Nursery-linked plantation outbreaks and evidence for multiple introductions of the pitch canker pathogen Fusarium circinatum into South Africa

In recent years, Pinus plantation forestry has been significantly hampered by outbreaks of pitch canker caused by the fungus Fusarium circinatum. In this study we investigated the role of Pinus host, geographic origin and reproductive mode in structuring the F. circinatum populations in plantations. For this purpose, 159 isolates originating from diseased plantation trees in the Western and Eastern Cape Provinces of South Africa, were genotyped using 10 microsatellite markers. Analyses of these data revealed 30 multilocus haplotypes and that the populations were distinct based on geographic origin as well as host. However, shared haplotypes were observed between populations, showing that these populations are connected possibly through the movement of haplotypes. A second aim was to determine whether the genetic variation found in these populations of the fungus could be attributed to outbreaks of the seedling disease caused by this pathogen in Pinus nurseries. To achieve this goal, an additional set of 43 isolates originating from pine seedling nurseries were genotyped and analysed. The results showed that the populations of F. circinatum in plantations most likely originated from the nursery outbreaks that occurred prior to the plantation outbreak. Inferences regarding reproductive mode further showed that sexual reproduction has little impact on the genetic makeup of the F. circinatum populations and that they primarily reproduce asexually. Overall the results of this study showed that the F. circinatum diversity in South Africa has arisen due to multiple introductions of the pathogen and is not due to sexual reproduction.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1365-30592017-04-30hb2016Forestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Characterization of host-specific genes from pine- and grass-associated species of the Fusarium fujikuroi species complex

SUPPLEMENTARY MATERIALS : FIGURE S1. Phylogenetic relationship of paralogs with regards to the respective host-range-associated gene. FCIR = Fusarium circinatum; FFRAC = Fusarium fracticaudum; FPIN = Fusarium pininemorale; FSUB = Fusarium subglutinans; FIGURE S2. Host-range-associated genes with ancestral origins that emerged within the FFSC. The investigated host-range-associated genes are highlighted in yellow; FCIR = Fusarium circinatum and FTEMP = Fusarium temperatum; FIGURE S3. Host-range-associated genes with ancestral origins that emerged within the FFSC and FOSC. The investigated host-range-associated genes are highlighted in yellow; FCIR = Fusarium circinatum and FTEMP = Fusarium temperatum; FIGURE S4. Host-range-associated genes with ancestral origins that emerged within the broader Fusarium outside the FFSC and FOSC. The investigated host-range associated genes are highlighted in yellow; FCIR = Fusarium circinatum and FTEMP = Fusarium temperatum; FIGURE S5. Host-range-associated genes with less than 10 ancestral origin hits and mostly Fusarium. The investigated host-range-associated genes are highlighted in yellow; FCIR = Fusarium circinatum and FTEMP = Fusarium temperatum; FIGURE S6. Host-range-associated genes with ancestral origins hits and mostly not Fusarium. The investigated host-range-associated genes are highlighted in yellow; FCIR = Fusarium circinatum and FTEMP = Fusarium temperatum; FIGURE S7. Host-range-associated genes with ancestral origins outside Fusarium but in the Ascomycetes. The investigated host-range-associated genes are highlighted in yellow; FCIR = Fusarium circinatum and FTEMP = Fusarium temperatum; FIGURE S8. Host-range-associated genes with ancestral origins outside Fungi. The investigated host-range-associated genes are highlighted in yellow; FCIR = Fusarium circinatum and FTEMP = Fusarium temperatum; FIGURE S9. The distribution of host-range-associated genes from pine-host-associated Fusarium species and conservation of synteny across and between chromosomes and genomes. Pine-host-associated genes distribution across each of the chromosomes as indicated by the blue lines. The conservation of synteny and inversion between the relevant genomes are indicated in the brown blocks and red lines. FCIR = F. circinatum; chromosome size is given in kbp; FIGURE S10. The distribution of hostrange- associated genes from Poaceae-host-associated Fusarium species and conservation of synteny across and between chromosomes and genomes. Poaceae-host-associated gene distribution across each of the chromosomes as indicated by the blue lines. The conservation of synteny and inversion between the relevant genomes are indicated in the brown blocks and red lines. FTEMP = F. temperatum; chromosome size is given in kbp; FIGURE S11. The syntenous relationship between genes from F. circinatum versus F. temperatum; FIGURE S12. The syntenous relationship between genes from F. temperatum and F. circinatum; TABLE S1. BUSCO results for the relevant Fusarium genomes; TABLE S2. The size difference between the chromosomes of four of the six Fusarium species; TABLE S3. Presence of telomeres at chromosomal ends for the two representative Fusarium species examined; TABLE S4. The Blast2GO data for the 72 unique pine-host-associated genes specifically for (A) Fusarium circinatum, (B) F. fracticaudum and (C) F. pininemorale; TABLE S5. The Blast2GO data for the 47 unique Poaceae-host-associated genes, specifically for (A) Fusarium konzum, (B) F. subglutinans and (C) F. temperatum; TABLE S6. The Fischer exact test data for (A) the 72 unique pine-host-associated genes and (B) the 47 unique Poaceae-host-associated genes; TABLE S7. The EST and RNA-seq data for F. circinatum, obtained from Wingfield et al. [52] and Phasha et al. [53], respectively; TABLE S8. The placement of host-range-associated genes in groups that infer their evolutionary origins; TABLE S9. The gene information for the unique F. circinatum genes, in terms of chromosome location, subtelomeric placement, ancestral origin and BLAST description; TABLE S10. The gene information for the unique F. temperatum genes, in terms of chromosome location, subtelomeric placement, ancestral origin and BLAST description; TABLE S11. The host-range-associated gene density for both F. circinatum and F. temperatum; TABLE S12. The SynChro data for genes downstream and upstream of the host-rangeassociated genes of both the pine- and Poaceae-host-associated Fusarium species; FCIR = Fusarium circinatum and FTEMP = Fusarium temperatum.The Fusarium fujikuroi species complex (FFSC) includes socioeconomically important pathogens that cause disease for numerous crops and synthesize a variety of secondary metabolites that can contaminate feedstocks and food. Here, we used comparative genomics to elucidate processes underlying the ability of pine-associated and grass-associated FFSC species to colonize tissues of their respective plant hosts. We characterized the identity, possible functions, evolutionary origins, and chromosomal positions of the host-range-associated genes encoded by the two groups of fungi. The 72 and 47 genes identified as unique to the respective genome groups were potentially involved in diverse processes, ranging from transcription, regulation, and substrate transport through to virulence/pathogenicity. Most genes arose early during the evolution of Fusarium/FFSC and were only subsequently retained in some lineages, while some had origins outside Fusarium. Although differences in the densities of these genes were especially noticeable on the conditionally dispensable chromosome of F. temperatum (representing the grass-associates) and F. circinatum (representing the pine-associates), the host-range-associated genes tended to be located towards the subtelomeric regions of chromosomes. Taken together, these results demonstrate that multiple mechanisms drive the emergence of genes in the grass- and pine-associated FFSC taxa examined. It also highlighted the diversity of the molecular processes potentially underlying niche-specificity in these and other Fusarium species.The South African Department of Science and Innovation’s South African Research Chair Initiative, the DSI-NRF Centre of Excellence in Plant Health Biotechnology at the Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, the Food Safety National Program at the United States Department of Agriculture, Agricultural Research Service.https://www.mdpi.com/journal/pathogensam2023BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Intra-species genomic variation in the pine pathogen Fusarium circinatum

Fusarium circinatum is an important global pathogen of pine trees. Genome plasticity has been observed in different isolates of the fungus, but no genome comparisons are available. To address this gap, we sequenced and assembled to chromosome level five isolates of F. circinatum. These genomes were analysed together with previously published genomes of F. circinatum isolates, FSP34 and KS17. Multi-sample variant calling identified a total of 461,683 micro variants (SNPs and small indels) and a total of 1828 macro structural variants of which 1717 were copy number variants and 111 were inversions. The variant density was higher on the sub-telomeric regions of chromosomes. Variant annotation revealed that genes involved in transcription, transport, metabolism and transmembrane proteins were overrepresented in gene sets that were affected by high impact variants. A core genome representing genomic elements that were conserved in all the isolates and a non-redundant pangenome representing all genomic elements is presented. Whole genome alignments showed that an average of 93% of the genomic elements were present in all isolates. The results of this study reveal that some genomic elements are not conserved within the isolates and some variants are high impact. The described genome-scale variations will help to inform novel disease management strategies against the pathogen.DATA AVAILABILTY STATEMENT : The Whole Genome Shotgun project for Fusarium circinatum CMWF1803 has been deposited at DDBJ/ENA/GenBank under the accession JAEHFH000000000. The version described in this paper is version JAEHFH010000000. The Whole Genome Shotgun project for Fusarium circinatum CMWF560 has been deposited at DDBJ/ENA/GenBank under the accession JAEHFI000000000. The version described in this paper is version JAEHFI010000000. The Whole Genome Shotgun project for Fusarium circinatum CMWF567 has been deposited at DDBJ/ENA/GenBank under the accession JADZLS000000000. The version described in this paper is version JADZLS010000000. The Whole Genome Shotgun project for Fusarium circinatum UG27 has been deposited at DDBJ/ENA/ GenBank under the accession JAELVK000000000. The version described in this paper is version JAELVK010000000. The Whole Genome Shotgun project for Fusarium circinatum UG10 has been deposited at DDBJ/ENA/GenBank under the accession JAGJRQ000000000. The version described in this paper is version JAGJRQ010000000.The South African Department of Science and Innovation’s South African Research Chair Initiative and the DSI-NRF Centre of Excellence in Plant Health Biotechnology at the Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria.http://www.mdpi.com/journal/jofBiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Identification and characterization of a QTL for growth of Fusarium circinatum on pine-based medium

SUPPLEMENTARY FILE S1: HPLC and GC-MS results showing the broad overview and primary metabolites identified in the pine-based media. SUPPLEMENTARY FILE S2: The primer sequences and PCR protocols used to amplify gene regions in this study. SUPPLEMENTARY FILE S3: Reference mapping of F. circinatum Illumina and MinIon raw reads mapped to the genomes of F circinatum KS17 and F. temperatum. SUPPLEMENTARY FILE S4: Genic information of the identified genes and indel region in the QTL region of F. circinatum. InterProScan and gene ontology information are provided for all genes in this region. Further information on the retrotransposons and repeats that are characteristic of the indel within the QTL region is provided.Fusarium circinatum is an economically important pathogen of pine and resides in the Fusarium fujikuroi species complex. Here we investigated the molecular processes underlying growth in F. circinatum by exploring the association between growth and the nutritional environment provided by the pine host. For this purpose, we subjected a mapping population consisting of F. circinatum X F. temperatum hybrid progeny to an analysis of growth rate on a pine-tissue derived medium. These data, together with the available genetic linkage map for F. circinatum, were then used to identify Quantitative Trait Loci (QTLs) associated with growth. The single significant QTL identified was then characterized using the available genome sequences for the hybrid progeny’s parental isolates. This revealed that the QTL localized to two non-homologous regions in the F. circinatum and F. temperatum genomes. For one of these, the F. circinatum parent contained a two-gene deletion relative to the F. temperatum parent. For the other region, the two parental isolates encoded different protein products. Analysis of repeats, G+C content, and repeat-induced point (RIP) mutations further suggested a retrotransposon origin for the two-gene deletion in F. circinatum. Nevertheless, subsequent genome and PCR-based analyses showed that both regions were similarly polymorphic within a collection of diverse F. circinatum. However, we observed no clear correlation between the respective polymorphism patterns and growth rate in culture. These findings support the notion that growth is a complex multilocus trait and raise the possibility that the identified QTL contains multiple small-effect QTLs, of which some might be dependent on the genetic backgrounds. This study improved our current knowledge of the genetic determinants of vegetative growth in F. circinatum and provided an important foundation for determining the genes and processes underpinning its ability to colonize its host environment.The South African Department of Science and Innovation’s South African Research Chair Initiative and the DSI-NRF Centre of Excellence in Plant Health Biotechnology at the Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria.https://www.mdpi.com/journal/jofam2023BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant PathologyZoology and Entomolog

Genome-wide macrosynteny among Fusarium species in the Gibberella fujikuroi complex revealed by amplified fragment length polymorphisms

The Gibberella fujikuroi complex includes many Fusarium species that cause significant losses in yield and quality of agricultural and forestry crops. Due to their economic importance, whole-genome sequence information has rapidly become available for species including Fusarium circinatum, Fusarium fujikuroi and Fusarium verticillioides, each of which represent one of the three main clades known in this complex. However, no previous studies have explored the genomic commonalities and differences among these fungi. In this study, a previously completed genetic linkage map for an interspecific cross between Fusarium temperatum and F. circinatum, together with genomic sequence data, was utilized to consider the level of synteny between the three Fusarium genomes. Regions that are homologous amongst the Fusarium genomes examined were identified using in silico and pyrosequenced amplified fragment length polymorphism (AFLP) fragment analyses. Homology was determined using BLAST analysis of the sequences, with 777 homologous regions aligned to F. fujikuroi and F. verticillioides. This also made it possible to assign the linkage groups from the interspecific cross to their corresponding chromosomes in F. verticillioides and F. fujikuroi, as well as to assign two previously unmapped supercontigs of F. verticillioides to probable chromosomal locations. We further found evidence of a reciprocal translocation between the distal ends of chromosome 8 and 11, which apparently originated before the divergence of F. circinatum and F. temperatum. Overall, a remarkable level of macrosynteny was observed among the three Fusarium genomes, when comparing AFLP fragments. This study not only demonstrates how in silico AFLPs can aid in the integration of a genetic linkage map to the physical genome, but it also highlights the benefits of using this tool to study genomic synteny and architecture.National Research Foundation of South Africahttp://www.plosone.orgtm201

IMA genome - F14 : Draft genome sequences of Penicillium roqueforti, Fusarium sororula, Chrysoporthe puriensis, and Chalaropsis populi

Draft genomes of Penicillium roqueforti, Fusarium sororula, Chalaropsis populi, and Chrysoporthe puriensis are presented. Penicillium roqueforti is a model fungus for genetics, physiological and metabolic studies, as well as for biotechnological applications. Fusarium sororula and Chrysoporthe puriensis are important tree pathogens, and Chalaropsis populi is a soilborne root-pathogen. The genome sequences presented here thus contribute towards a better understanding of both the pathogenicity and biotechnological potential of these species.The University of Pretoria, the Department of Science and Technology (DST)/National Research Foundation (NRF) Centre of Excellence in Tree Health Biotechnology (CTHB), South Africa, the Tree Protection Co-operative Programme (TPCP), the National Research Foundation and the DST-NRF SARChI chair in Fungal Genomics.http://www.imafungus.orgam2022BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Draft genomes of Amanita jacksonii, Ceratocystis albifundus, Fusarium circinatum, Huntiella omanensis, Leptographium procerum, Rutstroemia sydowiana, and Sclerotinia echinophila

The genomes of fungi provide an important resource to resolve issues pertaining to their taxonomy, biology, and evolution. The genomes of Amanita jacksonii, Ceratocystis albifundus, a Fusarium circinatum variant, Huntiella omanensis, Leptographium procerum, Sclerotinia echinophila, and Rutstroemia sydowiana are presented in this genome announcement. These seven genomes are from a number of fungal pathogens and economically important species. The genome sizes range from 27 Mb in the case of Ceratocystis albifundus to 51.9 Mb for Rutstroemia sydowiana. The latter also encodes for a predicted 17 350 genes, more than double that of Ceratocystis albifundus. These genomes will add to the growing body of knowledge of these fungi and provide a value resource to researchers studying these fungi.The US Department of Agriculture (USDA) Agricultural Research Service, grants from the Natural Sciences and Engineering Research Council of Canada (NSERC) and the Royal Ontario Museum to J.M.M.; Graduate Scholarships from the Consejo Nacional de Ciencia y Tecnologia (Mexico) and the University of Toronto to SSR; and a Undergraduate Student Research Award from NSERC to M.S. Financial support was provided by members of the Tree Protection Cooperative Program (TPCP), the Department of Science and Technology (DST)/ National Research Foundation (NRF) Centre of Excellence in Tree Health Biotechnology, and the Genomics Research Institute of the University of Pretoria. This project was supported by multiple grants from the NRF, South Africa, including the grant specific unique reference number (UID) 83924.http://www.imafungus.orgam201

Autoantibodies neutralizing type I IFNs are present in ~4% of uninfected individuals over 70 years old and account for ~20% of COVID-19 deaths

Publisher Copyright: © 2021 The Authors, some rights reserved.Circulating autoantibodies (auto-Abs) neutralizing high concentrations (10 ng/ml; in plasma diluted 1:10) of IFN-alpha and/or IFN-omega are found in about 10% of patients with critical COVID-19 (coronavirus disease 2019) pneumonia but not in individuals with asymptomatic infections. We detect auto-Abs neutralizing 100-fold lower, more physiological, concentrations of IFN-alpha and/or IFN-omega (100 pg/ml; in 1:10 dilutions of plasma) in 13.6% of 3595 patients with critical COVID-19, including 21% of 374 patients >80 years, and 6.5% of 522 patients with severe COVID-19. These antibodies are also detected in 18% of the 1124 deceased patients (aged 20 days to 99 years; mean: 70 years). Moreover, another 1.3% of patients with critical COVID-19 and 0.9% of the deceased patients have auto-Abs neutralizing high concentrations of IFN-beta. We also show, in a sample of 34,159 uninfected individuals from the general population, that auto-Abs neutralizing high concentrations of IFN-alpha and/or IFN-omega are present in 0.18% of individuals between 18 and 69 years, 1.1% between 70 and 79 years, and 3.4% >80 years. Moreover, the proportion of individuals carrying auto-Abs neutralizing lower concentrations is greater in a subsample of 10,778 uninfected individuals: 1% of individuals 80 years. By contrast, auto-Abs neutralizing IFN-beta do not become more frequent with age. Auto-Abs neutralizing type I IFNs predate SARS-CoV-2 infection and sharply increase in prevalence after the age of 70 years. They account for about 20% of both critical COVID-19 cases in the over 80s and total fatal COVID-19 cases.Peer reviewe

First fungal genome sequence from Africa : a preliminary analysis

Some of the most significant breakthroughs in the biological sciences this century will emerge from the development of next generation sequencing technologies. The ease of availability of DNA sequence made possible through these new technologies has given researchers opportunities to study organisms in a manner that was not possible with Sanger sequencing. Scientists will, therefore, need to embrace genomics, as well as develop and nurture the human capacity to sequence genomes and utilise the ’tsunami‘ of data that emerge from genome sequencing. In response to these challenges, we sequenced the genome of Fusarium circinatum, a fungal pathogen of pine that causes pitch canker, a disease of great concern to the South African forestry industry. The sequencing work was conducted in South Africa, making F. circinatum the first eukaryotic organism for which the complete genome has been sequenced locally. Here we report on the process that was followed to sequence, assemble and perform a preliminary characterisation of the genome. Furthermore, details of the computer annotation and manual curation of this genome are presented. The F. circinatum genome was found to be nearly 44 million bases in size, which is similar to that of four other Fusarium genomes that have been sequenced elsewhere. The genome contains just over 15 000 open reading frames, which is less than that of the related species, Fusarium oxysporum, but more than that for Fusarium verticillioides. Amongst the various putative gene clusters identified in F. circinatum, those encoding the secondary metabolites fumosin and fusarin appeared to harbour evidence of gene translocation. It is anticipated that similar comparisons of other loci will provide insights into the genetic basis for pathogenicity of the pitch canker pathogen. Perhaps more importantly, this project has engaged a relatively large group of scientists including students in a significant genome project that is certain to provide a platform for growth in this important area of research in the future.We thank the National Research Foundation (NRF) of South Africa, members of the Tree Protection Co-operative Programme, the THRIP initiative of the Department of Trade and Industry and the Department of Science and Technology (DST)/NRF Centre of Excellence in Tree Health Biotechnology and the Oppenheimer Foundation for funding.http://www.sajs.co.zanf201

The risk of COVID-19 death is much greater and age dependent with type I IFN autoantibodies

SignificanceThere is growing evidence that preexisting autoantibodies neutralizing type I interferons (IFNs) are strong determinants of life-threatening COVID-19 pneumonia. It is important to estimate their quantitative impact on COVID-19 mortality upon SARS-CoV-2 infection, by age and sex, as both the prevalence of these autoantibodies and the risk of COVID-19 death increase with age and are higher in men. Using an unvaccinated sample of 1,261 deceased patients and 34,159 individuals from the general population, we found that autoantibodies against type I IFNs strongly increased the SARS-CoV-2 infection fatality rate at all ages, in both men and women. Autoantibodies against type I IFNs are strong and common predictors of life-threatening COVID-19. Testing for these autoantibodies should be considered in the general population