Biology subjects

Johannesson, H.

Publications and source records attributed to Johannesson, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Elevated substitution rates and increased purifying selection associated with thermophily in Chaetomiaceae fungi

Understanding the genomic consequences of thermal adaptation in fungi is crucial, as rising global temperatures are expected to have negative impacts on food safety and human health. The family Chaetomiaceae contains a large number of thermophilic fungal taxa, but previous studies have reported inconsistent optimal growth temperatures (OGT) for the same strains, obtained with various laboratory methods. Here we applied a standardized laboratory approach to measure OGT across strains of 17 Chaetomiaceae species and used a phylogenomic approach to test associations between OGT, rates of genome evolution, and strength of purifying selection. Compared to mesophiles, thermophilic fungi showed faster nucleotide substitution rates. In addition, thermophiles showed lower dN/dS ratios than mesophiles, suggesting stronger purifying selection on conserved orthologs. We hypothesize that the elevated substitution rates are linked to high growth rates, as thermophilic fungi grew significantly faster than mesophilic ones. Our results show that selective pressures may act at different temperatures for distinct genomic characteristics. Genome size was lower at OGT [≥] 35{degrees}C compared to mesophilic species, while GC content did not show a large difference between mesophiles and thermotolerant species, but increased in thermophilic species with an OGT [≥] 45{degrees}C.

evolutionary biology↗

bioRxiv2026

Living in a metal-rich world: Enhanced growth and reduced metal accumulation in Fusarium fungi from the Kiirunavaara iron ore mine

BackgroundHuman activities such as mining generally lead to increased heavy metal concentrations in the environment. While traditional remediation techniques are often costly, the use of fungi as bioremediators, known as mycoremediation, is increasingly gaining attention as a sustainable approach for removal of heavy metals. Here, we evaluated heavy metal levels inside the Kiirunavaara iron ore mine in Northern Sweden and analysed fungal responses to various metal concentrations by comparing growth and metal uptake in mine-derived isolates and closely related control isolates. ResultsSediments inside the mine were enriched in heavy metals compared to those from the outlet of the mine to natural lakes. Six Fusarium isolates were recovered from contaminated mining environments: five isolates from inside the mine were identified as Fusarium oxysporum, and one isolate from the outlet was identified as Fusarium tricinctum. Isolates from the mine and outlet showed overall higher survival and biomass production in presence of copper, iron, and zinc across a range of concentrations (up to 1000 mg/L) compared to control isolates. At the same time, these isolates often exhibited reduced relative metal uptake. As a result, mycoremediation potential, assessed as total uptake in the grown mycelium, was isolate-dependent. ConclusionsBased on these results, we conclude that Fusarium isolates from the Kiirunavaara mine show increased growth in media enriched with heavy metals compared to closely related control isolates. We additionally show that mycoremediation potential is not necessarily associated with environmental origin. Instead, mycoremediation potential should be evaluated on a case-by-case basis for each isolate and based on specific needs for mycoremediation.

microbiology↗

bioRxiv2025

A recent shift in centromere size and DNA content in Podospora pseudocomata co-occurs with the loss of a fungal genome defense system

The centromere of the eukaryotic chromosome is necessary for the accurate segregation during cell division. Yet, centromeric DNA is highly variable and rapidly evolving. In fungi, centromeres range from point- to regional centromeres, some of which are hundreds of thousands of base pairs long and filled with transposable elements. As fungi have evolved several specialized defense mechanisms against transposable elements, these regional centromeres are intriguing sites for investigating the connection between genome defense and centromere evolution. Here, we investigated the structure of the centromeres of seven species of the Podospora anserina species complex, which is made up of closely related filamentous ascomycetes that diverged less than 1 MYA. We discovered that one species in the complex, P. pseudocomata, lacks the genomic signature of the specialized genome defense mechanism called Repeat Induced Point mutations (RIP). We identified the centromeric regions in P. anserina and P. pseudocomata using chromatin immunoprecipitation targeting the centromere-specific histone variant cenH3, and using comparative genomics we inferred the size of centromeric regions in the other species. We found that while the centromere structure in the complex is generally well conserved, the centromeric regions of P. pseudocomata has gone through a rapid change. Specifically, the size of the centromeres in P. pseudocomata are 35-46 kb, which is significantly smaller than those of the other species (44-90 kb), and the DNA-transposon discoglosse is the most abundant TE family instead of the typical LTR-retrotransposon crapaud. Taken together, our data strongly indicates a link between genome defense and centromere evolution in fungi.

genomics↗

bioRxiv2025

Patterns and drivers of genome-wide codon usage bias in the fungal order Sordariales

Here we present a study on amino acid composition, codon usage bias (CUB), and levels of selection driving codon usage in Sordariales fungi. We found that GC ending codons are used more often than AT ending codons in all Sordariales genomes, but the strength of CUB differs amongst families. The families Podosporaceae and Sordariaceae contain relatively low genome-wide levels of CUB, while the highest levels of CUB are found in Chaetomiaceae and the "BLLNS"-group, a monophyletic group of five other Sordariales families. Based on genomic clustering, and ancestral state reconstruction of GC nucleotides at the third codon position, we hypothesize that Podosporaceae and Sordariaceae represent the ancestral state of amino acid composition and CUB. The Chaetomiaceae and BLLNS have most likely diverged from this state, with increased natural selection driving use of specific codons, resulting in higher genome-wide CUB. We expect that the higher levels of CUB in Chaetomiaceae genomes might have been caused by ecological niche specialization, including high optimal growth temperature of some Chaetomiaceae species.

genomics↗

bioRxiv2025

Reconstructing NOD-like receptor alleles with high internal conservation in Podospora anserina using long-read sequencing

NOD-like receptors (NLRs) are intracellular immune receptors that detect pathogen-associated cues and trigger defense mechanisms, including regulated cell death. In filamentous fungi, some NLRs mediate heterokaryon incompatibility, a self/non-self recognition process that prevents the vegetative fusion of genetically distinct individuals, reducing the risk of parasitism. The het-d and het-e NLRs in Podospora anserina are highly polymorphic incompatibility genes (het genes) whose products recognize different alleles of the het-c gene via a sensor domain composed of WD40 repeats. These repeats display unusually high sequence identity maintained by concerted evolution. However, some sites within individual repeats are hypervariable and under diversifying selection. Despite extensive genetic studies, inconsistencies in the reported WD40 domain sequence have hindered functional and evolutionary analyses. Here we demonstrate that the WD40 domain can be accurately reconstructed from long-read sequencing (Oxford Nanopore and PacBio) data, but not from Illumina-based assemblies. Functional alleles are usually formed by 11 highly conserved repeats, with different repeat combinations underlying the same phenotypic het-d and het-e incompatibility reactions. Protein structure models suggest that their WD40 domain folds into two 7-blade {beta}-propellers composed of the highly conserved repeats, as well as three cryptic divergent repeats at the C-terminus. We additionally show that one particular het-e allele does not have an incompatibility reaction with common het-c alleles, despite being 11-repeats long. Our findings provide a robust foundation for future research into the molecular mechanisms and evolutionary dynamics of het NLRs, while also highlighting both the fragility and the flexibility of {beta}-propellers as immune sensor domains.

genomics↗

bioRxiv2024

Multipartite complexity of the lichen symbiosis revealed by metagenome and transcriptome analysis of Xanthoria parietina

Lichens are composite symbiotic associations of fungi, algae, and bacteria that result in large, anatomically complex organisms adapted to many of the worlds most challenging environments. How such intricate, self-replicating lichen architectures develop from simple microbial components remains unknown because of their recalcitrance to experimental manipulation. Here we report a metagenomic and metatranscriptomic analysis of the lichen Xanthoria parietina at different developmental stages. We identified 168 genomes of symbionts and lichen-associated microbes within a lichen thallus, including representatives of green algae, three different classes of fungi, and 14 bacterial phyla. By analyzing occurrence of individual species across lichen thalli from diverse environments, we defined both substrate-specific and core microbial components of the lichen. Meta-transcriptomic analysis of the principal fungal symbiont from three different developmental stages of a lichen, compared to axenically grown fungus, revealed differential gene expression profiles indicative of lichen-specific transporter functions, specific cell signalling, transcriptional regulation and secondary metabolic capacity. Putative immunity-related proteins and lichen-specific structurally conserved secreted proteins resembling fungal pathogen effectors were also identified, consistent with a role for immunity modulation in lichen morphogenesis.

bioinformatics↗

bioRxiv2023

High-quality genome assemblies of four members of the Podospora anserina species complex

The filamentous fungus Podospora anserina is a model organism used extensively in the study of molecular biology, senescence, prion biology, meiotic drive, mating-type chromosome evolution, and plant biomass degradation. It has recently been established that P. anserina is a member of a complex of seven, closely related species. In addition to P. anserina, high-quality genomic resources are available for two of these taxa. Here we provide chromosome-level annotated assemblies of the four remaining species of the complex, as well as a comprehensive dataset of annotated assemblies from a total of 28 Podospora genomes. We find that all seven species have genomes of around 35 Mbp arranged in seven chromosomes that are mostly collinear and less than 2% divergent from each other at genic regions. We further attempt to resolve their phylogenetic relationships, finding significant levels of phylogenetic conflict as expected from a rapid and recent diversification. SignificanceHere we provide a dataset of 28 annotated genomes from the P. anserina species complex, including chromosome-level assemblies of four species that lacked a reference genome. With this dataset in hand, biologists can take advantage of the molecular tools available for P. anserina to study evolutionary dynamics at the interphase between micro- and macroevolution, with particular emphasis on trait evolution, genome architecture, and speciation.

genomics↗

bioRxiv2023

Purifying Selection and Persistent Polymorphism among Nuclei in the Multinucleate Arbuscular Mycorrhizal (AM) Fungi

Arbuscular mycorrhizal (AM) fungi form obligate symbiosis with the roots of the majority of land plants and are found in all terrestrial ecosystems. The source and structure of genetic variation in AM fungi has remained an enigma due to difficulties in the axenic cultivation and generation of high-quality genome assemblies from most species. Furthermore, how AM fungi survives long-term without a single nuclear stage per cell life history is puzzling, prompting hypotheses on selection at the nuclear level which functions to purge deleterious mutations. In this study, we aimed to characterize both intra- and inter-organismal genetic variation in AM fungi by analyzing genomic information from individual nuclei of three strains from two species of the genus Claroideoglomus. We observed overall low levels of genetic variation within the strains, most of which represent rare variants likely kept at low frequency by purifying selection. We also observed variants that have been maintained as polymorphic across both strains and species. The results in this study affirm our conceptual understanding that nuclei in AM fungal strains function as populations of asexually reproducing units. Further, we propose that selection acts on different levels within the organism, with strong signals of purifying selection on nuclei within strain.

evolutionary biology↗

bioRxiv2021

In-depth phylogenomic analysis of arbuscular mycorrhizal fungi based on a comprehensive set of de novo genome assemblies

O_LIMorphological characters and nuclear ribosomal DNA (rDNA) phylogenies have so far been the basis of the current classifications of arbuscular mycorrhizal (AM) fungi. Improved understanding of the phylogeny and evolutionary history of AM fungi requires extensive ortholog sampling and analyses of genome and transcriptome data from a wide range of taxa. C_LIO_LITo circumvent the need for axenic culturing of AM fungi we gathered and combined genomic data from single nuclei to generate de novo genome assemblies covering seven families of AM fungi. Comparative analysis of the previously published Rhizophagus irregularis DAOM197198 assembly confirm that our novel workflow generates high-quality genome assemblies suitable for phylogenomic analysis. Predicted genes of our assemblies, together with published protein sequences of AM fungi and their sister clades, were used for phylogenomic analyses. C_LIO_LIBased on analyses of sets of orthologous genes, we highlight three alternative topologies among families of AM fungi. In the main topology, Glomerales is polyphyletic and Claroideoglomeraceae, is the basal sister group to Glomeraceae and Diversisporales. C_LIO_LIOur results support family level classification from previous phylogenetic studies. New evolutionary relationships among families where highlighted with phylogenomic analysis using the hitherto most extensive taxon sampling for AM fungi. C_LI

genomics↗

bioRxiv2020

The plot thickens: haploid and triploid-like thalli, hybridization, and biased mating type ratios in Letharia

The study of the reproductive biology of lichen fungal symbionts has been traditionally challenging due to their complex and symbiotic lifestyles. Against the common belief of haploidy, a recent genomic study found a triploid-like signal in Letharia. Here, we used genomic data from a pure culture and from thalli, together with a PCR survey of the MAT locus, to infer the genome organization and reproduction in Letharia. We found that the read count variation in the four Letharia specimens, including the pure culture derived from a single sexual spore of L. lupina, is consistent with haploidy. By contrast, the L. lupina read counts from a thallus metagenome are triploid-like. Characterization of the mating-type locus revealed a conserved heterothallic configuration across the genus, along with auxiliary genes that we identified. We found that the mating-type distributions are balanced in North America for L. vulpina and L. lupina, suggesting widespread sexual reproduction, but highly skewed in Europe for L. vulpina, consistent with predominant asexuality. Taken together, we propose that Letharia fungi are heterothallic and typically haploid, and provide evidence that triploid-like individuals are rare hybrids between L. lupina and an unknown Letharia lineage, reconciling classic systematic and genetic studies with recent genomic observations.

evolutionary biology↗

bioRxiv2020

Meiotic drive is associated with sexual incompatibility in Neurospora

Meiotic drive is the phenomenon whereby selfish elements bias their transmission to progeny at ratios above 50:50, violating Mendels law of equal segregation. The model fungus Neurospora carries three different meiotic drivers, called Spore killers. Two of these, Sk-2 and Sk-3, are multilocus spore killers that constitute large haplotypes and are found in the species N. intermedia. Here we used molecular markers to determine that all N. intermedia isolates from New Zealand in fact belong to the sister species N. metzenbergii. Additionally, we use laboratory crosses to demonstrate that Sk-2 and Sk-3 are involved in sexual incompatibility between N. intermedia and N. metzenbergii.. Our experiments revealed that while crosses between these two species normally produced viable progeny at appreciable rates, when strains of N. intermedia carried Sk-2 or Sk-3 the proportion of viable progeny dropped substantially and in some crosses, no viable progeny were observed. Backcrossings supported that the incompatibility is tightly linked to the Sk haplotype. Finally, it appears that Sk-2 and Sk-3 have accumulated different incompatibility phenotypes when crossed with N. metzenbergii strains, consistent with their independent evolutionary history. This research illustrates how meiotic drive can contribute to reproductive isolation between populations, and thereby speciation.

evolutionary biology↗

bioRxiv2020

Transposon- and genome dynamics in the fungal genus Neurospora: insights from nearly gapless genome assemblies

BackgroundA large portion of nuclear DNA is composed of transposable element (TE) sequences, whose transposition is controlled by diverse host defense strategies in order to maintain genomic integrity. One such strategy is the fungal-specific Repeat-Induced Point (RIP) mutation that hyper-mutates repetitive DNA sequences. While RIP is found across Fungi, it has been shown to vary in efficiency. To date, detailed information on the TE landscapes and associated RIP patterns exist only in a few species belonging to highly divergent lineages. ResultWe investigated 18 nearly gapless genome assemblies of ten Neurospora species, which diverged from a common ancestor about 7 MYA, to determine genome-wide TE distribution and their associated RIP patterns. We showed that the TE contents between 8.7-18.9% covary with genome sizes that range between 37.8-43.9 Mb. Degraded copies of Long Terminal Repeat (LTR) retrotransposons were abundant among the identified TEs, and these are distributed across the genome at varying frequencies. In all investigated genomes, TE sequences had signs of numerous C-to-T substitutions, suggesting that RIP occurred in all species. RIP signatures in all genomes correlated with TE-dense regions. ConclusionsEssentially gapless genome assemblies allowed us to identify TEs in Neurospora genomes, and reveal that TEs contribute to genome size variation in this group. Our study suggests that TEs and RIP are highly correlated in Neurospora, and hence, the pattern of interaction is conserved over the investigated evolutionary timescale. We show that RIP signatures can be used to facilitate the identification of TE-rich region in the genome.

genomics↗

bioRxiv2020

AnVIL: An overlap-aware genome assembly scaffolder for linked reads

10X Genomics Chromium linked reads contain information that can be used to link sequences together into scaffolds in draft genome assemblies. Existing software for this purpose perform the scaffolding by joining sequences together with a gap between them, not considering potential contig overlaps. Such overlaps can be particularly prominent in genome drafts assembled from long-read sequencing data where an overlap-layout-consensus (OLC) algorithm has been used. Ignoring overlapping contig ends may result in genes and other features being incomplete or fragmented in the resulting scaffolds. We developed the application ARBitR to generate scaffolds from genome drafts using 10X Chromium data, with a focus on minimizing the number of gaps in resulting scaffolds by incorporating an OLC step to resolve junctions between linked contigs. We tested the performance of ARBitR on three published and simulated datasets and compared to the previously published tools ARCS and ARKS. The results revealed that ARBitR performed similarly considering contiguity statistics, and the advantage of the overlapping step was revealed by fewer long and short variants in ARBitR produced scaffolds, in addition to a higher proportion of completely assembled LTR retrotransposons. We expect ARBitR to have broad applicability in genome assembly projects that utilize 10X Chromium linked reads. Availability and implementationARBitR is written and implemented in Python3 for Unix-like operative systems. All source code is available at https://github.com/markhilt/ARBitR under the GNU General Public License v3. Contactmarkus.hiltunen@ebc.uu.se Supplementary informationavailable online

bioinformatics↗

bioRxiv2020

Invasion and maintenance of spore killing in ascomycete fungi

Meiotic drivers are selfish genetic elements that are able to become over-represented among the products of meiosis. This transmission advantage makes it possible for them to spread in a population even when they impose fitness costs on their host organisms. Whether a meiotic driver can invade a population, and subsequently reach fixation or coexist in a stable polymorphism, depends on the one hand on the biology of the host organism, including its life-cycle, mating system, and population structure, and on the other hand on the specific fitness effects of the driving allele on the host. Here, we present a population genetic model for spore killing, a type of drive specific to fungi. We show how ploidy level, rate of selfing, and efficiency of spore killing affect the invasion probability of a driving allele and the conditions for its stable coexistence with the non-driving allele. Our model can be adapted to different fungal life-cycles, and is applied here to two well-studied genera of filamentous ascomycetes known to harbor spore killing elements, Neurospora and Podospora. We discuss our results in the light of recent empirical findings for these two systems.

evolutionary biology↗

bioRxiv2020

The Enterprise: A massive transposon carrying Spok meiotic drive genes

The genomes of eukaryotes are full of parasitic sequences known as transposable elements (TEs). Most TEs studied to date are relatively small (50 - 12000 bp), but can contribute to very large proportions of genomes. Here we report the discovery of a giant tyrosine-recombinase-mobilized DNA transposon, Enterprise, from the model fungus Podospora anserina. Previously, we described a large genomic feature called the Spok block which is notable due to the presence of meiotic drive genes of the Spok gene family. The Spok block ranges from 110 kb to 247 kb and can be present in at least four different genomic locations within P. anserina, despite what is an otherwise highly conserved genome structure. We have determined that the reason for its varying positions is that the Spok block is not only capable of meiotic drive, but is also capable of transposition. More precisely, the Spok block represents a unique case where the Enterprise has captured the Spoks, thereby parasitizing a resident genomic parasite to become a genomic hyperparasite. Furthermore, we demonstrate that Enterprise (without the Spoks) is found in other fungal lineages, where it can be as large as 70 kb. Lastly, we provide experimental evidence that the Spok block is deleterious, with detrimental effects on spore production in strains which carry it. In contrast to the selfish role of the Enterprise in P. anserina, we hypothesize that the mobility of the Enterprise may also play an adaptive role in fungi when Enterprise undergoes horizontal transfer while carrying metabolic genes. This union of meiotic drivers and a transposon has created a selfish element of impressive size in Podospora, challenging our perception of how TEs influence genome evolution and broadening the horizons in terms of what the upper limit of transposition may be.

genomics↗

bioRxiv2020

An introgressed gene causes meiotic drive in Neurospora sitophila

Meiotic drive elements cause their own preferential transmission following meiosis. In fungi this phenomenon takes the shape of spore killing, and in the filamentous ascomycete Neurospora sitophila, the Sk-1 spore killer element is found in many natural populations. In this study, we identify the gene responsible for spore killing in Sk-1 by generating both long and short-read genomic data and by using these data to perform a genome wide association test. Through molecular dissection, we show that a single 405 nucleotide long open reading frame generates a product that both acts as a poison capable of killing sibling spores and as an antidote that rescues spores that produce it. By phylogenetic analysis, we demonstrate that the gene is likely to have been introgressed from the closely related species N. hispaniola, and we identify three subclades of N. sitophila, one where Sk-1 is fixed, another where Sk-1 is absent, and a third where both killer and sensitive strain are found. Finally, we show that spore killing can be suppressed through an RNA interference based genome defense pathway known as meiotic silencing by unpaired DNA. Spk-1 is not related to other known meiotic drive genes, and similar sequences are only found within Neurospora. These results shed new light on the diversity of genes capable of causing meiotic drive, their origin and evolution and their interaction with the host genome. Significance StatementIn order to survive, most organisms have to deal with parasites. Such parasites can be other organisms, or sometimes, selfish genes found within the host genome itself. While much is known about parasitic organisms, the interaction with their hosts and their ability to spread within and between species, much less is known about selfish genes. We here identify a novel selfish "spore killer" gene in the fungus Neurospora sitophila. The gene appears to have evolved within the genus, but has entered the species through hybridization and introgression. We also show that the host can counteract the gene through RNA interference. These results shed new light on the diversity of selfish genes in terms of origin, evolution and host interactions.

evolutionary biology↗

bioRxiv2019

From single nuclei to whole genome assembly

A large proportion of Earth's biodiversity constitutes organisms that cannot be cultured, have cryptic life-cycles and/or live submerged within their substrates1-4. Genomic data are key to unravel both their identity and function5. The development of metagenomic methods6,7 and the advent of single cell sequencing8-10 have revolutionized the study of life and function of cryptic organisms by upending the need for large and pure biological material, and allowing generation of genomic data from complex or limited environmental samples. Genome assemblies from metagenomic data have so far been restricted to organisms with small genomes, such as bacteria11, archaea12 and certain eukaryotes13. On the other hand, single cell technologies have allowed the targeting of unicellular organisms, attaining a better resolution than metagenomics8,9,14-16, moreover, it has allowed the genomic study of cells from complex organisms one cell at a time17,18. However, single cell genomics are not easily applied to multicellular organisms formed by consortia of diverse taxa, and the generation of specific workflows for sequencing and data analysis is needed to expand genomic research to the entire tree of life, including sponges19, lichens3,20, intracellular parasites21,22, and plant endophytes23,24. Among the most important plant endophytes are the obligate mutualistic symbionts, arbuscular mycorrhizal (AM) fungi, that pose an additional challenge with their multinucleate coenocytic mycelia25. Here, the development of a novel single nuclei sequencing and assembly workflow is reported. This workflow allows, for the first time, the generation of reference genome assemblies from large scale, unbiased sorted, and sequenced AM fungal nuclei circumventing tedious, and often impossible, culturing efforts. This method opens infinite possibilities for studies of evolution and adaptation in these important plant symbionts and demonstrates that reference genomes can be generated from complex non-model organisms by isolating only a handful of their nuclei.

genomics↗

bioRxiv2019

Combinations of Spok genes create multiple meiotic drivers in Podospora

Meiotic drive is the preferential transmission of a particular allele at a given locus during sexual reproduction. The phenomenon is observed as spore killing in a variety of fungal lineages, including Podospora. In natural populations of Podospora anserina, seven spore killers (Psks) have been identified through classical genetic analyses. Here we show that the Spok gene family underlie the Psk spore killers. The combination of the various Spok genes at different chromosomal locations defines the spore killers and creates a killing hierarchy within the same population. We identify two novel Spok homologs that are located within a complex region (the Spok block) that reside in different chromosomal locations in given natural strains. We confirm that the individual SPOK proteins perform both the killing and resistance functions and show that these activities are dependent on distinct domains, a nuclease and a kinase domain respectively. Genomic data and phylogenetic analysis across ascomycetes suggest that the Spok genes disperse via cross-species transfer, and evolve by duplication and diversification within several lineages.

genetics↗