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Maximum clade credibility chronogram for the major groups of Ascomycota. The chronogram is the result from the BEAST analysis of Scenario 4. Each node represents the mean divergence time estimate and bars show their associated 95% credibility interval. Numbers corresponding to dated groups shown in Table 3 are written above the nodes.
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Establishing the dates for the origin and main diversification events in the phylogeny of Ascomycota is among the most crucial remaining goals in understanding the evolution of Fungi. There have been several analyses of divergence times in the fungal tree of life in the last two decades, but most have yielded contrasting results for the origin of t...
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Many insects with long-proboscid mouthparts are among the pollinators of seed plants. Several cases of the long-proboscid pollination mode are known between fossil insects (e.g., true flies, scorpionflies, and lacewings) and various extinct gymnosperm lineages, beginning in the Early Permian and increasing during the Middle Jurassic to Early Cretac...
Citations
... We identified two examples of HGT within ascomycete fungi where the same elements have recently generated introns among highly divergent lineages (Fig. 3A). Xylaria and Lasiodiplodia last shared a common ancestor approximately 350 MYA (29,30). Nonetheless, each species' genome contains an introner family with 83.8% sequence similarity across the complete 134bp sequence between elements found in either lineage ( Fig. 3B; table S4). ...
Specialized transposable elements (TEs), introners, are one of the major drivers of intron gain in diverse eukaryotes. However, the molecular mechanism(s) and evolutionary processes driving introner propagation within and between lineages remain elusive. We analyze 8716 genomes, revealing 1093 introner families in 201 species spanning 1.7 billion years of evolution. Introners are derived from functionally diverse TEs including families of terminal-inverted-repeat DNA TEs, retrotransposons, cryptons, and helitrons as well as mobile elements with unknown molecular mechanisms. We identify eight cases where introners recently transferred between divergent host species, and show that giant viruses that integrate into genomes may facilitate introner transfer across lineages. We propose that intron gain is an inevitable consequence of TE activity in eukaryotic lineages, thereby resolving a key mystery of genome structure evolution.
... The 3′ region of the cytochrome B assembly factor CBP3 illustrates this. Experiments have shown that the RNA-binding protein Puf3 binds 3′ UTR of this gene in S. cerevisiae and the far diverged (about 500 Mya [20]) Neurospora crassa [21]. Moreover, we found that the Puf3 consensus binding motif can be found 3′ to the stop of the CBP3 homolog in almost all yeasts. ...
Background
The rise of large-scale multi-species genome sequencing projects promises to shed new light on how genomes encode gene regulatory instructions. To this end, new algorithms are needed that can leverage conservation to capture regulatory elements while accounting for their evolution.
Results
Here, we introduce species-aware DNA language models, which we trained on more than 800 species spanning over 500 million years of evolution. Investigating their ability to predict masked nucleotides from context, we show that DNA language models distinguish transcription factor and RNA-binding protein motifs from background non-coding sequence. Owing to their flexibility, DNA language models capture conserved regulatory elements over much further evolutionary distances than sequence alignment would allow. Remarkably, DNA language models reconstruct motif instances bound in vivo better than unbound ones and account for the evolution of motif sequences and their positional constraints, showing that these models capture functional high-order sequence and evolutionary context. We further show that species-aware training yields improved sequence representations for endogenous and MPRA-based gene expression prediction, as well as motif discovery.
Conclusions
Collectively, these results demonstrate that species-aware DNA language models are a powerful, flexible, and scalable tool to integrate information from large compendia of highly diverged genomes.
... The reconciled species tree was generated from single-copy orthologs and accounted for 64,810 individual sites. The tree was then made ultrametric with r8s (Sanderson 2003), constraining the Microascaceae node between 171 and 241 MYA, the Onygenales node between 83 and 193 MYA, the Eurotiales node between 73 and 169 MYA, and the Dothideomycetes crown between 93 and 252 MYA (Prieto and Wedin 2013;Hyde et al. 2020). Rates and times were estimated with the penalized likelihood and truncated Newton methods. ...
Emerging fungal pathogens are a global challenge for humankind. Many efforts have been made to understand the mechanisms underlying pathogenicity in bacteria, and OMICs techniques are largely responsible for those advancements. By contrast, our limited understanding of opportunism and antifungal resistance is preventing us from identifying, limiting and interpreting the emergence of fungal pathogens. The genus Scedosporium (Microascaceae) includes fungi with high tolerance to environmental pollution, whilst some species can be considered major human pathogens, such as Scedosporium apiospermum and Scedosporium boydii. However, unlike other fungal pathogens, little is known about the genome evolution of these organisms. We sequenced two novel genomes of Scedosporium aurantiacum and Scedosporium minutisporum isolated from extreme, strongly anthropized environments. We compared all the available Scedosporium and Microascaceae genomes, that we systematically annotated and characterized ex novo in most cases. The genomes in this family were integrated in a Phylum-level comparison to infer the presence of putative, shared genomic traits in filamentous ascomycetes with pathogenic potential. The analysis included the genomes of 100 environmental and clinical fungi, revealing poor evolutionary convergence of putative pathogenicity traits. By contrast, several features in Microascaceae and Scedosporium were detected that might have a dual role in responding to environmental challenges and allowing colonization of the human body, including chitin, melanin and other cell wall related genes, proteases, glutaredoxins and magnesium transporters. We found these gene families to be impacted by expansions, orthologous transposon insertions, and point mutations. With RNA-seq, we demonstrated that most of these anciently impacted genomic features responded to the stress imposed by an antifungal compound (voriconazole) in the two environmental strains S. aurantiacum MUT6114 and S. minutisporum MUT6113. Therefore, the present genomics and transcriptomics investigation stands on the edge between stress resistance and pathogenic potential, to elucidate whether fungi were pre-adapted to infect humans. We highlight the strengths and limitations of genomics applied to opportunistic human pathogens, the multifactoriality of pathogenicity and resistance to drugs, and suggest a scenario where pressures other than anthropic contributed to forge filamentous human pathogens.
Supplementary Information
The online version contains supplementary material available at 10.1186/s43008-023-00128-3.
... It has been widely used and it is still used in dating the fungal tree of life 26 . However, whether it is basal to the Ascomycota or nested within the subphylum Pezizomycotina is contentious and its position varies depending on the studies and data used leading to strikingly different age estimates for the same divergence events (e.g., 26,[64][65][66][67][68][69]. For example, Lücking et al. 66 considered using this fossil to calibrate three alternative positions in the Ascomycota tree: origin of Sordariomycetes, divergence of Pezizomycotina, and origin of Pezizomycotina. ...
Fungi are integral to well-functioning ecosystems, and their broader impact on Earth systems is widely acknowledged. Fossil evidence from the Rhynie Chert (Scotland, UK) shows that Fungi were already diverse in terrestrial ecosystems over 407-million-years-ago, yet evidence for the occurrence of Dikarya ( the subkingdom of Fungi that includes the phyla Ascomycota and Basidiomycota ) in this site is scant. Here we describe a particularly well-preserved asexual fungus from the Rhynie Chert which we examined using brightfield and confocal microscopy. We document Potteromyces asteroxylicola gen. et sp. nov. that we attribute to Ascomycota incertae sedis (Dikarya) . The fungus forms a stroma-like structure with conidiophores arising in tufts outside the cuticle on aerial axes and leaf-like appendages of the lycopsid plant Asteroxylon mackiei . It causes a reaction in the plant that gives rise to dome-shaped surface projections. This suite of features in the fungus together with the plant reaction tissues provides evidence of it being a plant pathogenic fungus. The fungus evidently belongs to an extinct lineage of ascomycetes that could serve as a minimum node age calibration point for the Ascomycota as a whole, or even the Dikarya crown group, along with some other Ascomycota previously documented in the Rhynie Chert.
... Ancient and ongoing evolutionary processes generated the diversity of resource use and growth traits that we observe. The deep evolutionary origins of taxa constituting slow-and fast-growing assemblages is demonstrated by their distinction at the class and order level (Fig 3), divergences encompassing over 120-300 million years [98][99][100][101]. Within the Sordariomycetes, a fungal class often represented in endophytic communities of grasses [12, 65,68,89,[102][103][104], differences in growth traits characterize taxa belonging to different orders (Fig 3). ...
Eukaryotic hosts harbor tremendously diverse microbiomes that affect host fitness and response to environmental challenges. Fungal endophytes are prominent members of plant microbiomes, but we lack information on the diversity in functional traits affecting their interactions with their host and environment. We used two culturing approaches to isolate fungal endophytes associated with the widespread, dominant prairie grass Andropogon gerardii and characterized their taxonomic diversity using rDNA barcode sequencing. A randomly chosen subset of fungi representing the diversity of each leaf was then evaluated for their use of different carbon compound resources and growth on those resources. Applying community phylogenetic analyses, we discovered that these fungal endophyte communities are comprised of phylogenetically distinct assemblages of slow- and fast-growing fungi that differ in their use and growth on differing carbon substrates. Our results demonstrate previously undescribed and cryptic functional diversity in carbon resource use and growth in fungal endophyte communities of A. gerardii.
... The data by gene was partitioned, with unlinked partitions with the GTR + G substitution model for each partition, and base frequencies were estimated simultaneously, using four gamma categories. The uncorrelated lognormal relaxed clock model was used, which allows rates of molecular evolution to be uncorrelated across the tree (Prieto et al. 2013). For the trees, a Yule tree prior was used, which assumes a constant speciation rate per lineage, and a randomly generated starting tree. ...
Rhytisma Fr. is the type genus of Rhytismataceae (Rhytismatales, Leotiomycetes, Ascomycota). Rhytisma-like species include members of Cryptomyces, Rhytisma and Vladracula. They are parasites on leaves of broadleaf trees and cause tar spot diseases. In this study, a phylogeny based on the large subunit of the ribosomal rRNA gene (nrLSU) and the mitochondrial small subunit (mtSSU) is presented, including sequences of 39 newly collected specimens from East Asia, Europe, and temperate as well as tropical America. Based on analyses of morphology, phylogeny as well as host-specificity and diversification time estimates, the family Rhytismataceae sensu stricto is proposed, and eight genera are accepted in this narrow family, including four novel genera (Densorhytisma, Fanglania, Johnstoniella and Shiqia), the type genus Rhytisma, and the reinstated genera Lophodermina, Placuntium and Xyloma. Lophodermina clusters within the main Rhytisma clade in our analyses, but is divergent in morphological terms, not having large compound stromata. Thirty species are recognized, including seven novel species (Fanglania hubeiensis, F. parasitica, Johnstoniella yunnanensis, Rhytisma japonicum, Rh. taiwanense, Xyloma globosum, and X. shennongjiaense), fifteen new combinations (Densorhytisma anhuiense, D. huangshanense, F. concova, F. himalensis, F. ilicis-integrae, F. ilicis-latifoliae, F. ilicis-pedunculosae, J. lonicerae, Rh. annuliforme, Shiqia menziesii, S. yuexiensis, X. filamentosum, X. maximum, X. muelleri, and X. polare), one new name (J. xylostei), seven known species (Lophodermina melaleuca, Placuntium andromedae, Rhytisma acerinum, Rh. americanum, Rh. punctatum, X. salicinum, and X. umbonatum). In addition, seven immature specimens were studied but not assigned to existing species, herein referred to as Fanglania sp. 1, Johnstoniella sp. 1, Johnstoniella sp. 2, Placuntium sp. 1, Placuntium sp. 2, Rhytisma sp. 1, and Xyloma sp. 1. The systematic positions of Cryptomyces maximus, Cr. muelleri and Vladracula annuliformis are re-assigned based on phylogenetic analysis. One Rhytisma-like species from tropical America was segregated from Rhytismataceae s.str., thus a novel genus Neorhytisma was established to accommodate this species, with the one new combinations Neorhytisma panamense. The results of the molecular phylogenetic analysis indicate that Rhytisma-like species are host-specific at genus level. Apparently, Rhytisma-like species coevolved with their hosts, and Rhytisma-like species on Ericaceae seem to be in the process of host jumping. Morphological characteristics of ascomata are important for the delimitation of species and genera of Rhytisma-like species. This study provides a key to genera and species of recognized Rhytisma-like species worldwide.
... existing hypotheses suggest that ancestral nitrilases diversified in animals and plants before horizontal transfer into microbial lineages (Pace and Brenner, 2001). The last common ancestors of crown Viridiplantae, crown Metazoa, and crown Ascomycota are predicted to be, at maximum, 972 Ma (Morris et al., 2018), 834 Ma (Dos Reis et al., 2015), and 671 Ma (Prieto and Wedin, 2013), respectively-all younger than the lowest bound of the youngest predicted age distribution for nitrilases. The predicted age of the nitrilases in the tree is therefore inconsistent with the diversification of these enzymes within eukaryotes. ...
In addition to its role as a toxic environmental contaminant, cyanide has been hypothesized to play a key role in prebiotic chemistry and early biogeochemical evolution. While cyanide-hydrolyzing enzymes have been studied and engineered for bioremediation, the extant diversity of these enzymes remains underexplored. Additionally, the age and evolution of microbial cyanide metabolisms is poorly constrained. Here we provide comprehensive phylogenetic and molecular clock analyses of the distribution and evolution of the Class I nitrilases, thiocyanate hydrolases, and nitrile hydratases. Molecular clock analyses indicate that bacterial cyanide-reducing nitrilases were present by the Paleo- to Mesoproterozoic, and were subsequently horizontally transferred into eukaryotes. These results present a broad diversity of microbial enzymes that could be optimized for cyanide bioremediation.
... In any case, resinicolous Chaenothecopsis species from various ambers prove that this ecological mode on conifer resin has existed within the genus for at least 35 million years (Rikkinen and Poinar 2000;Tuovila et al. 2013;. Recent estimates of divergence times of the Ascomycota place the separation of Mycocaliales and Eurotiomycetes in the Carboniferous (Prieto and Wedin 2013;Beimforde et al. 2014) and the origin of the Mycocaliciales crown group in the late Jurassic, when diverse conifer lineages were present (Lubna et al. 2021). It is possible that Mycocaliciales could have colonized conifers at an early stage of conifer evolution in the Permian, and it might well be that the resinicolous ecology evolved at a very early stage within Mycocaliciales. ...
The order Mycocaliciales (Ascomycota) comprises fungal species with diverse, often highly specialized substrate ecologies. Particularly within the genus Chaenothecopsis , many species exclusively occur on fresh and solidified resins or other exudates of vascular plants. In New Zealand, the only previously known species growing on plant exudate is Chaenothecopsis schefflerae , found on several endemic angiosperms in the family Araliaceae. Here we describe three new species; Chaenothecopsis matai Rikkinen, Beimforde, Tuovila & A.R. Schmidt, C. nodosa Beimforde, Tuovila, Rikkinen & A.R. Schmidt, and C. novae-zelandiae Rikkinen, Beimforde, Tuovila & A.R. Schmidt, all growing on exudates of endemic New Zealand conifers of the Podocarpaceae family, particularly on Prumnopitys taxifolia . Phylogenetic analyses based on ribosomal DNA regions (ITS and LSU) grouped them into a distinct, monophyletic clade. This, as well as the restricted host range, suggests that all three taxa are endemic to New Zealand. Copious insect frass between the ascomata contain ascospores or show an early stage of ascomata development, indicating that the fungi are spread by insects. The three new species represent the first evidence of Chaenothecopsis from any Podocarpaceae species and the first from any gymnosperm exudates in New Zealand.
... However, there is a fossil record referred to Alternaria described as Polycellaesporonites alternariatus (Kalgutkar & Sigler) Kalgutkar & Janson (≡ Piriurella alternariata Kalgutkar & Sigler). Polycellaesporonites alternariatus was first described as Piriurella alternariata by Kalgutkar & Sigler [123] for the fungal fossilproduced dictyosporae spore group. The species was referred to Alternaria in forming muriform, ovoid to obclavate, rostrate, pale brown to brown conidia, arising singly or in clusters, with transverse septa more prominent and thicker than the longitudinal or oblique septa. ...
... The species was referred to Alternaria in forming muriform, ovoid to obclavate, rostrate, pale brown to brown conidia, arising singly or in clusters, with transverse septa more prominent and thicker than the longitudinal or oblique septa. The broader basal region distally tapered to a short or cylindrical beak with or without a dark thickened tip [123] . The species was found from Iceberg Bay formation at Kanguk Peninsula, Axel Heiberg Island and Northwest Territories, Canada with an estimated age during the late Palaeocene or early Eocene (40.4-58.7 MYA) [123] . ...
... The broader basal region distally tapered to a short or cylindrical beak with or without a dark thickened tip [123] . The species was found from Iceberg Bay formation at Kanguk Peninsula, Axel Heiberg Island and Northwest Territories, Canada with an estimated age during the late Palaeocene or early Eocene (40.4-58.7 MYA) [123] . However, the link between P. alternariatus and Alternaria has not yet been confirmed due to Alternaria being variable in shape, size and septation of conidium and was shown to be a species complex [11][12][13][14]22,55,123] . ...
Alternaria, a genus of ascomycetes, comprises major plant pathogens, saprobes and are common allergens to humans. There are more than 360 accepted species in the genus, which are currently divided into 29 sections. This paper aims to elaborate the taxonomy of Alternaria with multi-locus phylogenetic trees derived by analyses of a concatenated DNA sequence dataset consisting of ITS, LSU, TEF1-α, RPB2, GAPDH and Alt-a1 loci. Eighteen new species viz. Alternariaarctoseptata, A. arundinis,A. baoshanensis, A. breviconidiophora,A. brevirostra,A. ellipsoidialis,A. eupatoriicola,A. falcata,A. lathyri, A. macilenta,A.macroconidia,A. minimispora,A. nodulariconidiophora, A. oblongoellipsoidea, A. orobanches, A. phragmiticola,A.phytolaccae and A. salicicola are introduced and classified in sect. Alternaria, sect. Infectoriae, sect. Porri and sect. Radicina.Alternaria alternata andA. doliconidium are also described herein with new host and geographical records, in China, Italy, and Thailand. This study further explores the utility of divergent time estimates to gain additional insights into the evolutionary relationships of Alternaria in Pleosporales.
... However, there is a fossil record referred to Alternaria described as Polycellaesporonites alternariatus (Kalgutkar & Sigler) Kalgutkar & Janson (≡ Piriurella alternariata Kalgutkar & Sigler). Polycellaesporonites alternariatus was first described as Piriurella alternariata by Kalgutkar & Sigler [123] for the fungal fossilproduced dictyosporae spore group. The species was referred to Alternaria in forming muriform, ovoid to obclavate, rostrate, pale brown to brown conidia, arising singly or in clusters, with transverse septa more prominent and thicker than the longitudinal or oblique septa. ...
... The species was referred to Alternaria in forming muriform, ovoid to obclavate, rostrate, pale brown to brown conidia, arising singly or in clusters, with transverse septa more prominent and thicker than the longitudinal or oblique septa. The broader basal region distally tapered to a short or cylindrical beak with or without a dark thickened tip [123] . The species was found from Iceberg Bay formation at Kanguk Peninsula, Axel Heiberg Island and Northwest Territories, Canada with an estimated age during the late Palaeocene or early Eocene (40.4-58.7 MYA) [123] . ...
... The broader basal region distally tapered to a short or cylindrical beak with or without a dark thickened tip [123] . The species was found from Iceberg Bay formation at Kanguk Peninsula, Axel Heiberg Island and Northwest Territories, Canada with an estimated age during the late Palaeocene or early Eocene (40.4-58.7 MYA) [123] . However, the link between P. alternariatus and Alternaria has not yet been confirmed due to Alternaria being variable in shape, size and septation of conidium and was shown to be a species complex [11][12][13][14]22,55,123] . ...
