Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses

Population Genomics Reveals an Emerging Lineage of Xanthomonas perforans on Pepper

Xanthomonas perforans-the dominant causal agent of bacterial leaf spot of tomato-is an emerging pathogen of pepper, indicative of a potential host expansion across the southeastern United States. However, studies of the genetic diversity and evolution of X. perforans from pepper remain limited. In this study, the whole-genome sequences of 35 X. perforans strains isolated from pepper from four fields and two transplant facilities across southwest Florida between 2019 and 2021 were used to compare genomic divergence, evolution, and variation in type III secreted effectors. Phylogenetic analysis based on core genes revealed that all 35 X. perforans strains formed one genetic cluster with pepper and tomato strains from Alabama and Turkey and were closely related to strains isolated from tomato in Indiana, Mexico, and Louisiana. The in planta population growth of tomato strains isolated from Indiana, Mexico, Louisiana, and Turkey in pepper leaf mesophyll was on par with pepper X. perforans and X. euvesicatoria strains. Molecular clock analysis of the 35 Florida strains dated their emergence to approximately 2017. While strains varied in copper tolerance, all sequenced strains harbored the avrHah1 transcription activation-like effector located on a conjugative plasmid, not previously reported in Florida. Our findings suggest that there is a geographically distributed lineage of X. perforans strains on tomato that has the genetic background to cause disease on pepper. Moreover, this study clarifies potential adaptive variants of X. perforans on pepper that could help forecast the emergence of such strains and enable immediate or preemptive intervention.

Herbarium specimen sequencing allows precise dating of Xanthomonas citri pv. citri diversification history

Herbarium collections are an important source of dated, identified and preserved DNA, whose use in comparative genomics and phylogeography can shed light on the emergence and evolutionary history of plant pathogens. Here, we reconstruct 13 historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri (Xci) from infected Citrus herbarium specimens. Following authentication based on ancient DNA damage patterns, we compare them with a large set of modern genomes to estimate their phylogenetic relationships, pathogenicity-associated gene content and several evolutionary parameters. Our results indicate that Xci originated in Southern Asia ~11,500 years ago (perhaps in relation to Neolithic climate change and the development of agriculture) and diversified during the beginning of the 13th century, after Citrus diversification and before spreading to the rest of the world (probably via human-driven expansion of citriculture through early East-West trade and colonization).

Genetic Divergence and Population Structure of Xanthomonas albilineans Strains Infecting Saccharum spp. Hybrid and Saccharum officinarum

Leaf scald caused by Xanthomonas albilineans (Xa) is a major bacterial disease in sugarcane that represents a threat to the global sugar industry. Little is known about the population structure and genetic evolution of this pathogen. In this study, 39 Xa strains were collected from 6 provinces in China. Of these strains, 15 and 24 were isolated from Saccharum spp. hybrid and S. officinarum plants, respectively. Based on multilocus sequence analysis (MLSA), with five housekeeping genes, these strains were clustered into two distinct phylogenetic groups (I and II). Group I included 26 strains from 2 host plants, Saccharum spp. hybrid and S. officinarum collected from 6 provinces, while Group II consisted of 13 strains from S. officinarum plants in the Zhejiang province. Among the 39 Xa strains, nucleotide sequence identities from 5 housekeeping genes were: ABC (99.6-100%), gyrB (99.3-100%), rpoD (98.4-100%), atpD (97.0-100%), and glnA (97.6-100%). These strains were clustered into six groups (A-F), based on the rep-PCR fingerprinting, using primers for ERIC2, BOX A1R, and (GTG)5. UPGMA and PCoA analyses revealed that group A had the most strains (24), followed by group C with 11 strains, while there was 1 strain each in groups B and D-F. Neutral tests showed that the Xa population in S. officinarum had a trend toward population expansion. Selection pressure analysis showed purification selection on five concatenated housekeeping genes from all tested strains. Significant genetic differentiation and infrequent gene flow were found between two Xa populations hosted in Saccharum spp. hybrids and S. officinarum. Altogether, these results provide evidence of obvious genetic divergence and population structures among Xa strains from China.

Citrus Canker Pathogen, Its Mechanism of Infection, Eradication, and Impacts

Citrus canker is a ravaging bacterial disease threatening citrus crops. Its major types are Asiatic Canker, Cancrosis B, and Cancrosis C, caused by Xanthomonas citri pv. citri (Xcc), Xanthomonas citri pv. aurantifolii pathotype-B (XauB), and pathotype-C (XauC), respectively. The bacterium enters its host through stomata and wounds, from which it invades the intercellular spaces in the apoplast. It produces erumpent corky necrotic lesions often surrounded by a chlorotic halo on the leaves, young stems, and fruits, which causes dark spots, defoliation, reduced photosynthetic rate, rupture of leaf epidermis, dieback, and premature fruit drop in severe cases. Its main pathogenicity determinant gene is pthA, whose variants are present in all citrus canker-causing pathogens. Countries where citrus canker is not endemic adopt different methods to prevent the introduction of the pathogen into the region, eradicate the pathogen, and minimize its dissemination, whereas endemic regions require an integrated management program to control the disease. The main aim of the present manuscript is to shed light on the pathogen profile, its mechanism of infection, and fruitful strategies for disease management. Although an adequate method to completely eradicate citrus canker has not been introduced so far, many new methods are under research to abate the disease.

Intraspecies characterization of bacteria via evolutionary modeling of protein domains

The ability to detect and characterize bacteria within a biological sample is crucial for the monitoring of infections and epidemics, as well as for the study of human health and its relationship with commensal microorganisms. To this aim, a commonly used technique is the 16S rRNA gene targeted sequencing. PCR-amplified 16S sequences derived from the sample of interest are usually clustered into the so-called Operational Taxonomic Units (OTUs) based on pairwise similarities. Then, representative OTU sequences are compared with reference (human-made) databases to derive their phylogeny and taxonomic classification. Here, we propose a new reference-free approach to define the phylogenetic distance between bacteria based on protein domains, which are the evolving units of proteins. We extract the protein domain profiles of 3368 bacterial genomes and we use an ecological approach to model their Relative Species Abundance distribution. Based on the model parameters, we then derive a new measurement of phylogenetic distance. Finally, we show that such model-based distance is capable of detecting differences between bacteria in cases in which the 16S rRNA-based method fails, providing a possibly complementary approach , which is particularly promising for the analysis of bacterial populations measured by shotgun sequencing.

Genome dynamics mediated by repetitive and mobile elements in Xanthomonas citri pv. durantae

Xanthomonas is a highly evolved group of phytopathogenic bacteria infecting nearly 400 host plants having vast genomic resources available with heterogenicity in representation from different species and pathovars. Unfortunately, the wealth of data is extremely biased and restricted to a few Xanthomonas pathogens that infect economically important plants, while those reported to infect the most diverse plants remain neglected. In the present study, we report the first complete genome sequence of Xanthomonas citri pv. durantae that was reported to infect Duranta repens L. or golden dewdrop, a hedge plant of ornamental importance native to the American region. Phylogenomic analysis with its closest relatives placed it amongst X. citri pv. citri A* pathotype strains and further comparative studies revealed various large unique genomic regions of chromosomal origin. The association of integrative and conjugative elements and prophages with unique genomic regions suggests the role of mobilome in genome dynamics. A large number of IS elements and transcription activator-like effectors encoding genes on each of the four plasmids indicate the further scope of diversification in Xanthomonas .

Complete Genome and Molecular Characterization of a New Cyprinid Herpesvirus 2 (CyHV-2) SH-01 Strain Isolated from Cultured Crucian Carp

Cyprinid herpesvirus 2 (CyHV-2) is a causative factor of herpesviral hematopoietic necrosis (HVHN) in farmed crucian carp (Carassius carassius) and goldfish (Carassius auratus). In this study, we analyzed the genomic characteristics of a new strain, CyHV-2 SH-01, isolated during outbreaks in crucian carp at a local fish farm near Shanghai, China. CyHV-2 SH-01 exhibited a high sensitivity to goldfish and crucian carp in our previous research. The complete genome of SH-01 is 290,428 bp with 154 potential open reading frames (ORFs) and terminal repeat (TR) regions at both ends. Compared to the sequenced genomes of other CyHVs, Carassius auratus herpesvirus (CaHV) and Anguillid herpesvirus 1 (AngHV-1), several variations were found in SH-01, including nucleotide mutations, deletions, and insertions, as well as gene duplications, rearrangements, and horizontal transfers. Overall, the genome of SH-01 shares 99.60% of its identity with that of ST-J1. Genomic collinearity analysis showed that SH-01 has a high degree of collinearity with another three CyHV-2 isolates, and it is generally closely related to CaHV, CyHV-1, and CyHV-3, although it contains many differences in locally collinear blocks (LCBs). The lowest degree of collinearity was found with AngHV-1, despite some homologous LCBs, indicating that they are evolutionarily the most distantly related. The results provide new clues to better understand the CyHV-2 genome through sequencing and sequence mining.

Clustered Regularly Interspaced Short Palindromic Repeats in Xanthomonas citri—Witnesses to a Global Expansion of a Bacterial Pathogen over Time

Xanthomonas citri pv. citri, a Gram-negative bacterium, is the causal agent of citrus canker, a significant threat to citrus production. Understanding of global expansion of the pathogen and monitoring introduction into new regions are of interest for integrated disease management at the local and global level. Genetic diversity can be assessed using genomic approaches or information from partial gene sequences, satellite markers or clustered regularly interspaced short palindromic repeats (CRISPR). Here, we compared CRISPR loci from 355 strains of X. citri pv. citri, including a sample from ancient DNA, and generated the genealogy of the spoligotypes, i.e., the absence/presence patterns of CRISPR spacers. We identified 26 novel spoligotypes and constructed their likely evolutionary trajectory based on the whole-genome information. Moreover, we analyzed ~30 additional pathovars of X. citri and found that the oldest part of the CRISPR array was present in the ancestor of several pathovars of X. citri. This work presents a framework for further analyses of CRISPR loci and allows drawing conclusions about the global spread of the citrus canker pathogen, as exemplified by two introductions in West Africa.

Deep Population Genomics Reveals Systematic and Parallel Evolution at a Lipopolysaccharide Biosynthetic Locus in Xanthomonas Pathogens That Infect Rice and Sugarcane

The advent of high-throughput sequencing and population genomics has enabled researchers to investigate selection pressure at hypervariable genomic loci encoding pathogen-associated molecular pattern (PAMP) molecules like lipopolysaccharide (LPS). Xanthomonas is a model and a major group of phytopathogenic bacteria that infect hosts in tissue-specific manner. Our in-depth population-based genomic investigation revealed the emergence of major lineages in two Xanthomonas pathogens that infect xylem of rice and sugarcane is associated with the acquisition and later large-scale replacement by distinct type of LPS cassettes. In the population of the rice xylem pathogen, Xanthomonas oryzae pv. oryzae (Xoo) and sugarcane pathogens Xanthomonas sacchari (Xsac) and Xanthomonas vasicola (Xvv), the BXO8 type of LPS cassette is replaced by a BXO1 type of cassette in Xoo and by Xvv type LPS cassette in Xsac and Xvv. These findings suggest a wave of parallel evolution at an LPS locus mediated by horizontal gene transfer (HGT) events during its adaptation and emergence. Aside from xylem pathogens, two closely related lineages of Xoo that infect parenchyma of rice and Leersia hexandra grass have acquired an LPS cassette from Xanthomonas pathogens that infect parenchyma of citrus, walnut, and strawberries, indicating yet another instance of parallel evolution mediated by HGT at an LPS locus. Our targeted and megapopulation-based genome dynamic studies revealed the acquisition and dominance of specific types of LPS cassettes in adaptation and success of a major group of phytopathogenic bacteria. IMPORTANCE Lipopolysaccharide (LPS) is a major microbe associated molecular pattern and hence a major immunomodulator. As a major and outer member component, it is expected that LPS is a frontline defense mechanism to deal with different host responses. Limited studies have indicated that LPS loci are also highly variable at strain and species level in plant-pathogenic bacteria, suggesting strong selection pressure from plants and associated niches. The advent of high-throughput genomics has led to the availability of a large set of genomic resources at taxonomic and population levels. This provides an exciting and important opportunity to carryout megascale targeted and population-based comparative genomic/association studies at important loci like those encoding LPS biosynthesis to understand their role in the evolution of the host, tissue specificity, and also predominant lineages. Such studies will also fill major gap in understanding host and tissue specificity in pathogenic bacteria. Our pioneering study uses the Xanthomonas group of phytopathogens that are known for their characteristic host and tissue specificity. The present deep phylogenomics of diverse Xanthomonas species and its members revealed lineage association and dominance of distinct types of LPS in accordance with their origin, host, tissue specificity, and evolutionary success.

Pathotyping Citrus Ornamental Relatives with Xanthomonas citri pv. citri and X. citri pv. aurantifolii Refines Our Understanding of Their Susceptibility to These Pathogens

Xanthomonas citri pv. citri (Xcc) and X. citri pv. aurantifolii (Xca) are causal agents of Citrus Bacterial Canker (CBC), a devastating disease that severely affects citrus plants. They are harmful organisms not reported in Europe or the Mediterranean Basin. Host plants are in the Rutaceae family, including the genera Citrus, Poncirus, and Fortunella, and their hybrids. In addition, other genera of ornamental interest are reported as susceptible, but results are not uniform and sometimes incongruent. We evaluated the susceptibility of 32 ornamental accessions of the Rutaceae family belonging to the genera Citrus, Fortunella, Atalantia, Clausena, Eremocitrus, Glycosmis, Microcitrus, Murraya, Casimiroa, Calodendrum, and Aegle, and three hybrids to seven strains of Xcc and Xca. Pathotyping evaluation was assessed by scoring the symptomatic reactions on detached leaves. High variability in symptoms and bacterial population was shown among the different strains in the different hosts, indicative of complex host–pathogen interactions. The results are mostly consistent with past findings, with the few discrepancies probably due to our more complete experimental approach using multiple strains of the pathogen and multiple hosts. Our work supports the need to regulate non-citrus Rutaceae plant introductions into areas, like the EU and Mediterranean, that are currently free of this economically important pathogen.

Genome Sequence Resource of Xanthomonas citri pv. citri from Formalin-Fixed Citrus Leaves Specimen Showing Canker Lesions Collected in 1982

Xanthomonas citri pv. citri is the causative agent of citrus canker, one of the most devastating diseases threatening global citrus production. Here, we present the genome sequence of X. citri pv. citri strain GD82 from a formalin-fixed citrus leaf specimen showing canker lesions collected in 1982 in Guangdong Province, China. The GD82 genome consisted of 5,197,217 bp with G+C content of 64.8%, along with four circular plasmids: pXAC33 (32,377 bp), pXAC64 (63,972 bp), pXAC47 (47,810 bp), and pGD82.1 (219,560 bp). This is the oldest X. citri pv. citri genome from historical citrus canker specimens in China, which will enrich the current X. citri pv. citri genome database and facilitate genomic evolution research of X. citri pv. citri.

Comparative Genomic Analysis Uncovered Evolution of Pathogenicity Factors, Horizontal Gene Transfer Events, and Heavy Metal Resistance Traits in Citrus Canker Bacterium Xanthomonas citri subsp. citri

Background: Worldwide citrus production is severely threatened by Asiatic citrus canker which is caused by the proteobacterium Xanthomonas citri subsp. citri. Foliar sprays of copper-based bactericides are frequently used to control plant bacterial diseases. Despite the sequencing of many X. citri strains, the genome diversity and distribution of genes responsible for metal resistance in X. citri subsp. citri strains from orchards with different management practices in Taiwan are not well understood. Results: The genomes of three X. citri subsp. citri strains including one copper-resistant strain collected from farms with different management regimes in Taiwan were sequenced by Illumina and Nanopore sequencing and assembled into complete circular chromosomes and plasmids. CRISPR spoligotyping and phylogenomic analysis indicated that the three strains were located in the same phylogenetic lineages and shared ∼3,000 core-genes with published X. citri subsp. citri strains. These strains differed mainly in the CRISPR repeats and pathogenicity-related plasmid-borne transcription activator-like effector (TALE)-encoding pthA genes. The copper-resistant strain has a unique, large copper resistance plasmid due to an unusual ∼40 kbp inverted repeat. Each repeat contains a complete set of the gene cluster responsible for copper and heavy metal resistance. Conversely, the copper sensitive strains carry no metal resistance genes in the plasmid. Through comparative analysis, the origin and evolution of the metal resistance clusters was resolved. Conclusion: Chromosomes remained constant among three strains collected in Taiwan, but plasmids likely played an important role in maintaining pathogenicity and developing bacterial fitness in the field. The evolution of pathogenicity factors and horizontal gene transfer events were observed in the three strains. These data suggest that agricultural management practices could be a potential trigger for the evolution of citrus canker pathogens. The decrease in the number of CRISPR repeats and pthA genes might be the result of adaptation to a less stressful environment. The metal resistance genes in the copper resistant X. citri strain likely originated from the Mauritian strain not the local copper-resistant X. euvesicatoria strain. This study highlights the importance of plasmids as 'vehicles' for exchanging genetic elements between plant pathogenic bacteria and contributing to bacterial adaptation to the environment.

PthAW1, a Transcription Activator-Like Effector of Xanthomonas citri subsp. citri, Promotes Host-Specific Immune Responses

Citrus canker disease caused by Xanthomonas citri subsp. citri is one of the most destructive diseases in citrus. X. citri subsp. citri pathotypes display different host ranges. X. citri subsp. citri strain A (Xcc^A) causes canker disease in most commercial citrus varieties, whereas strain AW (Xcc^AW), which is genetically similar to Xcc^A, infects only lime and alemow. Understanding the mechanism that determines the host range of pathogens is critical to investigating and utilizing host resistance. We hypothesized that Xcc^AW would undergo mutations in genes that restrict its host range when artificially inoculated into incompatible citrus varieties. To test this hypothesis, we used an experimental evolution approach to identify phenotypic traits and genetic loci associated with the adaptation of Xcc^AW to incompatible sweet orange. Repeated inoculation and reisolation cycles improved the ability of three independent Xcc^AW strains to colonize sweet orange. Adapted Xcc^AW strains displayed increased expression of type III secretion system and effector genes. Genome sequencing analysis indicated that two of the adapted strains harbored mutations in pthAW1, a transcription activator-like effector (TALE) gene, that corresponded to the removal of one or two repeats from the central DNA-binding repeat region. Introduction of the original but not the adapted pthAW1 variants into Xcc^A abolished its ability to cause canker symptoms in sweet orange, Meyer lemon, and clementine but not in other Xcc^AW-resistant citrus varieties. The original pthAW1, when expressed in Xcc^A, induced ion leakage and the expression of pathogenesis-related genes but had no effect on CsLOB1 expression in sweet orange. Our study has identified a novel host-specific avirulence TALE and demonstrated active adaptive rearrangements of the TALE repeat array during host adaptation.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

The transcriptome landscapes of citrus leaf in different developmental stages

The temporal expression profiles of citrus leaves explain the sink-source transition of immature leaves to mature leaves and provide knowledge regarding the differential responses of mature and immature leaves to biotic stress such as citrus canker and Asian citrus psyllid (Diaphorina citri). Citrus is an important fruit crop worldwide. Different developmental stages of citrus leaves are associated with distinct features, such as differences in susceptibilities to pathogens and insects, as well as photosynthetic capacity. Here, we investigated the mechanisms underlying these distinctions by comparing the gene expression profiles of mature and immature citrus leaves. Immature (stages V3 and V4), transition (stage V5), and mature (stage V6) Citrus sinensis leaves were chosen for RNA-seq analyses. Carbohydrate biosynthesis, photosynthesis, starch biosynthesis, and disaccharide metabolic processes were enriched among the upregulated differentially expressed genes (DEGs) in the V5 and V6 stages compared with that in the V3 and V4 stages. Glucose level was found to be higher in V5 and V6 than in V3 and V4. Among the four stages, the largest number of DEGs between contiguous stages were identified between V5 and V4, consistent with a change from sink to source, as well as with the sucrose and starch quantification data. The differential expression profiles related to cell wall synthesis, secondary metabolites such as flavonoids and terpenoids, amino acid biosynthesis, and immunity between immature and mature leaves may contribute to their different responses to Asian citrus psyllid infestation. The expression data suggested that both the constitutive and induced gene expression of immunity-related genes plays important roles in the greater resistance of mature leaves against Xanthomonas citri compared with immature leaves. The gene expression profiles in the different stages can help identify stage-specific promoters for the manipulation of the expression of citrus traits according to the stage. The temporal expression profiles explain the sink-source transition of immature leaves to mature leaves and provide knowledge regarding the differential responses to biotic stress.

First historical genome of a crop bacterial pathogen from herbarium specimen: Insights into citrus canker emergence

Over the past decade, ancient genomics has been used in the study of various pathogens. In this context, herbarium specimens provide a precious source of dated and preserved DNA material, enabling a better understanding of plant disease emergences and pathogen evolutionary history. We report here the first historical genome of a crop bacterial pathogen, Xanthomonas citri pv. citri (Xci), obtained from an infected herbarium specimen dating back to 1937. Comparing the 1937 genome within a large set of modern genomes, we reconstructed their phylogenetic relationships and estimated evolutionary parameters using Bayesian tip-calibration inferences. The arrival of Xci in the South West Indian Ocean islands was dated to the 19th century, probably linked to human migrations following slavery abolishment. We also assessed the metagenomic community of the herbarium specimen, showed its authenticity using DNA damage patterns, and investigated its genomic features including functional SNPs and gene content, with a focus on virulence factors.

A comparative genomic analysis of Xanthomonas arboricola pv. juglandis strains reveal hallmarks of mobile genetic elements in the adaptation and accelerated evolution of virulence

Xanthomonas arboricola pv. juglandis (Xaj) is the most significant aboveground walnut bacterial pathogen. Disease management uses copper-based pesticides which induce pathogen resistance. We examined the genetic repertoire associated with adaptation and virulence evolution in Xaj. Comparative genomics of 32 Xaj strains reveal the possible acquisition and propagation of virulence factors via insertion sequences (IS). Fine-scale annotation revealed a Tn3 transposon (TnXaj417) encoding copper resistance genes acquired by horizontal gene transfer and associated with adaptation and tolerance to metal-based pesticides commonly used to manage pathogens in orchard ecosystems. Phylogenomic analysis reveals IS involvement in acquisition and diversification of type III effector proteins ranging from two to eight in non-pathogenic strains, 16 to 20 in pathogenic strains, besides six other putative effectors with a reduced identity degree found mostly among pathogenic strains. Yersiniabactin, xopK, xopAI, and antibiotic resistance genes are also located near ISs or inside genomic islands and structures resembling composite transposons.

Trends in Molecular Diagnosis and Diversity Studies for Phytosanitary Regulated Xanthomonas

Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide variety of non-specific symptoms, making their identification difficult. The coexistence of phylogenetically close strains, but drastically different in their phenotype, poses an added challenge to diagnosis. Data on future climate change scenarios predict an increase in the severity of epidemics and a geographical expansion of pathogens, increasing pressure on plant health services. In this context, the effectiveness of integrated disease management strategies strongly depends on the availability of rapid, sensitive, and specific diagnostic methods. The accumulation of genomic information in recent years has facilitated the identification of new DNA markers, a cornerstone for the development of more sensitive and specific methods. Nevertheless, the challenges that the taxonomic complexity of this genus represents in terms of diagnosis together with the fact that within the same bacterial species, groups of strains may interact with distinct host species demonstrate that there is still a long way to go. In this review, we describe and discuss the current molecular-based methods for the diagnosis and detection of regulated Xanthomonas, taxonomic and diversity studies in Xanthomonas and genomic approaches for molecular diagnosis.

Comparative Genomics of Xanthomonas citri pv. citri A* Pathotype Reveals Three Distinct Clades with Varying Plasmid Distribution

Citrus bacterial canker (CBC) is an important disease of citrus cultivars worldwide that causes blister-like lesions on host plants and leads to more severe symptoms such as plant defoliation and premature fruit drop. The causative agent, Xanthomonas citri pv. citri, exists as three pathotypes—A, A*, and A^w—which differ in their host range and elicited host response. To date, comparative analyses have been hampered by the lack of closed genomes for the A* pathotype. In this study, we sequenced and assembled six CBC isolates of pathotype A* using second- and third-generation sequencing technologies to produce complete, closed assemblies. Analysis of these genomes and reference A, A*, and A^w sequences revealed genetic groups within the A* pathotype. Investigation of accessory genomes revealed virulence factors, including type IV secretion systems and heavy metal resistance genes, differentiating the genetic groups. Genomic comparisons of closed genome assemblies also provided plasmid distribution information for the three genetic groups of A*. The genomes presented here complement existing closed genomes of A and A^w pathotypes that are publicly available and open opportunities to investigate the evolution of X. citri pv. citri and the virulence factors that contribute to this serious pathogen.

Development and comparative validation of genomic-driven PCR-based assays to detect Xanthomonas citri pv. citri in citrus plants

Background

Asiatic Citrus Canker, caused by Xanthomonas citri pv. citri, severely impacts citrus production worldwide and hampers international trade. Considerable regulatory procedures have been implemented to prevent the introduction and establishment of X. citri pv. citri into areas where it is not present. The effectiveness of this surveillance largely relies on the availability of specific and sensitive detection protocols. Although several PCR- or real-time PCR-based methods are available, most of them showed analytical specificity issues. Therefore, we developed new conventional and real-time quantitative PCR assays, which target a region identified by comparative genomic analyses, and compared them to existing protocols.

Results

Our assays target the X. citri pv. citri XAC1051 gene that encodes for a putative transmembrane protein. The real-time PCR assay includes an internal plant control (5.8S rDNA) for validating the assay in the absence of target amplification. A receiver-operating characteristic approach was used in order to determine a reliable cycle cut-off for providing accurate qualitative results. Repeatability, reproducibility and transferability between real-time devices were demonstrated for this duplex qPCR assay (XAC1051-2qPCR). When challenged with an extensive collection of target and non-target strains, both assays displayed a high analytical sensitivity and specificity performance: LOD_95% = 754 CFU ml^− 1 (15 cells per reaction), 100% inclusivity, 97.2% exclusivity for XAC1051-2qPCR; LOD_95% = 5234 CFU ml^− 1 (105 cells per reaction), 100% exclusivity and inclusivity for the conventional PCR. Both assays can detect the target from naturally infected citrus fruit. Interestingly, XAC1051-2qPCR detected X. citri pv. citri from herbarium citrus samples. The new PCR-based assays displayed enhanced analytical sensitivity and specificity when compared with previously published PCR and real-time qPCR assays.

Conclusions

We developed new valuable detection assays useful for routine diagnostics and surveillance of X. citri pv. citri in citrus material. Their reliability was evidenced through numerous trials on a wide range of bacterial strains and plant samples. Successful detection of the pathogen was achieved from both artificially and naturally infected plants, as well as from citrus herbarium samples, suggesting that these assays will have positive impact both for future applied and academic research on this bacterium.

Xanthomonas diversity, virulence and plant-pathogen interactions

Xanthomonas spp. encompass a wide range of plant pathogens that use numerous virulence factors for pathogenicity and fitness in plant hosts. In this Review, we examine recent insights into host-pathogen co-evolution, diversity in Xanthomonas populations and host specificity of Xanthomonas spp. that have substantially improved our fundamental understanding of pathogen biology. We emphasize the virulence factors in xanthomonads, such as type III secreted effectors including transcription activator-like effectors, type II secretion systems, diversity resulting in host specificity, evolution of emerging strains, activation of susceptibility genes and strategies of host evasion. We summarize the genomic diversity in several Xanthomonas spp. and implications for disease outbreaks, management strategies and breeding for disease resistance.