Karyotype evolution in Fusarium

FunFEA: an R package for fungal functional enrichment analysis

BACKGROUND

The functional annotation of fungal genomes is critical for understanding their biological processes and ecological roles. While existing tools support functional enrichment analysis from publicly available annotations of well-established model organisms, few are tailored to the specific needs of the fungal research community. Furthermore, many tools struggle with processing functional annotations of novel species, for which no publicly available functional annotations are yet available.

RESULTS

FunFEA is an R package designed for functional enrichment analysis of fungal genomes. It supports COG/KOG (Clusters of Orthologous Genes), GO (Gene Ontology), and KEGG (Kyoto Encyclopedia of Genes and Genomes) annotations, and generates background frequency models from publicly available annotations for overrepresentation analysis, within a set of experimentally defined genes or proteins. Additionally, FunFEA can process eggNOG-mapper annotations, thus enabling functional enrichment analysis of novel genomes. The package offers a suite of tools for generation of background frequency models, functional enrichment analysis, as well as visualization of enriched functional categories. On release, the package includes precomputed models for 65 commonly used fungal strains in academic research and strains listed on the WHO fungal priority pathogens list.

CONCLUSIONS

FunFEA fills a critical need for a specialized tool in fungal genomics, providing valuable insights into fungal biology. Additionally, its ability to process eggNOG-mapper annotations makes it an essential resource for researchers, helping to drive further exploration of fungal functional diversity and pathways and derive biological insights from novel genomes.

The Fusarium graminearum Effector Protease FgTPP1 Suppresses Immune Responses and Facilitates Fusarium Head Blight Disease

Most plant pathogens secrete effector proteins to circumvent host immune responses, thereby promoting pathogen virulence. One such pathogen is the fungus Fusarium graminearum, which causes Fusarium head blight (FHB) disease on wheat and barley. Transcriptomic analyses revealed that F. graminearum expresses many candidate effector proteins during early phases of the infection process, some of which are annotated as proteases. However, the contributions of these proteases to virulence remain poorly defined. Here, we characterize an F. graminearum endopeptidase, FgTPP1 (FGSG_11164), that is highly upregulated during wheat spikelet infection and is secreted from fungal cells. To elucidate the potential role of FgTPP1 in F. graminearum virulence, we generated FgTPP1 deletion mutants (ΔFgtpp1) and performed FHB infection assays. Deletion of FgTPP1 reduced the virulence of F. graminearum as assessed by spikelet bleaching. Infection with wild-type F. graminearum induced full bleaching in about 50% of the spikes at 10 to 11 days postinfection, whereas this fraction was reduced to between 18 and 27% when using ΔFgtpp1 mutants. Transient expression of green fluorescent protein-tagged FgTPP1 revealed that FgTPP1 localizes, in part, to chloroplasts and attenuates chitin-mediated activation of mitogen-activated protein kinase signaling, reactive oxygen species production, and cell death induced by an autoactive disease resistance protein when expressed in planta. Notably, the FgTPP1 protein is conserved across the Ascomycota phylum, suggesting that it may be a core effector among ascomycete plant pathogens. These properties make FgTPP1 an ideal candidate for decoy substrate engineering, with the goal of engineering resistance to FHB. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

The jet-like chromatin structure defines active secondary metabolism in fungi

Eukaryotic genomes are spatially organized within the nucleus in a nonrandom manner. However, fungal genome arrangement and its function in development and adaptation remain largely unexplored. Here, we show that the high-order chromosome structure of Fusarium graminearum is sculpted by both H3K27me3 modification and ancient genome rearrangements. Active secondary metabolic gene clusters form a structure resembling chromatin jets. We demonstrate that these jet-like domains, which can propagate symmetrically for 54 kb, are prevalent in the genome and correlate with active gene transcription and histone acetylation. Deletion of GCN5, which encodes a core and functionally conserved histone acetyltransferase, blocks the formation of the domains. Insertion of an exogenous gene within the jet-like domain significantly augments its transcription. These findings uncover an interesting link between alterations in chromatin structure and the activation of fungal secondary metabolism, which could be a general mechanism for fungi to rapidly respond to environmental cues, and highlight the utility of leveraging three-dimensional genome organization in improving gene transcription in eukaryotes.

Chromosome-Level Assemblies for the Pine Pitch Canker Pathogen Fusarium circinatum

The pine pitch canker pathogen, Fusarium circinatum, is globally regarded as one of the most important threats to commercial pine-based forestry. Although genome sequences of this fungus are available, these remain highly fragmented or structurally ill-defined. Our overall goal was to provide high-quality assemblies for two notable strains of F. circinatum, and to characterize these in terms of coding content, repetitiveness and the position of telomeres and centromeres. For this purpose, we used Oxford Nanopore Technologies MinION long-read sequences, as well as Illumina short sequence reads. By leveraging the genomic synteny inherent to F. circinatum and its close relatives, these sequence reads were assembled to chromosome level, where contiguous sequences mostly spanned from telomere to telomere. Comparative analyses unveiled remarkable variability in the twelfth and smallest chromosome, which is known to be dispensable. It presented a striking length polymorphism, with one strain lacking substantial portions from the chromosome's distal and proximal regions. These regions, characterized by a lower gene density, G+C content and an increased prevalence of repetitive elements, contrast starkly with the syntenic segments of the chromosome, as well as with the core chromosomes. We propose that these unusual regions might have arisen or expanded due to the presence of transposable elements. A comparison of the overall chromosome structure revealed that centromeric elements often underpin intrachromosomal differences between F. circinatum strains, especially at chromosomal breakpoints. This suggests a potential role for centromeres in shaping the chromosomal architecture of F. circinatum and its relatives. The publicly available genome data generated here, together with the detailed metadata provided, represent essential resources for future studies of this important plant pathogen.

Fusarium abutilonis and F. guadeloupense, two novel species in the Fusarium buharicum clade supported by multilocus molecular phylogenetic analyses

This study was conducted to elucidate evolutionary relationships and species diversity within the Fusarium buharicum species complex (FBSC). We also evaluate the potential of these species to produce mycotoxins and other bioactive secondary metabolites. Maximum likelihood and maximum parsimony analyses of sequences from portions of four marker loci (ITS rDNA, TEF1, RPB1, and RPB2) and the combined 4495 bp data set support recognition of seven genealogically exclusive species within the FBSC. Two of the three newly discovered species are formally described as F. abutilonis and F. guadeloupense based on concordance of gene genealogies and morphological data. Fusarium abutilonis induces leaf, stem, and root lesions on several weedy Malvaceae (Abution theophrasti, Anoda cristata, Sida spinosa) and a fabaceous host (Senna obtusifolia) in North America and also was recovered from soil in New Caledonia. Fusarium abutilonis, together with its unnamed sister, Fusarium sp. ex common marsh mallow (Hibiscus moscheutos) from Washington state, and F. buharicum pathogenic to cotton and kenaf in Russia and Iran, respectively, were strongly supported as a clade of malvaceous pathogens. The four other species of the FBSC are not known to be phytopathogenic; however, F. guadeloupense was isolated from human blood in Texas and soil in Guadeloupe. The former isolate is unique because it represents the only known case of a fusarial infection disseminated hematogenously by a species lacking microconidia and the only documented fusariosis caused by a member of the FBSC. Whole genome sequence data and extracts of cracked maize kernel cultures were analyzed to assess the potential of FBSC isolates to produce mycotoxins, pigments, and phytohormones.

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.

Effectiveness of the Influence of Selected Essential Oils on the Growth of Parasitic Fusarium Isolated from Wheat Kernels from Central Europe

The aim of the study was to determine the effectiveness of selected seven commercial essential oils (EsO) (grapefruit, lemongrass, tea tree (TTO), thyme, verbena, cajeput, and Litsea cubeba) on isolates of common Central European parasitic fungal species of Fusarium obtained from infected wheat kernels, and to evaluate the oils as potential natural fungicides. The study was conducted in 2 stages. At each stage, the fungicidal activity of EsO (with concentrations of 0.025; 0.05; 0.125; 0.25; 0.50; 1.0, and 2.0%) against Fusarium spp. was evaluated using the disc plate method and zones of growth inhibition were measured. At the first stage, the fungistatic activity of EsO was evaluated against four species of Fusarium from the Polish population (F. avenaceum FAPL, F. culmorum FCPL, F. graminearum FGPL and F. oxysporum FOPL). The correlation coefficient between the mycelial growth rate index (T) and the fungistatic activity (FA) was calculated. At the second stage, on the basis of the mycelium growth rate index, the effectiveness of the EsO in limiting the development of Fusarium isolates from the German population (F. culmorum FC1D, F. culmorum FC2D, F. graminearum FG1D, F. graminearum FG2D and F. poae FP0D) was assessed. The first and second stage results presented as a growth rate index were then used to indicate essential oils (as potential natural fungicides) effectively limiting the development of various common Central European parasitic species Fusarium spp. Finally, the sensitivity of four Fusarium isolates from the Polish population and five Fusarium isolates from the German population was compared. The data were compiled in STATISTICA 13.0 (StatSoft, Inc, CA, USA) at the significance level of 0.05. Fusarium isolates from the German population were generally more sensitive than those from the Polish population. The sensitivity of individual Fusarium species varied. Their vulnerability, regardless of the isolate origin, in order from the most to the least sensitive, is as follows: F. culmorum, F. graminearum, F. poae, F. avenaceum and F. oxysporum. The strongest fungicidal activity, similar to Funaben T, showed thyme oil (regardless of the concentration). Performance of citral oils (lemongrass and Litsea cubeba) was similar but at a concentration above 0.025%.

Apicidin biosynthesis is linked to accessory chromosomes in Fusarium poae isolates

BACKGROUND

Fusarium head blight is a disease of global concern that reduces crop yields and renders grains unfit for consumption due to mycotoxin contamination. Fusarium poae is frequently associated with cereal crops showing symptoms of Fusarium head blight. While previous studies have shown F. poae isolates produce a range of known mycotoxins, including type A and B trichothecenes, fusarins and beauvericin, genomic analysis suggests that this species may have lineage-specific accessory chromosomes with secondary metabolite biosynthetic gene clusters awaiting description.

METHODS

We examined the biosynthetic potential of 38 F. poae isolates from Eastern Canada using a combination of long-read and short-read genome sequencing and untargeted, high resolution mass spectrometry metabolome analysis of extracts from isolates cultured in multiple media conditions.

RESULTS

A high-quality assembly of isolate DAOMC 252244 (Fp157) contained four core chromosomes as well as seven additional contigs with traits associated with accessory chromosomes. One of the predicted accessory contigs harbours a functional biosynthetic gene cluster containing homologs of all genes associated with the production of apicidins. Metabolomic and genomic analyses confirm apicidins are produced in 4 of the 38 isolates investigated and genomic PCR screening detected the apicidin synthetase gene APS1 in approximately 7% of Eastern Canadian isolates surveyed.

CONCLUSIONS

Apicidin biosynthesis is linked to isolate-specific putative accessory chromosomes in F. poae. The data produced here are an important resource for furthering our understanding of accessory chromosome evolution and the biosynthetic potential of F. poae.

Phylogenomic Analysis of a 55.1-kb 19-Gene Dataset Resolves a Monophyletic Fusarium that Includes the Fusarium solani Species Complex

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. In 2013, the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus Fusarium into seven genera, including the FSSC described as members of the genus Neocosmospora, with subsequent justification in 2018 based on claims that the 2013 concept of Fusarium is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a genus Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus Neocosmospora were recombined in genus Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural, and practical taxonomic option available.

The Chromosome-Scale Genome Resource for Two Endophytic Fusarium species, F. culmorum and F. pseudograminearum

Genus Fusarium (Ascomycota, Hypocreales, Nectriaceae) includes many economically important plant pathogens that cause devastating diseases of a wide range of crops and trees. Interestingly, there is increasing evidence that some Fusarium species also live as endophytes and benefit plant growth and stress tolerance. In this work, we sequence the whole genomes of endophytic F. culmorum and F. pseudograminearum, isolated from a coastal dunegrass (Leymus mollis), using long-read single-molecule real-time sequencing technology. Their genomes are assembled into four chromosomes and a mitochondrial genome with a total assembly size of 40.05 and 42.90 M, respectively. This resource should not only facilitate functional studies designed to better understand what makes the two Fusarium species such successful plant-beneficial fungi but should also reveal their genome evolution and 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.

Fusarium solani species complex infection in elasmobranchs: A case report for rough-tail stingray with valid antifungal therapy

Fusarium species are common plant and animal pathogens. For humans, there are two dominant species complexes, F. solani species complex (FSSC) and F. oxysporum species complex (FOSC), which both infect immunocompromised individuals. However, there are few reports related to elasmobranchs infected by Fusarium species. In this study, we report a case of a rough-tail stingray from an ocean park infected by FSSC diagnosed using histopathology and microscopic observation, with morphological characteristics and molecular techniques used to identify the pathogen. Histopathology showed fungal hyphae invading stingray tissues, while micro/macroconidia were found under the microscope. We identified this pathogen as FSSC 12 through phylogenetic analysis using internal transcribed spacer (ITS) and elongation factor 1-alpha (EF1-α) sequences. Furthermore, we report that application of voriconazole (orally) and terbinafine (topically) constituted an effective therapy, curing the stingray.

Phylogenetic diversity, trichothecene potential, and pathogenicity within Fusarium sambucinum species complex

The Fusarium sambucinum species complex (FSAMSC) is one of the most taxonomically challenging groups of fusaria, comprising prominent mycotoxigenic plant pathogens and other species with various lifestyles. Among toxins produced by members of the FSAMSC, trichothecenes pose the most significant threat to public health. Herein a global collection of 171 strains, originating from diverse hosts or substrates, were selected to represent FSAMSC diversity. This strain collection was used to assess their species diversity, evaluate their potential to produce trichothecenes, and cause disease on wheat. Maximum likelihood and Bayesian analyses of a combined 3-gene dataset used to infer evolutionary relationships revealed that the 171 strains originally received as 48 species represent 74 genealogically exclusive phylogenetically distinct species distributed among six strongly supported clades: Brachygibbosum, Graminearum, Longipes, Novel, Sambucinum, and Sporotrichioides. Most of the strains produced trichothecenes in vitro but varied in type, indicating that the six clades correspond to type A, type B, or both types of trichothecene-producing lineages. Furthermore, five strains representing two putative novel species within the Sambucinum Clade produced two newly discovered type A trichothecenes, 15-keto NX-2 and 15-keto NX-3. Strains of the two putatively novel species together with members of the Graminearum Clade were aggressive toward wheat when tested for pathogenicity on heads of the susceptible cultivar Apogee. In planta, the Graminearum Clade strains produced nivalenol or deoxynivalenol and the aggressive Sambucinum Clade strains synthesized NX-3 and 15-keto NX-3. Other strains within the Brachygibbosum, Longipes, Novel, Sambucinum, and Sporotrichioides Clades were nonpathogenic or could infect the inoculated floret without spreading within the head. Moreover, most of these strains did not produce any toxin in the inoculated spikelets. These data highlight aggressiveness toward wheat appears to be influenced by the type of toxin produced and that it is not limited to members of the Graminearum Clade.

Monascus sanguineus May Be a Natural Nothospecies

The genus Monascus has important economic and ecological values. In 2016, we isolated a strain M. sanguineus. After studying the phylogenetic relationship of Monascus, we believe that M. sanguineus is an independent species and speculate that it is a natural nothospecies. Recently, the morphological characteristics and sequences of seven genes (ITS, LSU, β-tubulin, calmodulin, RNA polymerase II subunit, β-ketoacyl synthase, and mating-type locus 1-1) of 15 Monascus strains were analyzed, including sequencing of multiple clones of five protein genes in four M. sanguineus strains. Two types of haplotypes (A and B) were observed in the five protein genes of M. sanguineus. Haplotype A was closely related to M. ruber, and haplotype B may be derived from an unknown Monascus species. The results demonstrated that M. sanguineus including type strains may be a natural nothospecies. This study laid the foundation for further exploration of the M. sanguineus genome, and the study may be of significant importance for the Monascus fermentation industry.

Dynamics in Secondary Metabolite Gene Clusters in Otherwise Highly Syntenic and Stable Genomes in the Fungal Genus Botrytis

Fungi of the genus Botrytis infect >1,400 plant species and cause losses in many crops. Besides the broad host range pathogen Botrytis cinerea, most other species are restricted to a single host. Long-read technology was used to sequence genomes of eight Botrytis species, mostly pathogenic on Allium species, and the related onion white rot fungus, Sclerotium cepivorum. Most assemblies contained <100 contigs, with the Botrytis aclada genome assembled in 16 gapless chromosomes. The core genome and pan-genome of 16 Botrytis species were defined and the secretome, effector, and secondary metabolite repertoires analyzed. Among those genes, none is shared among all Allium pathogens and absent from non-Allium pathogens. The genome of each of the Allium pathogens contains 8-39 predicted effector genes that are unique for that single species, none stood out as potential determinant for host specificity. Chromosome configurations of common ancestors of the genus Botrytis and family Sclerotiniaceae were reconstructed. The genomes of B. cinerea and B. aclada were highly syntenic with only 19 rearrangements between them. Genomes of Allium pathogens were compared with ten other Botrytis species (nonpathogenic on Allium) and with 25 Leotiomycetes for their repertoire of secondary metabolite gene clusters. The pattern was complex, with several clusters displaying patchy distribution. Two clusters involved in the synthesis of phytotoxic metabolites are at distinct genomic locations in different Botrytis species. We provide evidence that the clusters for botcinic acid production in B. cinerea and Botrytis sinoallii were acquired by horizontal transfer from taxa within the same genus.

Evolution of Fusarium tricinctum and Fusarium avenaceum mitochondrial genomes is driven by mobility of introns and of a new type of palindromic microsatellite repeats

Background

Increased contamination of European and Asian wheat and barley crops with “emerging” mycotoxins such as enniatins or beauvericin, produced by Fusarium avenaceum and Fusarium tricinctum, suggest that these phylogenetically close species could be involved in future food-safety crises.

Results

The mitochondrial genomes of F. tricinctum strain INRA104 and F. avenaceum strain FaLH27 have been annotated. A comparative analysis was carried out then extended to a set of 25 wild strains. Results show that they constitute two distinct species, easily distinguished by their mitochondrial sequences. The mitochondrial genetic variability is mainly located within the intergenic regions. Marks of variations show they have evolved (i) by Single Nucleotide Polymorphisms (SNPs), (ii) by length variations mediated by insertion/deletion sequences (Indels), and (iii) by length mutations generated by DNA sliding events occurring in mononucleotide (A)_n or (T)_n microsatellite type sequences arranged in a peculiar palindromic organization. The optionality of these palindromes between both species argues for their mobility. The presence of Indels and SNPs in palindrome neighbouring regions suggests their involvement in these observed variations. Moreover, the intraspecific and interspecific variations in the presence/absence of group I introns suggest a high mobility, resulting from several events of gain and loss during short evolution periods. Phylogenetic analyses of intron orthologous sequences suggest that most introns could have originated from lateral transfers from phylogenetically close or distant species belonging to various Ascomycota genera and even to the Basidiomycota fungal division.

Conclusions

Mitochondrial genome evolution between F. tricinctum and F. avenaceum is mostly driven by two types of mobile genetic elements, implicated in genome polymorphism. The first one is represented by group I introns. Indeed, both genomes harbour optional (inter- or intra-specifically) group I introns, all carrying putatively functional hegs, arguing for a high mobility of these introns during short evolution periods. The gain events were shown to involve, for most of them, lateral transfers between phylogenetically distant species. This study has also revealed a new type of mobile genetic element constituted by a palindromic arrangement of (A) n and (T) n microsatellite sequences whose presence was related to occurrence of SNPs and Indels in the neighbouring regions.

Karyotypic instability of endoprophase and mitotic cells of Amoeba sp. strain Cont from the "proteus-type" group (Amoebozoa, Euamoebida, Amoebidae)

We performed karyotyping of Amoeba sp. strain Cont. Based on the results of a cytological analysis, we concluded that the chromosome number of Amoeba sp. strain Cont in mitosis was unstable. In all cases they appeared to be hypergaploid (the basic chromosome number is 30), with monosomy of all chromosomes except four shortest ones. The presence of "extrachromosomes" in the nucleus could prolong until the beginning of the anaphase. It was only then that they were ejected from the nucleus and the euploidy (haploidy) was restored. The stage of endoprophase nucleus was revealed in the cell cycle of Amoeba sp. strain Cont. This stage has not yet been found in other amoebae from the "proteus-type" group that had been previously studied (A. proteus strain B and A. borokensis). The maximum number of endoreplication rounds in the strain Cont amoebae nuclear cycle was 4 or 5. The regular extrusion of chromosomes from the nucleus into the cytoplasm occurred in each of the endoreplication rounds. Comparative cytological analysis of A. proteus strain B, A. borokensis and Amoeba sp. strain Cont karyotypes indicated that strain Cont, though rather close to the former two amoebae, is actually a distinct species.

Neotypification of Fusarium chlamydosporum - a reappraisal of a clinically important species complex

Fusarium chlamydosporum represents a well-defined morpho-species of both phytopathological and clinical importance. Presently, five phylo-species lacking Latin binomials have been resolved in the F. chlamydosporum species complex (FCSC). Naming these phylo-species is complicated due to the lack of type material for F. chlamydosporum. Over the years a number of F. chlamydosporum isolates (which were formerly identified based on morphology only) have been accessioned in the culture collection of the Westerdijk Fungal Biodiversity Institute. The present study was undertaken to correctly identify these 'F. chlamydosporum' isolates based on multilocus phylogenetic inference supported by morphological characteristics. Closer scrutiny of the metadata associated with one of these isolates allowed us to propose a neotype for F. chlamydosporum. Phylogenetic inference revealed the presence of nine phylo-species within the FCSC in this study. Of these, eight could be provided with names supported by subtle morphological characters. In addition, a new species, as F. nodosum, is introduced in the F. sambucinum species complex and F. chlamydosporum var. fuscum is raised to species level, as F. coffeatum, in the F. incarnatum-equiseti species complex (FIESC).

QTL mapping of mycelial growth and aggressiveness to distinct hosts in Ceratocystis pathogens

Some species of Ceratocystis display strong host specificity, such as C. fimbriata sensu stricto that is restricted to sweet potato (Ipomoea batatas) as host. In contrast, the closely related C. manginecans, infects Acacia mangium and Mangifera indica but is not pathogenic to I. batatas. Despite the economic importance of these fungi, knowledge regarding the genetic factors that influence their pathogenicity and host specificity is limited. A recent inheritance study, based on an interspecific cross between C. fimbriata and C. manginecans and the resultant 70 F₁ progeny, confirmed that traits such as mycelial growth rate, spore production and aggressiveness on A. mangium and I. batatas are regulated by multiple genes. In the present study, a quantitative trait locus (QTL) analysis was performed to determine the genomic loci associated with these traits. All 70 progeny isolates were genotyped with SNP markers and a linkage map was constructed. The map contained 467 SNPs, distributed across nine linkage groups, with a total length of 1203 cm. Using the progeny genotypes and phenotypes, one QTL was identified on the linkage map for mycelial growth rate, one for aggressiveness to A. mangium and two for aggressiveness to I. batatas (P < 0.05). Two candidate genes, likely associated with mycelial growth rate, were identified in the QTL region. The three QTLs associated with aggressiveness to different hosts contained candidate genes involved in protein processing, detoxification and regions with effector genes and high transposable element density. The results provide a foundation for studies considering the function of genes regulating various quantitative traits in Ceratocystis.