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Best scoring ML tree with RAxML and GARLI bootstrap values respectively above (green) and below (red) the nodes. Values below 50 % were removed and branches with more than 90 % bootstrap for both methods are thickened without values. Environmental sources relevant to the papers in this volume are indicated in the key (R-Rock; M-Marine; F-Freshwater; D-Dung; B-Bamboo). Nutritional characters are indicated by colour as per the key.
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We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41 families (six newly described in this volume) in Dothideomycetes. All currently accepted orders in the class are represented for the first time in addition to numerous previously unplaced lineages. Subclass Pleosporomycetidae...
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Most reconstruction methods for genomes of ancient origin that are used today require a closely related reference. In order to identify genomic rearrangements or the deletion of whole genes, de novo assembly has to be used. However, because of inherent problems with ancient DNA, its de novo assembly is highly complicated. In order to tackle the div...
Citations
... The phylogenetic analysis of the nrLSU DNA locus showed that sequences of A. parasitica are located in a well-supported subclade together with other species of Pleosporales s.l., such as Ellismarsporium parvum (Zhang et al. 2020). Many species of the Dothideomycetes, especially the asexual genera, are known to be polyphyletic (Schoch et al. 2009). To confirm the systematic hypothesis and to determine the placement of A. parasitica at family level, the use of multi-loci phylogenies is necessary in the future. ...
Atractilina Dearn. & Barthol. and Spiropes Cif. are genera of asexual fungi that comprise species mainly hyperparasitic on black mildews (Meliolales, Ascomycota). Although a common group of anamorphic fungi, they have been described up to now only by morphology and their systematic position is unknown. The present study provides a morphological treatise of all known species of Atractilina and Spiropes hyperparasitic on Meliolales, including insights into their systematic position, based on DNA sequences generated here for the first time. The study was conducted, based on 33 herbarium specimens and 23 specimens recently collected in Benin and Panama. The obtained DNA sequence data (28S rDNA and ITS rDNA) of A. parasitica and of two species of Spiropes show systematic placements in the Dothideomycetes and Leotiomycetes, respectively. The sequence data of the two Spiropes spp. do not group together. Moreover, the anamorph-teleomorph connection between Atractilina parasitica and Malacaria meliolicola, a pseudothecioid fungus, is confirmed. Three species in the genus Spiropes are proposed as new to science, namely S. angylocalycis, S. carpolobiae and S. croissantiformis. Four species are reported for Benin for the first time, three species for Panama and one species for mainland America. Atractilina and Spiropes are currently two genera with highly heterogeneous species and they might have to be split in the future, once the taxonomic concepts are validated by morphology and molecular sequence data.
... Dothideomycetes have been well studied in the past, and their higher-level classification has also been revisited (Pem et al. 2019, 2021. Schoch et al. (2009) studied the phylogenetic position of 41 families in Dothideomycetes. Subsequently, Lumbsch & Huhndorf (2010), in the Outline of Ascomycota, included 41 families and 249 genera, and 116 remaining genera were placed as incertae sedis in Dothideomycetes. ...
Meristematic fungi are mainly defined as having aggregates of thick-walled, melanised cells enlarging and reproducing by isodiametric division. Dothideomycetes black meristematic and meristematic-like fungi have been allied to Myriangiales, which currently has two accepted families, Myriangiaceae and Elsinoaceae, with fungi mainly regarded as pathogens, parasites, saprobes and epiphytes of different plant species. This study aimed to verify the phylogenetic position using four nuclear markers (SSU, LSU, ITS and RPB2) of the incertae sedis genera associated with Myriangiales, namely Endosporium, Gobabebomyces, Lembosiniella and Phaeosclera, and the new genus, Endophytium gen. nov. (including E. albocacti sp. nov. and E. cacti sp. nov.), established for endophytic fungi occurring in cacti in Brazil. Based on morphology, lifestyle and phylogenetic inferences, these black meristematic and meristematic-like fungi cannot be accommodated in Myriangiales. Combining these results, three new orders and two new families are introduced: Endophytiales ord. nov. (including Endophytiaceae fam. nov. for Endophytium gen. nov.), Endosporiales ord. nov. (including Endosporiaceae for Endosporium) and Phaeosclerales ord. nov. (including Phaeoscleraceae fam. nov. for Phaeosclera). Gobabebomyces and Lembosiniella remained incertae sedis due to their disposition in the phylogenetic tree, that moved among clades accordingly with the gene analysed. Our results show that the inclusion of endophytic fungi obtained from plants in dry forests can contribute to the discovery of new taxa, clarify the phylogenetic position of allied taxa and confer information to the estimation of national and global fungal diversity.
... Though Sordariomycetes and Dothideomycetes may share common early ancestors in Ascomycota (Wijayawardene et al. 2018), horizontal gene transfer may still occur in Dothideomycetes that was transferred from Sordariomycetes. Lineage-specific genetic content was commonly found among organisms, including in different classes of fungi (Sipos et al. 2017;Cai et al. 2006;Schoch et al. 2009). Previous study had found nearly 8.5% of genes in Dothideomycetes were not found in other fungi classes (Schoch et al. 2009). ...
... Lineage-specific genetic content was commonly found among organisms, including in different classes of fungi (Sipos et al. 2017;Cai et al. 2006;Schoch et al. 2009). Previous study had found nearly 8.5% of genes in Dothideomycetes were not found in other fungi classes (Schoch et al. 2009). In our ortholog gene analysis which included 38 Dothideomycete species and 48 Sordariomycetes species we identified 31,297 ortholog gene groups in these species. ...
Botryosphaeriaceae (Botryosphaeriales, Dothideomycetes, Ascomycota) encompasses commonly encountered opportunistic pathogens that cause stem cankers on woody plants. Lifestyles of Botryosphaeriaceae species could vary as endophytes, pathogens and saprobes and one species can have one or more lifestyles. Therefore, this family is an excellent candidate to study the relationships among lifestyles and lifestyle changes. It is postulated that this family has saprobic ancestors, and the mechanisms by which they evolved from nonpathogenic ancestors to woody pathogens remain unclear. Here, we present an analysis of 18 Botryosphaeriaceae genomes, including four newly generated high-quality genomes of Botryosphaeriaceae strains. We compared Botryosphaeriaceae genomes with phylogenetically closely related Dothideomycetes taxa including plant pathogens and saprobes which revealed significant net gene family expansion in Botryosphaeriaceae . This gene expansion is prominent in the early ancestors before the divergence of genera of Botryosphaeriaceae . This expansion affected the pathogenicity-related genes and detoxification genes. Furthermore, we analysed horizontal gene transfer, which is a mechanism of transfer to genetic material between organisms that are not in a parent–offspring relationship and identified widespread putative intra-kingdom horizontal gene transfer events in this family. Most were transferred during the evolution of ancient ancestors of Botryosphaeriaceae , before the divergence of the modern genera and were enriched in pathogenicity-related genes and detoxification genes. Furthermore, The RNA sequencing analysis of the Botryosphaeriaceae species Lasiodiplodia theobromae revealed that pathogenicity-related genes and detoxification genes, including those obtained through gene family expansion and horizontal gene transfers, were significantly induced after the infection of plant hosts rather than before infection. These insights reveal critical roles for gene family expansion and horizontal gene transfers in the evolutionary adaptation of Botryosphaeriaceae in the infection of woody plants. We postulate that the pathogenic lifestyle of Botryosphaeriaceae species evolved from saprobic or endophytic lifestyles in the early divergence of this family. However, there are few endophytic genomes available for closely related species of Botryosphaeriaceae , thus further studies are necessary to clarify the evolutionary relationships of the endophytes.
... The trees were rooted on the outgroup, Pyrenophora teres f. maculata, due to its genomic similarity and distinct phylogenetic relationship with the Alternaria spp. (Schoch et al. 2009). A statistical test for congruence between the NJ and ML trees was conducted using the non-parametric bootstrapping method with 500 replicates (Arnaoudova et al. 2010). ...
Demethylation inhibitors (DMI) fungicides are commonly used to mitigate fungal diseases in crops by inhibiting ergosterol biosynthesis. Alternaria alternata and Alternaria tenuissima are fungal plant pathogens being controlled with DMIs. However, with unregulated use of fungicides, reports on reduced sensitivity to DMIs have been documented in these fungal species. Previous studies have shown the accumulation of point mutations in CYP51 and CYP61 genes that are involved in ergosterol biosynthesis to the development of resistance to DMI fungicides. Understanding the phylogeographic trends of isolates based on the DMI gene targets is critical to identify sustainable management strategies against fungicide resistance. In this study, a phylogenetic approach was used to determine the association of geographic origin of isolates with fungicide resistance across A. alternata and A. tenuissima isolates. Phylogeographic and haplotype analyses revealed genetic patterns in CYP51 and CYP61, associated with DMI resistance. Generally, clusters formed within specific geographic areas such as Asia and North America. Moreover, nucleotide variation estimates revealed the presence of polymorphic nucleotide bases in response to DMI exposure as a selection pressure. These results provided insights in further testing in vitro assays regarding the selection patterns associated with specific regions.
... Dothideomycetes are the largest and phylogenetically the most diverse group of Ascomycota, composed of saprotrophs, plant pathogens, endophytes, lichen-forming fungi, as well as fungicolous and lichenicolous species (Crous et al. 2022;Haridas et al. 2020;Schoch et al. 2009). Despite the intensive study of Dothideomycetes in recent decades, they still include poorly known lineages. ...
Acrospermales represent one of the least studied lineages of Dothideomycetes and are characterized by diverse ecological strategies, including saprotrophic, epiphytic, fungicolous, lichenicolous, and bryophilous lifestyles. The order is composed of two teleomorphic genera, Acrospermum and Oomyces, and five anamorphic genera of unclear relationships. The objectives of the study were to establish the phylogenetic position of Acrospermum species collected from lichens in the tropical forest of Bolivia and to infer the evolution of the lichenicolous lifestyle in Acrospermales. Our results reveal that the examined specimens from Bolivia represent a new species, A. bolivianum, which is well characterized by its phylogenetic distinctness, morphological characteristics, and host selection. The new species is the first lichenicolous member of Acrospermum and forms a well-supported clade sister to the bryophilous Acrospermum adeanum. The evolution of lifestyles, concluded by phylogenetic analyses and ancestral state reconstructions, indicated that the saprotrophic lifestyle is ancestral to Acrospermales. This corresponds to their close relationship to other saprotrophic lineages of Dothideomycetes and indicates that the wide spectrum of nutritional strategies, currently observed in Acrospermales, may be a result of more recent shifts in their ecology. Our results also suggest that the lichenicolous lifestyle in Acrospermales appeared independently at least two times. Lichenicolous species are represented in our data set by Acrospermum bolivianum and Gonatophragmium physciae, which evolved from lichenicolous and plant-parasite ancestors, respectively. The genus Oomyces, represented by O. carneoalbus, was included for the first time in the phylogenetic analysis and showed a sister relationship to the remaining taxa of Acrospermales.
... Contrary to the hypothesis that we could identify potentially disease-protective taxa or microbiome features, only one of the eight microbial ASVs associated with disease progression was correlated with reduced lesion development (Fig. 7). This ASV could only be identified as belonging to the class Dothideomycetes, the largest class within the largest phylum of fungi (65), making it difficult to characterize any potentially protective traits. None of the numerous bacterial biocontrol agents successfully tested against Phytophthora spp. in cocoa [e.g., Paenibacillus polymyxa (19), Bacillus amyloliquefaciens, Pseudomonas aeruginosa, Chryseobacterium proteolyticum (66)] were found among the ASVs that differed in relative abundance between the two accessions or were correlated with lesion development. ...
The oomycete pathogen Phytophthora palmivora , which causes black pod rot (BPR) on cacao ( Theobroma cacao L.), is responsible for devastating yield losses worldwide. Genetic variation in resistance to Phytophthora spp. is well documented among cacao cultivars, but variation has also been observed in the incidence of BPR even among trees of the same cultivar. In light of evidence that the naturally occurring phyllosphere microbiome can influence foliar disease resistance in other host-pathogen systems, it was hypothesized that differences in the phyllosphere microbiome between two field accessions of the cultivar Gainesville II 164 could be responsible for their contrasting resistance to P. palmivora . Bacterial alpha diversity was higher but fungal alpha diversity was lower in the more resistant accession MITC-331, and the accessions harbored phyllosphere microbiomes with distinct community compositions. Six bacterial and 82 fungal amplicon sequence variants (ASVs) differed in relative abundance between MITC-333 and MITC-331, including bacterial putative biocontrol agents and a high proportion of fungal pathogens, and nine fungal ASVs were correlated with increased lesion development. The roles of contrasting light availability and host mineral nutrition, particularly potassium, are also discussed. Results of this preliminary study can be used to guide research into microbiome-informed integrated pest management strategies effective against Phytophthora spp. in cacao.
IMPORTANCE
Up to 40% of the world’s cacao is lost each year to diseases, the most devastating of which is black pod rot, caused by Phytophthora palmivora . Though disease resistance is often attributed to cacao genotypes (i.e., disease-resistant rootstocks), this study highlights the role of the microbiome in contributing to differences in resistance even among accessions of the same cacao cultivar. Future studies of plant-pathogen interactions may need to account for variation in the host microbiome, and optimizing the cacao phyllosphere microbiome could be a promising new direction for P. palmivora resistance research.
... This may be indicative of terrestrial contamination, for instance, if marine invertebrates ingested spores, but fungal phylogenies often show putatively marine fungi nested within clades of typically terrestrial lineages [65]. This led to a hypothesis that most marine fungi diversified before animals transitioned to a terrestrial lifestyle [65], but it has also been proposed that many truly marine isolates recently evolved from terrestrial ancestors [64,66]. Some fungi are capable of tolerating vastly different habitats [67], so may inhabit both marine and terrestrial environments. ...
Symbiotic relationships between microbes and animals are incredibly common. However, most studies focus on the bacterial symbionts of vertebrate hosts and ignore both eukaryotic symbionts and invertebrate hosts. Some of the technical limitations complicating research into eukaryotic symbionts have largely been overcome, but there is an added wrinkle when examining such microbes in microscopic invertebrates. Namely, it can be difficult to distinguish eukaryotes that have simply been eaten by these tiny animals from true symbionts. To overcome this, researchers recently used phylogenetic reconstruction to identify microbial taxa that fall within typically host-associated clades. and applied this to the potential eukaryotic microbiomes of 220 marine invertebrate specimens, spanning 9 phyla. They identified numerous previously undescribed lineages and expanded the known host range of several microbial taxa. A lack of reference sequences resulted in several cryptic clades within Apicomplexa and Ciliophora, which suggests that these invertebrates harbor uncharacterized symbionts. This study represents just a tiny peek into the world of invertebrates and their potential symbionts. Yet, it still suggests that, despite their size, microscopic invertebrates harbor protist and fungal symbionts and that further research is warranted to develop more robust inferences.
... Leaves were rehydrated to induce sporulation by incubating for 2-5 d in moist chambers as described above and maintained under 12 h ultraviolet (UV) light and 12 h dark. Newly emerging conidia and conidiophores were examined using a DM1000 compound microscope ( (White et al. 1990) or 28S with primers LROR/ LR5 (Schoch et al. 2009) was conducted with an initial denaturation temperature of 95 C for 3 min, followed by 34 cycles of 95 C for 30 s, 60 C for 30 s, and 72 C for 1 min, and a final extension at 72 C for 5 min. The TEF1 segment was PCR-amplified with primers EF983F/ EF2218R (Schoch et al. 2009), with an annealing temperature of 56 C and extension time of 90 s. ...
... Newly emerging conidia and conidiophores were examined using a DM1000 compound microscope ( (White et al. 1990) or 28S with primers LROR/ LR5 (Schoch et al. 2009) was conducted with an initial denaturation temperature of 95 C for 3 min, followed by 34 cycles of 95 C for 30 s, 60 C for 30 s, and 72 C for 1 min, and a final extension at 72 C for 5 min. The TEF1 segment was PCR-amplified with primers EF983F/ EF2218R (Schoch et al. 2009), with an annealing temperature of 56 C and extension time of 90 s. The RPB2 segment was PCR-amplified with primers 7cR (O'Donnell et al. 2007) and Rpr2, with an annealing temperature of 65 C and extension time of 60 s. ...
Bipolaris gigantea (= Drechslera gigantea) causes Bipolaris leaf spot (BLS), a devastating and widespread disease on industrial hemp (Cannabis sativa). An investigation of relationships of isolates from hemp and other plants indicated variation in ploidy that has not previously been reported for Bipolaris. Isolates were obtained from BLS lesions on hemp and nearby weeds in 11 Kentucky counties and were similar to each other in morphology and growth characteristics. In total, 23 isolates were analyzed by multilocus phylogenetics, of which seven were also chosen for whole genome shotgun sequencing. Genes for RNA polymerase II subunit 2 (RPB2), translation elongation factor 1-α (TEF1), and mating type (MAT1) indicated that 13 of the isolates were haploid with only a single allele each of RPB2 and TEF1 and either the MAT1-1 or MAT1-2 idiomorph, whereas 10 were apparently "heteroploid" with two alleles each of RPB2 and TEF1 and both MAT1 idiomorphs. Haploids all had identical RPB2 alleles except for a 1-bp difference in two isolates, identical TEF1 alleles, and (if present) identical MAT1-2 alleles. Those alleles were also present in each heteroploid along with either of two related but distinct alleles for each gene. In contrast, haploids and heteroploids shared allelic variation of MAT1-1. In total, four haploid and two heteroploid genotypes were identified. Genome sequence data assembled to 30-32 Mb for each of four haploid isolates, but 10-31 Mb larger sizes for each of three heteroploids depending on sequencing platform and assembly program. The haploids and heteroploids caused similar disease on hemp.
... Significant diversity of lichen-associated microfungi is also found in Dothideomycetes, although here the isolated strains are phylogenetically more heterogeneous. In Dothideomycetes, our samples were related to fungi with different lifestyles (Schoch et al. 2009;Hyde et al. 2013;Wijayawardene et al. 2014), as well as lichenicolous fungi such as Phoma caloplacae and P. cladonicola (Lawrey et al. 2012). Interestingly, most of the isolates retrieved in Dothideomycetes are related to fungi previously isolated from lichens or to rockinhabiting fungi from extreme environments, such as Elasticomyces elasticus or Saxomyces penninicus (Selbmann et al. 2008(Selbmann et al. , 2013Ruibal et al. 2011;Muggia et al. 2016Muggia et al. , 2017. ...
Lichens have been reappraised as self-sustaining and long-living ecosystems in which a multiplicity of microorganisms are housed, in addition to the main symbiotic partners. Lichen-associated microfungi can frequently occur cryptically, and their species diversity has recently been more fully elucidated by DNA metabarcoding studies and culture isolations. These lichen-associated fungi represent a wide array of major lineages in ascomycetes and basidiomycetes, including both filamentous and yeast species. Thanks to culture isolations, the morphology of a subset of the lichen-associated microfungal diversity has been studied. Metabarcoding analyses have shown high diversity of ascomycetous lichen-associated fungi in the two cosmopolitan rock-inhabiting lichens – Rhizoplaca melanophthalma and Tephromela atra – and many of these taxa were successfully isolated in culture. Based on DNA sequence data and morphological analyses, two new lineages within Chaetothyriales are here recognized. Both occur in lichens from dry habitats and are described here as the new species Cladophialophora endolichena Cometto, de Hoog, Muggia and Paracladophialophora lichenicola Cometto, de Hoog, Muggia. Other strains are placed in Pleostigmataceae, Trichomeriaceae , Pleosporales , Mycosphaerellales , Coniochaetales and Hypocreales , further filling gaps of knowledge of the high fungal diversity residing in lichen thalli.
... Genomic DNA sample of COAD 3424 was extracted from five days-old cultures grown in potato dextrose broth (Merk KGaA, Germany) using the Wizard® genomic DNA purification kit (Promega) following the manufacture´s protocol. For molecular identification, the primers ITS1/ITS 4 (White et al. 1990), EF 983/2218R (Schoch et al. 2009) and GPD1/GPD2 (Berbee et al. 1999) were used to amplify the internal transcribed spacer (ITS) regions of rDNA, part showing necrotic elongated light brown spots arised from the margin or tip of the leaves (J). Scale bar = 10 µm of translation elongation factor (TEF-1α) and part of the glyceraldehyde-3-phosphate dehydrogenase (GPDH) genes, respectively. ...
During a survey of the mycobiota of sourgrass (Digitaria insularis), a graminaceous weed from Brazil, severe foliage blight symptoms were observed on plants at different places of the state of Minas Gerais. A fungus identified as Bipolaris yamadae, after a polyphasic study, including analysis of ITS, GPDH and TEF-1α genes, was isolated from diseased tissues. Pathogenicity to sourgrass was confirmed through inoculations of healthy plants. This is the first report of B. yamadae causing foliage blight on D. insularis in Brazil and worldwide.
