulgaris.

The molecular interactions between Polymyxa betae, the protist vector of sugar beet viruses, beet necrotic yellow vein virus (BNYVV), the causal agent of rhizomania, and Beta vulgaris have not been extensively studied. Here, the transmission of BNYVV to sugar beet by P. betae zoospores was optimized using genetically characterized organisms. Molecular interactions of aviruliferous and viruliferous protist infection on sugar beet were highlighted by transcriptomic analysis. P. betae alone induced limited gene expression changes in sugar beet, as a biotrophic asymptomatic parasite. Most differentially expressed plant genes were down-regulated and included resistance gene analogs and cell wall peroxidases. Several enzymes involved in stress regulation, such as the glutathione-S-transferases, were significantly induced. With BNYVV, the first stages of the P. betae life cycle on sugar beet were accelerated with a faster increase of relative protist DNA level and an earlier appearance of sporangia and sporosori in plants roots. A clear activation of plant defenses and the modulation of genes involved in plant cell wall metabolism were observed. The P. betae transcriptome in the presence of BNYVV revealed induction of genes possibly involved in the switch to the survival stage. The interactions were different depending on the presence or absence of the virus. P. betae alone alleviates plant defense response, playing hide-and-seek with sugar beet and allowing for their mutual development. Conversely, BNYVV manipulates plant defense and promotes the rapid invasion of plant roots by P. betae. This accelerated colonization is accompanied by the development of thick-walled resting spores, supporting the virus survival. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

RNA silencing machinery contributes to inability of BSBV to establish infection in Nicotiana benthamiana: evidence from characterization of agroinfectious clones of Beet soil-borne virus.

Beet soil-borne virus (BSBV) is a sugar beet pomovirus frequently associated with Beet necrotic yellow veins virus, the causal agent of the rhizomania disease. BSBV has been detected in most of the major beet-growing regions worldwide, yet its impact on this crop remains unclear. With the aim to understand the life cycle of this virus and clarify its putative pathogenicity, agroinfectious clones have been engineered for each segment of its tripartite genome. The biological properties of these clones were then studied on different plant species. Local infection was obtained on agroinfiltrated leaves of Beta macrocarpa. On leaves of Nicotiana benthamiana, similar results were obtained, but only when heterologous viral suppressors of RNA silencing were co-expressed or in a transgenic line down regulated for both dicer-like protein 2 and 4. On sugar beet, local infection following agroinoculation was obtained on cotyledons, but not on other tested plant parts. Nevertheless, leaf symptoms were observed on this host via sap inoculation. Likewise, roots were efficiently mechanically infected, highlighting low frequency of root necrosis and constriction, and enabling the demonstration of transmission by the vector Polymyxa betae. Altogether, the entire viral cycle was reproduced, validating the constructed agroclones as efficient inoculation tools, paving the way for further studies on BSBV and its related pathosystem.

Muntingia yellow spot virus: a novel New World begomovirus infecting Muntingia calabura L.

The whole genome sequence of a begomovirus (family Geminiviridae) infecting Muntingia calabura L. (family Muntingiaceae) from the province of Guayas in Ecuador was determined in this work. The major symptom observed on this plant species was yellow spots on leaves. The nucleotide sequences of three DNA-A clones and one DNA-B clone were compared to those of other begomoviruses. The DNA-A clones displayed the highest similarity to isolates of pepper leafroll virus (PepLRV), with 87.4 to 88.1% sequence identity. Likewise, the DNA-B clone showed the highest similarity (79.3-79.6% sequence identity) to PepLRV isolates. According to the demarcation criteria for begomovirus species, the begomovirus described in this work, for which we propose the name "muntingia yellow spot virus", represents a novel species. To our best knowledge, this is the first report of a begomovirus infecting a plant of the family Muntingiaceae.

Banana Tree Infected with Banana Bunchy Top Virus Attracts Pentalonia nigronervosa Aphids Through Increased Volatile Organic Compounds Emission.

Banana plants are affected by various viral diseases, among which the most devastating is the "bunchy top", caused by the Banana bunchy top virus (BBTV) and transmitted by the aphid Pentalonia nigronervosa Coquerel. The effect of BBTV on attraction mechanisms of dessert and plantain banana plants on the vector remains far from elucidated. For that, attractiveness tests were carried out using a two columns olfactometer for apterous aphids, and a flight cage experiment for alate aphids. Volatile Organic Compounds (VOCs) emitted by either healthy or BBTV-infected banana plants were identified using a dynamic extraction system and gas-chromatography mass-spectrometry (GC-MS) analysis. Behavioral results revealed a stronger attraction of aphids towards infected banana plants (independently from the variety), and towards the plantain variety (independently from the infection status). GC-MS results revealed that infected banana plants produced VOCs of the same mixture as healthy banana plants but in much higher quantities. In addition, VOCs produced by dessert and plantain banana plants were different in nature, and plantains produced higher quantities than dessert banana trees. This work opens interesting opportunities for biological control of P. nigronervosa, for example by luring away the aphid from banana plants through manipulation of olfactory cues.

The Complete Genome Sequence of Xanthomonas theicola, the Causal Agent of Canker on Tea Plants, Reveals Novel Secretion Systems in Clade-1 Xanthomonads.

Xanthomonas theicola is the causal agent of bacterial canker on tea plants. There is no complete genome sequence available for X. theicola, a close relative of the species X. translucens and X. hyacinthi, thus limiting basic research for this group of pathogens. Here, we release a high-quality complete genome sequence for the X. theicola type strain, CFBP 4691T. Single-molecule real-time sequencing with a mean coverage of 264× revealed two contigs of 4,744,641 bp (chromosome) and 40,955 bp (plasmid) in size. Genome mining revealed the presence of nonribosomal peptide synthases, two CRISPR systems, the Xps type 2 secretion system, and the Hrp type 3 secretion system. Surprisingly, this strain encodes an additional type 2 secretion system and a novel type 3 secretion system with enigmatic function, hitherto undescribed for xanthomonads. Four type 3 effector genes were found on complete or partial transposons, suggesting a role of transposons in effector gene evolution and spread. This genome sequence fills an important gap to better understand the biology and evolution of the early-branching xanthomonads, also known as clade-1 xanthomonads.

Genome Resource of Barley Bacterial Blight and Leaf Streak Pathogen Xanthomonas translucens pv. translucens strain UPB886.

Xanthomonas translucens pv. translucens causes bacterial leaf streak and bacterial blight diseases of barley. This pathogen limits barley production globally but remains understudied, with limited genomic resources. To better understand the biology of this X. translucens subgroup, we sequenced the complete genome of the X. translucens pv. translucens strain UPB886.

Molecular Typing Reveals High Genetic Diversity of Xanthomonas translucens Strains Infecting Small-Grain Cereals in Iran.

This study provides a phylogeographic insight into the population diversity of Xanthomonas translucens strains causing bacterial leaf streak disease of small-grain cereals in Iran. Among the 65 bacterial strains isolated from wheat, barley, and gramineous weeds in eight Iranian provinces, multilocus sequence analysis and typing (MLSA and MLST) of four housekeeping genes (dnaK, fyuA, gyrB, and rpoD), identified 57 strains as X. translucens pv. undulosa, while eight strains were identified as X. translucens pv. translucens. Although the pathogenicity patterns on oat and ryegrass weed species varied among the strains, all X. translucens pv. undulosa strains were pathogenic on barley, Harding's grass, rye (except for XtKm35) and wheat, and all X. translucens pv. translucens strains were pathogenic on barley and Harding's grass, while none of the latter group was pathogenic on rye or wheat (except for XtKm18). MLST using the 65 strains isolated in Iran, as well as the sequences of the four genes from 112 strains of worldwide origin retrieved from the GenBank database, revealed higher genetic diversity (i.e., haplotype frequency, haplotype diversity, and percentage of polymorphic sites) among the Iranian population of X. translucens than among the North American strains of the pathogen. High genetic diversity of the BLS pathogen in Iran was in congruence with the fact that the Iranian Plateau is considered the center of origin of cultivated wheat. However, further studies using larger collections of strains are warranted to precisely elucidate the global population diversity and center of origin of the pathogen.IMPORTANCE Bacterial leaf streak (BLS) of small-grain cereals (i.e., wheat and barley) is one of the economically important diseases of gramineous crops worldwide. The disease occurs in many countries across the globe, with particular importance in regions characterized by high levels of precipitation. Two genetically distinct xanthomonads-namely, Xanthomonas translucens pv. undulosa and X. translucens pv. translucens-have been reported to cause BLS disease on small-grain cereals. As seed-borne pathogens, the causal agents are included in the A2 list of quarantine pathogens by the European and Mediterranean Plant Protection Organization (EPPO). Despite its global distribution and high economic importance, the population structure, genetic diversity, and phylogeography of X. translucens remain undetermined. This study, using MLSA and MLST, provides a global-scale phylogeography of X. translucens strains infecting small-grain cereals. Based on the diversity parameters, neutrality indices, and population structure, we observe higher genetic diversity of the BLS pathogen in Iran, which is geographically close to the center of origin of common wheat, than has so far been observed in other areas of the world, including North America. The results obtained in this study provide a novel insight into the genetic diversity and population structure of the BLS pathogen of small-grain cereals on a global scale.

Full genome sequence of a new polymycovirus infecting Fusarium redolens.

By screening a collection of Fusarium spp. for the presence of dsRNA, the Fusarium redolens strain A63-1 was found harboring a pattern of multiple dsRNA bands when analyzed by agarose gel electrophoresis. Using NextSeq Illumina sequencing, the full sequences of eight dsRNA molecules were determined, compared to databases, and gathered into a new viral genome. This novel virus shares similarities with mycoviruses that were recently grouped in the proposed family "Polymycoviridae". Hence, the name "Fusarium redolens polymycovirus 1" is proposed for this virus. Each viral dsRNA contains only one ORF, except dsRNA 7, which has an additional one. Based on amino acid sequence similarities, the functions of the proteins encoded by dsRNA 1-4 can be hypothesized. On the other hand, the putative proteins encoded by dsRNA 5-8 exhibit no relevant homology to known proteins. In this report, the full genome sequence of this new virus is presented along with a primary bioinformatics analysis.

Bottom-up regulation of a tritrophic system by Beet yellows virus infection: consequences for aphid-parasitoid foraging behaviour and development.

Effects of plants on herbivores can cascade up the food web and modulate the abundance of higher trophic levels. In agro-ecosystems, plant viruses can affect the interactions between crops, crop pests, and natural enemies. Little is known, however, about the effects of viruses on higher trophic levels, including parasitoids and their ability for pest regulation. We tested the hypothesis that a plant virus affects parasitoid foraging behaviour through cascading effects on higher trophic levels. We predicted that the semi-persistent Beet yellows virus (BYV) would influence plant (Beta vulgaris) quality, as well as aphid host (Aphis fabae) quality for a parasitoid Lysiphlebus fabarum. We determined amino acid and sugar content in healthy and infected plants (first trophic level), lipid content and body size of aphids (second trophic level) fed on both plants, as well as foraging behaviour and body size of parasitoids (third trophic level) that developed on aphids fed on both plants. Our results showed that virus infection increased sugars and decreased total amino acid content in B. vulgaris. We further observed an increase in aphid size without modification in host aphid quality (i.e., lipid content), and a slight effect on parasitoid behaviour through an increased number of antennal contacts with host aphids. Although the BYV virus clearly affected the first two trophic levels, it did not affect development or emergence of parasitoids. As the parasitoid L. fabarum does not seem to be affected by the virus, we discuss the possibility of using it for the development of targeted biological control against aphids.

The Epidemiology of Xylella fastidiosa; A Perspective on Current Knowledge and Framework to Investigate Plant Host-Vector-Pathogen Interactions.

Insect-transmitted plant diseases caused by viruses, phytoplasmas, and bacteria share many features in common regardless of the causal agent. This perspective aims to show how a model framework, developed originally for plant virus diseases, can be modified for the case of diseases incited by Xylella fastidiosa. In particular, the model framework enables the specification of a simple but quite general invasion criterion defined in terms of key plant, pathogen, and vector parameters and, importantly, their interactions, which determine whether or not an incursion or isolated outbreak of a pathogen will lead to establishment, persistence, and subsequent epidemic development. Hence, this approach is applicable to the wide range of X. fastidiosa-incited diseases that have recently emerged in southern Europe, each with differing host plant, pathogen subspecies, and vector identities. Of particular importance are parameters relating to vector abundance and activity, transmission characteristics, and behavior in relation to preferences for host infection status. Some gaps in knowledge with regard to the developing situation in Europe are noted.

Complete genome sequence of two tomato-infecting begomoviruses in Venezuela: evidence of a putative novel species and a novel recombinant strain.

At least six begomovirus species have been reported infecting tomato in Venezuela. In this study the complete genomes of two tomato-infecting begomovirus isolates (referred to as Trujillo-427 and Zulia-1084) were cloned and sequenced. Both isolates showed the typical genome organization of New World bipartite begomoviruses, with DNA-A genomic components displaying 88.8% and 90.3% similarity with established begomoviruses, for isolates Trujillo-427 and Zulia-1084, respectively. In accordance to the guidelines for begomovirus species demarcation, the Trujillo-427 isolate represents a putative new species and the name "Tomato wrinkled mosaic virus" is proposed. Meanwhile, Zulia-1084 represents a putative new strain classifiable within species Tomato chlorotic leaf distortion virus, for which a recombinant origin is suggested.

ICTV Virus Taxonomy Profile: Virgaviridae.

The family Virgaviridae is a family of plant viruses with rod-shaped virions, a ssRNA genome with a 3'-terminal tRNA-like structure and a replication protein typical of alpha-like viruses. Differences in the number of genome components, genome organization and the mode of transmission provide the basis for genus demarcation. Tobacco mosaic virus (genus Tobamovirus) was the first virus to be discovered (in 1886); it is present in high concentrations in infected plants, is extremely stable and has been extensively studied. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Virgaviridae, which is available at www.ictv.global/report/virgaviridae.

Molecular and biological characterization of a new Tomato mild yellow leaf curl Aragua virus strain producing severe symptoms in tomato.

Tomato mild yellow leaf curl Aragua virus (ToMYLCV) is a begomovirus first reported infecting tomato (Solanum lycopersicum) and milkweed (Euphorbia heterophylla) in Venezuela. In this study, a ToMYLCV isolate (Zulia-219) was completely sequenced and its host range was evaluated. The DNA-A and DNA-B components of isolate Zulia-219 showed 93 and 85% nucleotide sequence identity with the respective counterparts of the ToMYLCV type strain. According to current demarcation criteria for begomovirus species, Zulia-219 is a new strain of ToMYLCV. Interestingly, tomato plants inoculated with ToMYLCV Zulia-219 displayed severe symptoms, including severe chlorotic leaf curling, in contrast to mild symptoms associated with the type strain of this begomovirus. These results indicate potential risks associated with this new ToMYLCV strain for tomato production in Venezuela.

Characterization of the Xanthomonas translucens Complex Using Draft Genomes, Comparative Genomics, Phylogenetic Analysis, and Diagnostic LAMP Assays.

Prevalence of Xanthomonas translucens, which causes cereal leaf streak (CLS) in cereal crops and bacterial wilt in forage and turfgrass species, has increased in many regions in recent years. Because the pathogen is seedborne in economically important cereals, it is a concern for international and interstate germplasm exchange and, thus, reliable and robust protocols for its detection in seed are needed. However, historical confusion surrounding the taxonomy within the species has complicated the development of accurate and reliable diagnostic tools for X. translucens. Therefore, we sequenced genomes of 15 X. translucens strains representing six different pathovars and compared them with additional publicly available X. translucens genome sequences to obtain a genome-based phylogeny for robust classification of this species. Our results reveal three main clusters: one consisting of pv. cerealis, one consisting of pvs. undulosa and translucens, and a third consisting of pvs. arrhenatheri, graminis, phlei, and poae. Based on genomic differences, diagnostic loop-mediated isothermal amplification (LAMP) primers were developed that clearly distinguish strains that cause disease on cereals, such as pvs. undulosa, translucens, hordei, and secalis, from strains that cause disease on noncereal hosts, such as pvs. arrhenatheri, cerealis, graminis, phlei, and poae. Additional LAMP assays were developed that selectively amplify strains belonging to pvs. cerealis and poae, distinguishing them from other pathovars. These primers will be instrumental in diagnostics when implementing quarantine regulations to limit further geographic spread of X. translucens pathovars.

Bacillus cereus sensu lato antimicrobial arsenal: An overview.

The Bacillus cereus group contains genetically closed bacteria displaying a variety of phenotypic features and lifestyles. The group is mainly known through the properties of three major species: the entomopathogen Bacillus thuringiensis, the animal and human pathogen Bacillus anthracis and the foodborne opportunistic strains of B. cereus sensu stricto. Yet, the actual diversity of the group is far broader and includes multiple lifestyles. Another less-appreciated aspect of B. cereus members lies within their antimicrobial potential which deserves consideration in the context of growing emergence of resistance to antibiotics and pesticides, and makes it crucial to find new sources of antimicrobial molecules. This review presents the state of knowledge on the known antimicrobial compounds of the B. cereus group members, which are grouped according to their chemical features and biosynthetic pathways. The objective is to provide a comprehensive review of the antimicrobial range exhibited by this group of bacteria, underscoring the interest in its potent biocontrol arsenal and encouraging further research in this regard.

Preference of Pentalonia nigronervosa for infected banana plants tends to reverse after Banana bunchy top virus acquisition.

Pentalonia nigronervosa Coquerel (Hemiptera: Aphididae) is the vector of the Banana Bunchy Top Virus (BBTV), the most serious viral disease of banana (Musa spp.) in the world. Before acquiring the virus, the vector is more attracted to infected banana plants in response to the increased emissions of volatile organic compounds (VOCs). Here, we test the hypothesis that BBTV acquisition directly modifies the preference of P. nigronervosa for infected banana plants, and that the change in preference results from the alteration of the organs linked to the VOC detection or to the behaviour of the vector. We found that the preference of P. nigronervosa for infected banana plants reverses after virus acquisition in dessert banana, while it remains similar between healthy and infected banana plants before and after the acquisition of BBTV. At the same time, aphids reared on infected bananas had smaller forewing areas and hind tibia length than aphids reared on healthy bananas, although the number of secondary rhinaria on the antennae was lower on dessert banana-reared aphids than plantain-reared aphids, this was not affected by the infection status of the aphid. These results support the "vector manipulation hypothesis-VMH" of pathogens to promote their spread. They have implications for the BBTV management.

Pest categorisation of Pratylenchus loosi.

Following the EFSA commodity risk assessment of Malus domestica plants imported from Türkiye into the EU, the EFSA Panel on Plant Health performed a pest categorisation of Pratylenchus loosi (Nematoda: Pratylenchidae) for the EU. Pratylenchus loosi belongs to the order Rhabditida, subfamily Pratylenchidae. This nematode is not known to be present in the EU. The species is not included in the EU Commission Implementing Regulation 2019/2072. The pest occurs primarily in tropical, subtropical and warm temperate areas. It is widely distributed in Asian countries, with tea plants (Camellia sinensis) as the main host. The pest was reported from more than 60 plant species, but reports from hosts other than C. sinensis, e.g. citrus (Citrus spp.) and banana (Musa spp.), are associated with high uncertainty due to doubtful pest identification. Morphological and molecular methods are available for the identification of the pest. Pathways of entry are host plants for planting except seeds, as well as soil attached to plants for planting, machinery or footwear. Soil import to the EU is prohibited from third countries. The climatic preferences of P. loosi are compatible with the microclimatic conditions occurring in the areas of the EU where tea is grown outside. The impact of the nematode is primarily known for Asian countries, where it is a devastating pathogen on tea plants, but there is a key uncertainty on impacts on hosts other than tea. Considering the strong pathogenicity of the pest, its establishment in tea producing areas would have negative consequences for tea producers. Therefore, the Panel concludes that P. loosi satisfies all the criteria that are within the remit of EFSA to assess for it to be regarded as a potential Union quarantine pest.

Pest categorisation of Malacosoma parallela.

The EFSA Panel on Plant Health performed a pest categorisation of Malacosoma parallela (Staudinger) (Lepidoptera: Lasiocampidae) for the territory of the European Union, following commodity risk assessments of Berberis thunbergii, Malus domestica, Prunus persica and P. dulcis plants for planting from Türkiye, in which M. parallela came to attention as of possible concern. M. parallela is commonly known as the mountain ring silk moth and is a polyphagous leaf-eating pest in west-central Asia, primarily feeding on deciduous trees and shrubs, and known to cause serious damage to Malus, Prunus, and Quercus species. It is found at a range of altitudes from 130 m to 3000 m although most common above 1000 m. It is a univoltine species. Eggs are laid in masses on twigs and branches in the summer and larvae hatch the following spring to feed on buds and fresh leaves. Host plants can be completely defoliated. Plants for planting and cut branches provide pathways for entry, especially if infested with egg masses. Host availability and climate suitability suggest that parts of the EU would be suitable for establishment. Adults can fly and the pest could spread naturally within the EU although adults only live for a few days. Faster and more extensive spread is therefore more likely via egg masses moved on plants for planting. The introduction of M. parallela into the EU could lead to outbreaks causing damage to deciduous trees and shrubs in forests and orchards. Phytosanitary measures are available to inhibit the entry and spread of this species. M. parallela satisfies all the criteria that are within the remit of EFSA to assess for it to be regarded as a potential Union quarantine pest.