Charity Care in Ophthalmology, 2024.

PURPOSE: To review changes in the provision of charity eye care in the past 50 years with hypothesized resulting effects on surgical training and patient outcomes. DESIGN: Perspective. METHODS: Case report, comparison of experience in community and training program settings, and selected literature review. RESULTS: The population to which charity care applies has shrunk as broader insurance coverage has been legislated, but in 2023 remains at approximately 7.3% of the US population. In areas with ophthalmology training programs, house staff supervised by faculty provide most of the charity care. In areas without training programs, a shrinking pool of willing private practitioners provides charity care. Because there is no organized financial support behind provision of charity, nonanecdotal data needed to assess the problem and guide decision making are lacking. CONCLUSIONS: Charity eye care in ophthalmology in 2024 is a patchwork of transient, local efforts that have a few common themes: absent material basis for sustainability, a narrowing base of support by clinicians, transfer of care to training programs, and financial vetting of applicants by nonclinicians. Unless universal health care legislation passes, which would eliminate the issue, suggestions for improvement include broader voluntary participation by private practice ophthalmologists in charity eye care, allocation of charity care spending by nonprofit hospitals to support this effort, and clinician-determined criteria for provision of charitable surgery supported by involved hospital systems.

Early Detection of Fusarium Basal Rot Infection in Onions and Shallots Based on VOC Profiles Analysis.

Gas chromatography ion-mobility spectrometry (GC-IMS) technology is drawing increasing attention due to its high sensitivity, low drift, and capability for the identification of compounds. The noninvasive detection of plant pests and pathogens is an application area well suited to this technology. In this work, we employed GC-IMS technology for early detection of Fusarium basal rot in brown onion, red onion, and shallot bulbs and for tracking disease progression during storage. The volatile profiles of the infected and healthy control bulbs were characterized using GC-IMS and gas chromatography-time-of-flight mass spectrometry (GC-TOF-MS). GC-IMS data combined with principal component analysis and supervised methods provided discrimination between infected and healthy control bulbs as early as 1 day after incubation with the pathogen, classification regarding the proportion of infected to healthy bulbs in a sample, and prediction of the infection's duration with an average R2 = 0.92. Furthermore, GC-TOF-MS revealed several compounds, mostly sulfides and disulfides, that could be uniquely related to Fusarium basal rot infection.

Codesigning a systemic discharge intervention for inpatient mental health settings (MINDS): a protocol for integrating realist evaluation and an engineering-based systems approach.

INTRODUCTION: Transition following discharge from mental health hospital is high risk in terms of relapse, readmission and suicide. Discharge planning supports transition and reduces risk. It is a complex activity involving interacting systemic elements. The codesigning a systemic discharge intervention for inpatient mental health settings (MINDS) study aims to improve the process for people being discharged, their carers/supporters and staff who work in mental health services, by understanding, co-designing and evaluating implementation of a systemic approach to discharge planning. METHODS AND ANALYSIS: The MINDS study integrates realist research and an engineering-informed systems approach across three stages. Stage 1 applies realist review and evaluation using a systems approach to develop programme theories of discharge planning. Stage 2 uses an Engineering Better Care framework to codesign a novel systemic discharge intervention, which will be subjected to process and economic evaluation in stage 3. The programme theories and resulting care planning approach will be refined throughout the study ready for a future clinical trial. MINDS is co-led by an expert by experience, with researchers with lived experience co-leading each stage. ETHICS AND DISSEMINATION: MINDS stage 1 has received ethical approval from Yorkshire & The Humber-Bradford Leeds (Research Ethics Committee (22/YH/0122). Findings from MINDS will be disseminated via high-impact journal publications and conference presentations, including those with service user and mental health professional audiences. We will establish routes to engage with public and service user communities and National Health Service professionals including blogs, podcasts and short videos. TRIAL REGISTRATION NUMBER: MINDS is funded by the National Institute of Health Research (NIHR 133013) https://fundingawards.nihr.ac.uk/award/NIHR133013. The realist review protocol is registered on PROSPERO. PROSPERO REGISTRATION NUMBER: CRD42021293255.

First report of Fusarium oxysporum f. sp. lactucae Race 1 causing lettuce wilt in Northern Ireland.

In the UK, lettuce is produced both in the field and in greenhouses or polytunnels. In summer 2022, wilt symptoms were observed for the first time on lettuce (cv. Amica) grown in soil in part of a single 0.55 ha greenhouse in County Armagh, Northern Ireland (NI). Initial presentation of symptoms was stunting of plants, followed by wilting and yellowing of lower leaves in approx. 12% of the plants. Orange-brown discoloration of vascular tissue in the tap root of affected plants was also observed. To isolate the causal pathogen, sections (0.5 cm2) of symptomatic vascular tissue from 5 plants were surface sterilized in 70% ethanol for 45 s, washed twice in sterile water and placed on potato dextrose agar (PDA) amended with 20 µg mL-1 chlortetracycline. Plates were incubated at 20°C for 5 days and fungal colonies sub cultured onto PDA. Isolates from all five samples displayed morphology typical of Fusarium oxysporum and were cream to purple in colour with abundant microconidia and occasional macroconidia. DNA was extracted from 5 isolates and part of the translation elongation factor 1- α (EF1-α) gene amplified by PCR and sequenced as described by Taylor et al. (2016). All EF1-α sequences were identical (OQ241898) and matched with F. oxysporum f. sp. lactucae race 1 (MW316853.1, isolate 231274) and race 4 (MK059958.1, isolate IRE1) with 100% sequence identity using BLAST. Isolates were then identified as FOL race 1 (FOL1) using a race-specific PCR assay (Pasquali et al. 2007). Next, pathogenicity and race identity of one isolate (AJ773) was confirmed using a set of differential lettuce cultivars (Gilardi et al. 2017); Costa Rica No. 4 (CR; FOL1 resistant), Banchu Red Fire (BRF; FOL4 resistant) and Gisela (GI; FOL1 / FOL4 susceptible). Plants were inoculated with AJ773 (this study), ATCCMya-3040 (FOL1, Italy; Gilardi et al. 2017) and LANCS1 (FOL4, UK; Taylor et al., 2019). Roots of 16-day-old lettuce plants (8 replicates per cultivar/isolate) were trimmed and soaked in a spore suspension (1 x 106 conidia mL-1) for 10 min before transplanting into compost in 9 cm pots. Control plants for each cultivar were dipped in sterile water. Pots were placed in a glasshouse (25C day, 18C night). Inoculation with AJ773 and FOL1 ATCCMya-3040 resulted in typical symptoms of Fusarium wilt for BRF and GI 12-15 days after inoculation, while for FOL4 LANCS1, wilting was observed in CR and GI. Thirty-two days after inoculation, plants were cut longitudinally and vascular browning was observed in all plants where wilt was present. All uninoculated control plants, CR inoculated with FOL1 ATCCMya-3040 or AJ773, and BRF inoculated with FOL4 LANCS1 remained healthy. These results confirm the identity of isolate AJ773 from NI as FOL1. Koch's postulates were fulfilled by consistent re-isolation of F. oxysporum from BRF and GI plants and identifying as FOL1 using the race-specific PCR. No FOL was re-isolated from control plants of any cultivar. Fusarium wilt in England and the Republic of Ireland first reported by Taylor et al. (2019) was identified as FOL4 and has been confined to indoor lettuce production with further outbreaks caused by the same race. However, FOL1 was recently identified in Norway in a soil-grown glasshouse crop (Herrero et al. 2021). The presence of both FOL1 and FOL4 in neighbouring countries within the UK is a serious risk to lettuce production and is of particular importance to growers who rely on knowledge of cultivar resistance to specific FOL races to make decisions on which variety to plant.

The Impact of Trauma System Implementation on Patient Quality of Life and Economic Burden: A Systematic Review Study Protocol.

Background: Trauma accounts for 10% of global mortality, with increasing rates disproportionally affecting low- and middle-income countries. In an attempt to improve clinical outcomes after injury, trauma systems have been implemented in multiple countries over recent years. However, whilst many studies have subsequently demonstrated improvements in overall mortality outcomes, less is known about the impact trauma systems have on morbidity, quality of life, and economic burden. This systematic review seeks to assess the existing evidence base for trauma systems with these outcome measures. Methods: This review will include any study that assesses the impact implementation of a trauma system has on patient morbidity, quality of life, or economic burden. Any comparator study, including cohort, case-control, and randomised controlled studies, will be included, both retrospective or prospective in nature. Studies conducted from any region in the world and involving any age of patient will be included. We will collect data on any morbidity outcomes, health-related quality of life measures, or health economic assessments reported. We predict a high heterogeneity in these outcomes used and will therefore keep inclusion criteria broad. Discussion: Previous reviews have shown the significant improvements that can be achieved in mortality outcomes with the implementation of an organised trauma system, however the wider impact they can have on morbidity outcomes, quality of life measures, and the economic burden of trauma, is less well described. This systematic review will present all available data on these outcomes, helping to better characterise both the societal and economic impact of trauma system implementation. Highlights: Trauma systems are known to improve mortality rates, however less in known on the impact they have on morbidity outcomes, quality of life, and economic burdenWe aim to perform a systematic review to identify any comparator study that assesses the impact implementation of a trauma system on these outcomesUnderstanding the impact trauma systems can have on wider parameters, such as economic and quality of life outcomes, is crucial to allow governments globally to appropriately allocate often limited healthcare resources.PROSPERO registration number: CRD42022348529.

Can process mapping and a multisite Delphi of perioperative professionals inform our understanding of system-wide factors that may impact operative risk?

OBJECTIVES: To examine whether the use of process mapping and a multidisciplinary Delphi can identify potential contributors to perioperative risk. We hypothesised that this approach may identify factors not represented in common perioperative risk tools and give insights of use to future research in this area. DESIGN: Multidisciplinary, modified Delphi study. SETTING: Two centres (one tertiary, one secondary) in the UK during 2020 amidst coronavirus pressures. PARTICIPANTS: 91 stakeholders from 23 professional groups involved in the perioperative care of older patients. Key stakeholder groups were identified via process mapping of local perioperative care pathways. RESULTS: Response rate ranged from 51% in round 1 to 19% in round 3. After round 1, free text suggestions from the panel were combined with variables identified from perioperative risk scores. This yielded a total of 410 variables that were voted on in subsequent rounds. Including new suggestions from round two, 468/519 (90%) of the statements presented to the panel reached a consensus decision by the end of round 3. Identified risk factors included patient-level factors (such as ethnicity and socioeconomic status), and organisational or process factors related to the individual hospital (such as policies, staffing and organisational culture). 66/160 (41%) of the new suggestions did not feature in systematic reviews of perioperative risk scores or key process indicators. No factor categorised as 'organisational' is currently present in any perioperative risk score. CONCLUSIONS: Through process mapping and a modified Delphi we gained insights into additional factors that may contribute to perioperative risk. Many were absent from currently used risk stratification scores. These results enable an appreciation of the contextual limitations of currently used risk tools and could support future research into the generation of more holistic data sets for the development of perioperative risk assessment tools.

Preliminary Studies on Detection of Fusarium Basal Rot Infection in Onions and Shallots Using Electronic Nose.

The evaluation of crop health status and early disease detection are critical for implementing a fast response to a pathogen attack, managing crop infection, and minimizing the risk of disease spreading. Fusarium oxysporum f. sp. cepae, which causes fusarium basal rot disease, is considered one of the most harmful pathogens of onion and accounts for considerable crop losses annually. In this work, the capability of the PEN 3 electronic nose system to detect onion and shallot bulbs infected with F. oxysporum f. sp. cepae, to track the progression of fungal infection, and to discriminate between the varying proportions of infected onion bulbs was evaluated. To the best of our knowledge, this is a first report on successful application of an electronic nose to detect fungal infections in post-harvest onion and shallot bulbs. Sensor array responses combined with PCA provided a clear discrimination between non-infected and infected onion and shallot bulbs as well as differentiation between samples with varying proportions of infected bulbs. Classification models based on LDA, SVM, and k-NN algorithms successfully differentiate among various rates of infected bulbs in the samples with accuracy up to 96.9%. Therefore, the electronic nose was proved to be a potentially useful tool for rapid, non-destructive monitoring of the post-harvest crops.

Identification of genetic loci in lettuce mediating quantitative resistance to fungal pathogens.

KEY MESSAGE: We demonstrate genetic variation for quantitative resistance against important fungal pathogens in lettuce and its wild relatives, map loci conferring resistance and predict key molecular mechanisms using transcriptome profiling. Lactuca sativa L. (lettuce) is an important leafy vegetable crop grown and consumed globally. Chemicals are routinely used to control major pathogens, including the causal agents of grey mould (Botrytis cinerea) and lettuce drop (Sclerotinia sclerotiorum). With increasing prevalence of pathogen resistance to fungicides and environmental concerns, there is an urgent need to identify sources of genetic resistance to B. cinerea and S. sclerotiorum in lettuce. We demonstrated genetic variation for quantitative resistance to B. cinerea and S. sclerotiorum in a set of 97 diverse lettuce and wild relative accessions, and between the parents of lettuce mapping populations. Transcriptome profiling across multiple lettuce accessions enabled us to identify genes with expression correlated with resistance, predicting the importance of post-transcriptional gene regulation in the lettuce defence response. We identified five genetic loci influencing quantitative resistance in a F6 mapping population derived from a Lactuca serriola (wild relative) × lettuce cross, which each explained 5-10% of the variation. Differential gene expression analysis between the parent lines, and integration of data on correlation of gene expression and resistance in the diversity set, highlighted potential causal genes underlying the quantitative trait loci.

Systems approach to improving traumatic brain injury care in Myanmar: a mixed-methods study from lived experience to discrete event simulation.

OBJECTIVES: Traumatic brain injury (TBI) is a global health problem, whose management in low-resource settings is hampered by fragile health systems and lack of access to specialist services. Improvement is complex, given the interaction of multiple people, processes and institutions. We aimed to develop a mixed-method approach to understand the TBI pathway based on the lived experience of local people, supported by quantitative methodologies and to determine potential improvement targets. DESIGN: We describe a systems approach based on narrative exploration, participatory diagramming, data collection and discrete event simulation (DES), conducted by an international research collaborative. SETTING: The study is set in the tertiary neurotrauma centre in Yangon General Hospital, Myanmar, in 2019-2020 (prior to the SARS-CoV2 pandemic). PARTICIPANTS: The qualitative work involved 40 workshop participants and 64 interviewees to explore the views of a wide range of stakeholders including staff, patients and relatives. The 1-month retrospective admission snapshot covered 85 surgical neurotrauma admissions. RESULTS: The TBI pathway was outlined, with system boundaries defined around the management of TBI once admitted to the neurosurgical unit. Retrospective data showed 18% mortality, 71% discharge to home and an 11% referral rate. DES was used to investigate the system, showing its vulnerability to small surges in patient numbers, with critical points being CT scanning and observation ward beds. This explorative model indicated that a modest expansion of observation ward beds to 30 would remove the flow-limitations and indicated possible consequences of changes. CONCLUSIONS: A systems approach to improving TBI care in resource-poor settings may be supported by simulation and informed by qualitative work to ground it in the direct experience of those involved. Narrative interviews, participatory diagramming and DES represent one possible suite of methods deliverable within an international partnership. Findings can support targeted improvement investments despite coexisting resource limitations while indicating concomitant risks.

Diversity and Ecological Guild Analysis of the Oil Palm Fungal Microbiome Across Root, Rhizosphere, and Soil Compartments.

The rhizosphere microbiome is a major determinant of plant health, which can interact with the host directly and indirectly to promote or suppress productivity. Oil palm is one of the world's most important crops, constituting over a third of global vegetable oil production. Currently there is little understanding of the oil palm microbiome and its contribution to plant health and productivity, with existing knowledge based almost entirely on culture dependent studies. We investigated the diversity and composition of the oil palm fungal microbiome in the bulk soil, rhizosphere soil, and roots of 2-, 18-, and 35-year old plantations in Selangor, Malaysia. The fungal community showed substantial variation between the plantations, accounting for 19.7% of community composition, with compartment (root, rhizosphere soil, and bulk soil), and soil properties (pH, C, N, and P) contributing 6.5 and 7.2% of community variation, respectively. Rhizosphere soil and roots supported distinct communities compared to the bulk soil, with significant enrichment of Agaricomycetes, Glomeromycetes, and Lecanoromycetes in roots. Several putative plant pathogens were abundant in roots in all the plantations, including taxa related to Prospodicola mexicana and Pleurostoma sp. The mycorrhizal status and dependency of oil palm has yet to be established, and using 18S rRNA primers we found considerable between-site variation in Glomeromycotinian community composition, accounting for 31.2% of variation. There was evidence for the selection of Glomeromycotinian communities in oil palm roots in the older plantations but compartment had a weak effect on community composition, accounting for 3.9% of variation, while soil variables accounted for 9% of community variation. While diverse Mucoromycotinian fungi were detected, they showed very low abundance and diversity within roots compared to bulk soil, and were not closely related to taxa which have been linked to fine root endophyte mycorrhizal morphology. Many of the fungal sequences showed low similarity to established genera, indicating the presence of substantial novel diversity with significance for plant health within the oil palm microbiome.

Identification and Expression of Secreted In Xylem Pathogenicity Genes in Fusarium oxysporum f. sp. pisi.

Fusarium oxysporum is a soilborne fungal plant pathogen responsible for causing disease in many economically important crops with "special forms" (formae speciales) adapted to infect specific plant hosts. F. oxysporum f. sp. pisi (FOP) is the causal agent of Fusarium wilt disease of pea. It has been reported in every country where peas are grown commercially. Disease is generally controlled using resistant cultivars possessing single major gene resistance and therefore there is a constant risk of breakdown. The main aim of this work was to characterise F. oxysporum isolates collected from diseased peas in the United Kingdom as well as FOP isolates obtained from other researchers representing different races through sequencing of a housekeeping gene and the presence of Secreted In Xylem (SIX) genes, which have previously been associated with pathogenicity in other F. oxysporum f. spp. F. oxysporum isolates from diseased United Kingdom pea plants possessed none or just one or two known SIX genes with no consistent pattern of presence/absence, leading to the conclusion that they were foot-rot causing isolates rather than FOP. In contrast, FOP isolates had different complements of SIX genes with all those identified as race 1 containing SIX1, SIX6, SIX7, SIX9, SIX10, SIX11, SIX12, and SIX14. FOP isolates that were identified as belonging to race 2 through testing on differential pea cultivars, contained either SIX1, SIX6, SIX9, SIX13, SIX14 or SIX1, SIX6, SIX13. Significant upregulation of SIX genes was also observed in planta over the early stages of infection by different FOP races in pea roots. Race specific SIX gene profiling may therefore provide potential targets for molecular identification of FOP races but further research is needed to determine whether variation in complement of SIX genes in FOP race 2 isolates results in differences in virulence across a broader set of pea differential cultivars.

Assembly and characterisation of a unique onion diversity set identifies resistance to Fusarium basal rot and improved seedling vigour.

KEY MESSAGE: A unique, global onion diversity set was assembled, genotyped and phenotyped for beneficial traits. Accessions with strong basal rot resistance and increased seedling vigour were identified along with associated markers. Conserving biodiversity is critical for safeguarding future crop production. Onion (Allium cepa L.) is a globally important crop with a very large (16 Gb per 1C) genome which has not been sequenced. While onions are self-fertile, they suffer from severe inbreeding depression and as such are highly heterozygous as a result of out-crossing. Bulb formation is driven by daylength, and accessions are adapted to the local photoperiod. Onion seed is often directly sown in the field, and hence seedling establishment is a critical trait for production. Furthermore, onion yield losses regularly occur worldwide due to Fusarium basal rot caused by Fusarium oxysporum f. sp. cepae. A globally relevant onion diversity set, consisting of 10 half-sib families for each of 95 accessions, was assembled and genotyping carried out using 892 SNP markers. A moderate level of heterozygosity (30-35%) was observed, reflecting the outbreeding nature of the crop. Using inferred phylogenies, population structure and principal component analyses, most accessions grouped according to local daylength. A high level of intra-accession diversity was observed, but this was less than inter-accession diversity. Accessions with strong basal rot resistance and increased seedling vigour were identified along with associated markers, confirming the utility of the diversity set for discovering beneficial traits. The onion diversity set and associated trait data therefore provide a valuable resource for future germplasm selection and onion breeding.

Draft Genome Sequence of an Onion Basal Rot Isolate of Fusarium proliferatum.

Fusarium proliferatum is a component of the onion basal rot disease complex. We present an annotated F. proliferatum draft genome sequence, totaling 45.8 Mb in size, assembled into 597 contigs, with a predicted 15,418 genes. The genome contains 58 secondary metabolite clusters and homologs of the Fusarium oxysporum effector SIX2.

A Review of Risk Matrices Used in Acute Hospitals in England.

In healthcare, patient safety has received substantial attention and, in turn, a number of approaches to managing safety have been adopted from other high-risk industries. One of these has been risk assessment, predominantly through the use of risk matrices. However, while other industries have criticized the design and use of these risk matrices, the applicability of such criticism has not been investigated formally in healthcare. This study examines risk matrices as used in acute hospitals in England and the guidance provided for their use. It investigates the applicability of criticisms of risk matrices from outside healthcare through a document analysis of the risk assessment policies, procedures, and strategies used in English hospitals. The findings reveal that there is a large variety of risk matrices used, where the design of some might increase the chance of risk misprioritization. Additionally, findings show that hospitals may provide insufficient guidance on how to use risk matrices as well as what to do in response to the existing criticisms of risk matrices. Consequently, this is likely to lead to variation in the quality of risk assessment and in the subsequent deployment of resources to manage the assessed risk. Finally, the article outlines ways in which hospitals could use risk matrices more effectively.

Genomics Evolutionary History and Diagnostics of the Alternaria alternata Species Group Including Apple and Asian Pear Pathotypes.

The Alternaria section alternaria (Alternaria alternata species group) represents a diverse group of saprotroph, human allergens, and plant pathogens. Alternaria taxonomy has benefited from recent phylogenetic revision but the basis of differentiation between major phylogenetic clades within the group is not yet understood. Furthermore, genomic resources have been limited for the study of host-specific pathotypes. We report near complete genomes of the apple and Asian pear pathotypes as well as draft assemblies for a further 10 isolates representing Alternaria tenuissima and Alternaria arborescens lineages. These assemblies provide the first insights into differentiation of these taxa as well as allowing the description of effector and non-effector profiles of apple and pear conditionally dispensable chromosomes (CDCs). We define the phylogenetic relationship between the isolates sequenced in this study and a further 23 Alternaria spp. based on available genomes. We determine which of these genomes represent MAT1-1-1 or MAT1-2-1 idiomorphs and designate host-specific pathotypes. We show for the first time that the apple pathotype is polyphyletic, present in both the A. arborescens and A. tenuissima lineages. Furthermore, we profile a wider set of 89 isolates for both mating type idiomorphs and toxin gene markers. Mating-type distribution indicated that gene flow has occurred since the formation of A. tenuissima and A. arborescens lineages. We also developed primers designed to AMT14, a gene from the apple pathotype toxin gene cluster with homologs in all tested pathotypes. These primers allow identification and differentiation of apple, pear, and strawberry pathotypes, providing new tools for pathogen diagnostics.

Basal Rot of Narcissus: Understanding Pathogenicity in Fusarium oxysporum f. sp. narcissi.

Fusarium oxysporum is a globally distributed soilborne fungal pathogen causing root rots, bulb rots, crown rots and vascular wilts on a range of horticultural plants. Pathogenic F. oxysporum isolates are highly host specific and are classified as formae speciales. Narcissus is an important ornamental crop and both the quality and yield of flowers and bulbs can be severely affected by a basal rot caused by F. oxysporum f. sp. narcissi (FON); 154 Fusarium isolates were obtained from different locations and Narcissus cultivars in the United Kingdom, representing a valuable resource. A subset of 30 F. oxysporum isolates were all found to be pathogenic and were therefore identified as FON. Molecular characterisation of isolates through sequencing of three housekeeping genes, suggested a monophyletic origin with little divergence. PCR detection of 14 Secreted in Xylem (SIX) genes, previously shown to be associated with pathogenicity in other F. oxysporum f. spp., revealed different complements of SIX7, SIX9, SIX10, SIX12 and SIX13 within FON isolates which may suggest a race structure. SIX gene sequences were unique to FON and SIX10 was present in all isolates, allowing for molecular identification of FON for the first time. The genome of a highly pathogenic isolate was sequenced and lineage specific (LS) regions identified which harboured putative effectors including the SIX genes. Real-time RT-PCR, showed that SIX genes and selected putative effectors were expressed in planta with many significantly upregulated during infection. This is the first study to characterise molecular variation in FON and provide an analysis of the FON genome. Identification of expressed genes potentially associated with virulence provides the basis for future functional studies and new targets for molecular diagnostics.

Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae.

A reference-quality assembly of Fusarium oxysporum f. sp. cepae (Foc), the causative agent of onion basal rot has been generated along with genomes of additional pathogenic and non-pathogenic isolates of onion. Phylogenetic analysis confirmed a single origin of the Foc pathogenic lineage. Genome alignments with other F. oxysporum ff. spp. and non pathogens revealed high levels of syntenic conservation of core chromosomes but little synteny between lineage specific (LS) chromosomes. Four LS contigs in Foc totaling 3.9 Mb were designated as pathogen-specific (PS). A two-fold increase in segmental duplication events was observed between LS regions of the genome compared to within core regions or from LS regions to the core. RNA-seq expression studies identified candidate effectors expressed in planta, consisting of both known effector homologs and novel candidates. FTF1 and a subset of other transcription factors implicated in regulation of effector expression were found to be expressed in planta.

Shifts in diversification rates and host jump frequencies shaped the diversity of host range among Sclerotiniaceae fungal plant pathogens.

The range of hosts that a parasite can infect in nature is a trait determined by its own evolutionary history and that of its potential hosts. However, knowledge on host range diversity and evolution at the family level is often lacking. Here, we investigate host range variation and diversification trends within the Sclerotiniaceae, a family of Ascomycete fungi. Using a phylogenetic framework, we associate diversification rates, the frequency of host jump events and host range variation during the evolution of this family. Variations in diversification rate during the evolution of the Sclerotiniaceae define three major macro-evolutionary regimes with contrasted proportions of species infecting a broad range of hosts. Host-parasite cophylogenetic analyses pointed towards parasite radiation on distant hosts long after host speciation (host jump or duplication events) as the dominant mode of association with plants in the Sclerotiniaceae. The intermediate macro-evolutionary regime showed a low diversification rate, high frequency of duplication events and the highest proportion of broad host range species. Our findings suggest that the emergence of broad host range fungal pathogens results largely from host jumps, as previously reported for oomycete parasites, probably combined with low speciation rates. These results have important implications for our understanding of fungal parasites evolution and are of particular relevance for the durable management of disease epidemics.