Allopatric Plant Pathogen Population Divergence following Disease Emergence

Virulence Comparison of a Comprehensive Panel of Xylella fastidiosa Pierce's Disease Isolates from California

Xylella fastidiosa, the causal agent of Pierce's disease of grapevine, has been found in all major grape-growing regions in California, U.S.A. Large collections of X. fastidiosa isolates are available from these areas, which enable comparative studies of pathogen genetic traits and virulence. Owing to the significant resource requirements for experiments with X. fastidiosa in grapevine, however, most studies use only a single isolate to evaluate disease, and it is not clear how much variability between isolates impacts disease development in experimental or natural settings. In this study, a comprehensive panel of X. fastidiosa isolates from all California grape-growing regions was tested for virulence in susceptible grapevine and in the model host plant, tobacco. Seventy-one isolates were tested, 29 in both grapevine and tobacco. The results of this study highlight the inherent variability of inoculation experiments with X. fastidiosa, including variation in disease severity in plants inoculated with a single isolate, and variability between experimental replicates. There were limited differences in virulence between isolates that were consistent across experimental replicates, or across different host plants. This suggests that choice of isolate within the X. fastidiosa subsp. fastidiosa Pierce's disease group may not make any practical difference when testing in susceptible grape varieties, and that pathogen evolution has not significantly changed virulence of Pierce's disease isolates within California. The location of isolation also did not dictate relative disease severity. This information will inform experimental design for future studies of X. fastidiosa in grapevine and provide important context for genomic research.

Fungal Diseases in Yerba Mate: Status and Management Strategies

Yerba mate (Ilex paraguariensis St. Hil.), with its health benefits and socioeconomic significance, plays a crucial role in Argentina and other South American countries like Brazil and Paraguay. Its cultivation in the Province of Misiones (Argentina) supports various sectors, contributes to regional development, and provides employment opportunities. However, the transition from extractive practices to monoculture, accompanied with increased demand, has led to phytosanitary challenges. Imbalanced native microbiota, disease development, and pathogen dispersion have become prevalent issues. Understanding the known pathogens associated with yerba mate plants is crucial for developing effective agricultural strategies. The primary objective of this study is to synthesise current knowledge on prevalent fungal diseases in yerba mate cultivation, as well as to provide agricultural management recommendations for effective disease control. Fungal diseases can cause significant damage to different parts of the plant, resulting in economic losses. The proximity of neighbouring plantations to yerba mate crops may contribute to the cross-contamination of pathogens, emphasizing the need for comprehensive epidemiology and accurate diagnosis. Multiple fungal genera have been reported to cause pathologies in yerba mate. Among the fungi causing foliar diseases are Ceratobasidium niltonsouzanum, Cylindrocladium spathulatum, Pseudocercospora mate, Asterina sphaerelloides, Colletotrichum gloeosporioides aff var. yerbae, and Phyllosticta sp. Caulinary diseases are caused by Alternaria sp., Phoma sp., Colletotrichum sp., and Ceratocystis fimbriata. Regarding root rot, the genera Rhizoctonia sp., Pythium sp., Fusarium sp., and Rosellinia sp. have been reported. Proper crop management practices and monitoring are essential for effective disease control. To reduce reliance on chemical compounds, the use of biocontrol agents like Trichoderma sp. has shown promise in regulating phytopathogenic fungi populations. Continued research is vital to preserve the yerba mate industry and ensure its long-term viability while minimizing environmental impact.

Phylogeographic and Phylogenomic Structure of the Quarantine Plant Pathogen Colletotrichum liriopes, Including New Reports in the United States

Global agricultural trade has accelerated the emergence and re-emergence of new plant pathogens. In the United States, the fungal pathogen Colletotrichum liriopes is still considered a foreign quarantine pathogen that affects ornamental plants (i.e., Liriope spp.). Even though this species has been reported in East Asia on various asparagaceous hosts, its first and only report in the United States was in 2018. However, that study used only ITS nrDNA for identification, and no available culture or voucher specimen was maintained. The main objective of the present study was to determine the geographic and host distribution of specimens identified as C. liriopes. To accomplish this, new and existing isolates, sequences, and genomes obtained from various hosts and geographic locations (i.e., China, Colombia, Mexico, and the United States) were compared with the ex-type of C. liriopes. Multilocus phylogenetic (ITS, Tub2, GAPDH, CHS-1, and HIS3), phylogenomic, and splits tree analyses revealed that all the studied isolates/sequences form a well-supported clade with little intraspecific variation. Morphological characterizations support these findings. The minimum spanning network, low nucleotide diversity, and negative Tajima's D from both multilocus and genomic data suggest that there was a recent movement/invasion of a few East Asian genotypes to other countries where the ornamental plants are produced (e.g., South America) and subsequently to the importing countries, such as the United States. The study reveals that the geographic and host distribution of C. liriopes sensu stricto is expanded to the United States (i.e., at least Maryland, Mississippi, and Tennessee) and on various hosts in addition to Asparagaceae and Orchidaceae. The present study produces fundamental knowledge that can be used in efforts to reduce costs or losses from agricultural trade and to expand our understanding of pathogen movement.

The Multifaceted Role of Homologous Recombination in a Fastidious Bacterial Plant Pathogen

Homologous recombination plays a key function in the evolution of bacterial genomes. Within Xylella fastidiosa, an emerging plant pathogen with increasing host and geographic ranges, it has been suggested that homologous recombination facilitates host switching, speciation, and the development of virulence. We used 340 whole-genome sequences to study the relationship between inter- and intrasubspecific homologous recombination, random mutation, and natural selection across individual X. fastidiosa genes. Individual gene orthologs were identified and aligned, and a maximum likelihood (ML) gene tree was generated. Each gene alignment and tree pair were then used to calculate gene-wide and branch-specific r/m values (relative effect of recombination to mutation), gene-wide and branch-site nonsynonymous over synonymous substitution rates (dN/dS values; episodic selection), and branch length (as a proxy for mutation rate). The relationships between these variables were evaluated at the global level (i.e., for all genes among and within a subspecies), among specific functional classes (i.e., COGs), and between pangenome components (i.e., accessory versus core genes). Our analysis showed that r/m varied widely among genes as well as across X. fastidiosa subspecies. While r/m and dN/dS values were positively correlated in some instances (e.g., core genes in X. fastidiosa subsp. fastidiosa and both core and accessory genes in X. fastidiosa subsp. multiplex), low correlation coefficients suggested no clear biological significance. Overall, our results indicate that, in addition to its adaptive role in certain genes, homologous recombination acts as a homogenizing and a neutral force across phylogenetic clades, gene functional groups, and pangenome components. IMPORTANCE There is ample evidence that homologous recombination occurs frequently in the economically important plant pathogen Xylella fastidiosa. Homologous recombination has been known to occur among sympatric subspecies and is associated with host-switching events and virulence-linked genes. As a consequence, is it generally assumed that recombinant events in X. fastidiosa are adaptive. This mindset influences expectations of how homologous recombination acts as an evolutionary force as well as how management strategies for X. fastidiosa diseases are determined. Yet, homologous recombination plays roles beyond that of a source for diversification and adaptation. Homologous recombination can act as a DNA repair mechanism, as a means to facilitate nucleotide compositional change, as a homogenization mechanism within populations, or even as a neutral force. Here, we provide a first assessment of long-held beliefs regarding the general role of recombination in adaptation for X. fastidiosa. We evaluate gene-specific variations in homologous recombination rate across three X. fastidiosa subspecies and its relationship to other evolutionary forces (e.g., natural selection, mutation, etc.). These data were used to assess the role of homologous recombination in X. fastidiosa evolution.

Suspicions of two bridgehead invasions of Xylella fastidiosa subsp. multiplex in France

Of American origin, a wide diversity of Xylella fastidiosa strains belonging to different subspecies have been reported in Europe since 2013 and its discovery in Italian olive groves. Strains from the subspecies multiplex (ST6 and ST7) were first identified in France in 2015 in urban and natural areas. To trace back the most probable scenario of introduction in France, the molecular evolution rate of this subspecies was estimated at 3.2165 × 10^-7 substitutions per site per year, based on heterochronous genome sequences collected worldwide. This rate allowed the dating of the divergence between French and American strains in 1987 for ST6 and in 1971 for ST7. The development of a new VNTR-13 scheme allowed tracing the spread of the bacterium in France, hypothesizing an American origin. Our results suggest that both sequence types were initially introduced and spread in Provence-Alpes-Côte d'Azur (PACA); then they were introduced in Corsica in two waves from the PACA bridgehead populations.

Global predictions for the risk of establishment of Pierce's disease of grapevines

The vector-borne bacterium Xylella fastidiosa is responsible for Pierce's disease (PD), a lethal grapevine disease that originated in the Americas. The international plant trade is expanding the geographic range of this pathogen, posing a new threat to viticulture worldwide. To assess the potential incidence of PD, we have built a dynamic epidemiological model based on the response of 36 grapevine varieties to the pathogen in inoculation assays and on the vectors' distribution when this information is available. Key temperature-driven epidemiological processes, such as PD symptom development and recovery, are mechanistically modelled. Integrating into the model high-resolution spatiotemporal climatic data from 1981 onward and different infectivity (R₀) scenarios, we show how the main wine-producing areas thrive mostly in non-risk, transient, or epidemic-risk zones with potentially low growth rates in PD incidence. Epidemic-risk zones with moderate to high growth rates are currently marginal outside the US. However, a global expansion of epidemic-risk zones coupled with small increments in the disease growth rate is projected for 2050. Our study globally downscales the risk of PD establishment while highlighting the importance of considering climate variability, vector distribution, and an invasive criterion as factors to obtain better PD risk maps.

Xylella fastidiosa Outbreak in Israel: Population Genetics, Host Range, and Temporal and Spatial Distribution Analysis

Diseases caused by the insect-transmitted bacterium Xylella fastidiosa have been reported in the Americas since the 19th century, causing diseases such as Pierce's disease of grapevine, almond leaf scorch (ALS), and citrus variegated chlorosis. In the last decade X. fastidiosa was reported from different parts of the world, most notably from southern Italy, infecting olives. In 2017, X. fastidiosa was reported to be associated with ALS symptoms in Israel. Here, we investigated the causal agent of ALS in Israel, its genetic diversity, and host range, and we characterized the temporal and spatial distribution of the disease. X. fastidiosa subsp. fastidiosa sequence type 1 was isolated from symptomatic almond trees and was used to infect almond and grapevine by mechanical inoculation. The pathogen, however, did not infect olive, peach, cherry, plum, nectarine, clementine, and grapefruit plants. Genomic analysis of local isolates revealed that the local population is derived from a single introduction and that they are closely related to X. fastidiosa strains from grapevines in California. Distribution analyses revealed that ALS did not expand from 2017 to 2019; however, since 2020, newly symptomatic trees appeared in the tested orchards. Symptomatic trees were located primarily in clusters, and symptoms tended to spread within rows. Our study confirms that X. fastidiosa is the causal agent of ALS in Israel and describes its genetic and host range characteristics. Although there is no clear evidence yet for the identity of the vectors in Israel, ALS spread continues to threat the almond and grapevine industries in Israel.

Using Genomes and Evolutionary Analyses to Screen for Host-Specificity and Positive Selection in the Plant Pathogen Xylella fastidiosa

Xylella fastidiosa infects several economically important crops in the Americas, and it also recently emerged in Europe. Here, using a set of Xylella genomes reflective of the genus-wide diversity, we performed a pan-genome analysis based on both core and accessory genes for two purposes: (i) to test associations between genetic divergence and plant host species and (ii) to identify positively selected genes that are potentially involved in arms-race dynamics. For the former, tests yielded significant evidence for the specialization of X. fastidiosa to plant host species. This observation contributes to a growing literature suggesting that the phylogenetic history of X. fastidiosa lineages affects the host range. For the latter, our analyses uncovered evidence of positive selection across codons for 5.3% (67 of 1,257) of the core genes and 5.4% (201 of 3,691) of the accessory genes. These genes are candidates to encode interacting factors with plant and insect hosts. Most of these genes had unknown functions, but we did identify some tractable candidates, including nagZ_2, which encodes a beta-glucosidase that is important for Neisseria gonorrhoeae biofilm formation; cya, which modulates gene expression in pathogenic bacteria, and barA, a membrane associated histidine kinase that has roles in cell division, metabolism, and pili formation.

IMPORTANCEXylella fastidiosa causes devasting diseases to several critical crops. Because X. fastidiosa colonizes and infects many plant species, it is important to understand whether the genome of X. fastidiosa has genetic determinants that underlie specialization to specific host plants. We analyzed genome sequences of X. fastidiosa to investigate evolutionary relationships and to test for evidence of positive selection on specific genes. We found a significant signal between genome diversity and host plants, consistent with bacterial specialization to specific plant hosts. By screening for positive selection, we identified both core and accessory genes that may affect pathogenicity, including genes involved in biofilm formation.

Investigating plant disease outbreaks with long-read metagenomics: sensitive detection and highly resolved phylogenetic reconstruction applied to Xylella fastidiosa

Early disease detection is a prerequisite for enacting effective interventions for disease control. Strains of the bacterial plant pathogen Xylella fastidiosa have recurrently spread to new crops in new countries causing devastating outbreaks. So far, investigation of outbreak strains and highly resolved phylogenetic reconstruction have required whole-genome sequencing of pure bacterial cultures, which are challenging to obtain due to the fastidious nature of X. fastidiosa. Here, we show that culture-independent metagenomic sequencing, using the Oxford Nanopore Technologies MinION long-read sequencer, can sensitively and specifically detect the causative agent of Pierce’s disease of grapevine, X. fastidiosa subspecies fastidiosa. Using a DNA sample from a grapevine in Virginia, USA, it was possible to obtain a metagenome-assembled genome (MAG) of sufficient quality for phylogenetic reconstruction with SNP resolution. The analysis placed the MAG in a clade with isolates from Georgia, USA, suggesting introduction of X. fastidiosa subspecies fastidiosa to Virginia from the south-eastern USA. This proof of concept study, thus, revealed that metagenomic sequencing can replace culture-dependent genome sequencing for reconstructing transmission routes of bacterial plant pathogens.

Comparative Genomics of Xylella fastidiosa Explores Candidate Host-Specificity Determinants and Expands the Known Repertoire of Mobile Genetic Elements and Immunity Systems

Xylella fastidiosa causes diseases in many plant species. Originally confined to the Americas, infecting mainly grapevine, citrus, and coffee, X. fastidiosa has spread to several plant species in Europe causing devastating diseases. Many pathogenicity and virulence factors have been identified, which enable the various X. fastidiosa strains to successfully colonize the xylem tissue and cause disease in specific plant hosts, but the mechanisms by which this happens have not been fully elucidated. Here we present thorough comparative analyses of 94 whole-genome sequences of X. fastidiosa strains from diverse plant hosts and geographic regions. Core-genome phylogeny revealed clades with members sharing mostly a geographic region rather than a host plant of origin. Phylogenetic trees for 1605 orthologous CDSs were explored for potential candidates related to host specificity using a score of mapping metrics. However, no candidate host-specificity determinants were strongly supported using this approach. We also show that X. fastidiosa accessory genome is represented by an abundant and heterogeneous mobilome, including a diversity of prophage regions. Our findings provide a better understanding of the diversity of phylogenetically close genomes and expand the knowledge of X. fastidiosa mobile genetic elements and immunity systems.

Phylogenetics of Historical Host Switches in a Bacterial Plant Pathogen

Xylella fastidiosa is an insect-transmitted bacterial plant pathogen found across the Americas and, more recently, worldwide. X. fastidiosa infects plants of at least 563 species belonging to 82 botanical families. While the species X. fastidiosa infects many plants, particular strains have increased plant specificity. Understanding the molecular underpinnings of plant host specificity in X. fastidiosa is vital for predicting host shifts and epidemics. While there may exist multiple genetic determinants of host range in X. fastidiosa, the drivers of the unique relationships between X. fastidiosa and its hosts should be elucidated. Our objective with this study was to predict the ancestral plant hosts of this pathogen using phylogenetic and genomic methods based on a large data set of pathogen whole-genome data from agricultural hosts. We used genomic data to construct maximum-likelihood (ML) phylogenetic trees of subsets of the core and pan-genomes. With those trees, we ran ML ancestral state reconstructions of plant host at two taxonomic scales (genus and multiorder clades). Both the core and pan-genomes were informative in terms of predicting ancestral host state, giving new insight into the history of the plant hosts of X. fastidiosa. Subsequently, gene gain and loss in the pan-genome were found to be significantly correlated with plant host through genes that had statistically significant associations with particular hosts. IMPORTANCE Xylella fastidiosa is a globally important bacterial plant pathogen with many hosts; however, the underpinnings of host specificity are not known. This paper contains important findings about the usage of phylogenetics to understand the history of host specificity in this bacterial species, as well as convergent evolution in the pan-genome. There are strong signals of historical host range that give us insights into the history of this pathogen and its various invasions. The data from this paper are relevant in making decisions for quarantine and eradication, as they show the historical trends of host switching, which can help us predict likely future host shifts. We also demonstrate that using multilocus sequence type (MLST) genes in this system, which is still a commonly used process for policymaking, does not reconstruct the same phylogenetic topology as whole-genome data.

Genetic differentiation of Xylella fastidiosa following the introduction into Taiwan

The economically important plant pathogen Xylella fastidiosa has been reported in multiple regions of the globe during the last two decades, threatening a growing list of plants. Particularly, X. fastidiosa subspecies fastidiosa causes Pierce’s disease (PD) of grapevines, which is a problem in the USA, Spain, and Taiwan. In this work, we studied PD-causing subsp. fastidiosa populations and compared the genome sequences of 33 isolates found in Central Taiwan with 171 isolates from the USA and two from Spain. Phylogenetic relationships, haplotype networks, and genetic diversity analyses confirmed that subsp. fastidiosa was recently introduced into Taiwan from the Southeast USA (i.e. the PD-I lineage). Recent core-genome recombination events were detected among introduced subsp. fastidiosa isolates in Taiwan and contributed to the development of genetic diversity. The genetic diversity observed includes contributions through recombination from unknown donors, suggesting that higher genetic diversity exists in the region. Nevertheless, no recombination event was detected between X. fastidiosa subsp. fastidiosa and the endemic sister species Xylella taiwanensis, which is the causative agent of pear leaf scorch disease. In summary, this study improved our understanding of the genetic diversity of an important plant pathogenic bacterium after its invasion to a new region.

Phenotypic and Phylogenetic Characterization of Cu Homeostasis among Xylella fastidiosa Strains

Xylella fastidiosa is a bacterial pathogen causing severe diseases and asymptomatic colonization in more than 600 plants worldwide. Copper (Cu) is a widely used antimicrobial treatment for various plant diseases, including those affecting X. fastidiosa hosts. Cu homeostasis among X. fastidiosa strains from different geographical locations and host species has not been characterized. Here, we assessed minimum inhibitory concentration (MIC) of Cu for 54 X. fastidiosa strains. We observed strain-level variation in MIC values within each subspecies. We hypothesized that these differences could be explained by sequence variation in Cu homeostasis genes. Phylogenies based on copA, copB, copL, and cutC were created using 74 genomes (including 43 strains used in vitro) of X. fastidiosa, showing that the phylogenetic clustering of Cu homeostasis associated with clustering was based on core genome phylogenies, rather than on pattern of MIC. No association was found among Cu MIC, subspecies classification, and host and location of isolation, probably due to uneven and limited group of strains whose genomes are available. Further analysis focused on a subgroup of isolates from Georgia’s vineyards that shared similar Cu-related phenotypes. Further research is needed to better understand the distribution of Cu homeostasis for this pathogen.