Population genomics revealed cryptic species within host-specific zombie-ant fungi (Ophiocordyceps unilateralis)

International audienceThe identification and delimitation of species boundaries are essential for understanding speciation and adaptation processes and for the management of biodiversity as well as development for applications. Ophiocordyceps unilateralis sensu lato is a complex of fungal pathogens parasitizing Formicine ants, inducing zombie behaviors in their hosts. Previous taxonomic works with limited numbers of samples and markers led to the "one ant-one fun-gus" paradigm, resulting in the use of ant species as a proxy for fungal identification. Here, a population genomics study with sampling on three ant species across Thailand supported the existence of host-specific species in O. unilateralis s.l. with no footprints of long term introgression despite occasional host shifts and first-generation hybrids. We further detected genetic clusters within the previously delimited fungal species, with each little footprints of recombination, suggesting high levels of inbreeding. The clusters within each of O. camponoti-leonardi and O. camponoti-saundersi were supported by differentiation throughout the genome, suggesting they may constitute further cryptic species parasitizing the same host, challenging the one ant-one fungus paradigm. These genetic clusters had different geographical ranges, supporting different biogeographic influences between the north/center and the south of Thailand, reinforcing the scenario in which Thailand endured compartmentation during the latest Pleistocene glacial cycles

Resurrection and emendation of the Hypoxylaceae, recognised from a multigene phylogeny of the Xylariales

A multigene phylogeny was constructed, including a significant number of representative species of the main lineages in the Xylariaceae and four DNA loci the internal transcribed spacer region (ITS), the large subunit (LSU) of the nuclear rDNA, the second largest subunit of the RNA polymerase II (RPB2), and beta-tubulin (TUB2). Specimens were selected based on more than a decade of intensive morphological and chemotaxonomic work, and cautious taxon sampling was performed to cover the major lineages of the Xylariaceae; however, with emphasis on hypoxyloid species. The comprehensive phylogenetic analysis revealed a clear-cut segregation of the Xylariaceae into several major clades, which was well in accordance with previously established morphological and chemotaxonomic concepts. One of these clades contained Annulohypoxylon, Hypoxylon, Daldinia, and other related genera that have stromatal pigments and a nodulisporium-like anamorph. They are accommodated in the family Hypoxylaceae, which is resurrected and emended. Representatives of genera with a nodulisporium-like anamorph and bipartite stromata, lacking stromatal pigments (i.e. Biscogniauxia, Camillea, and Obolarina) appeared in a clade basal to the xylarioid taxa. As they clustered with Graphostroma platystomum, they are accommodated in the Graphostromataceae. The new genus Jackrogersella with J. multiformis as type species is segregated from Annulohypoxylon. The genus Pyrenopolyporus is resurrected for Hypoxylon polyporus and allied species. The genus Daldinia and its allies Entonaema, Rhopalostroma, Ruwenzoria, and Thamnomyces appeared in two separate subclades, which may warrant further splitting of Daldinia in the future, and even Hypoxylon was divided in several clades. However, more species of these genera need to be studied before a conclusive taxonomic rearrangement can be envisaged. Epitypes were designated for several important species in which living cultures and molecular data are available, in order to stabilise the taxonomy of the Xylariales.Fil: Wendt, Lucile. Helmholtz-Zentrum für Infektionsforschung GmbH. Department of Microbial Drugs; Alemania. German Centre for Infection Research; AlemaniaFil: Sir, Esteban Benjamin. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Unidad Ejecutora Lillo. Fundación Miguel Lillo. Unidad Ejecutora Lillo; ArgentinaFil: Kuhnert, Eric. Helmholtz-Zentrum für Infektionsforschung GmbH. Department of Microbial Drugs; Alemania. German Centre for Infection Research; AlemaniaFil: Heitkämper, Simone. Helmholtz-Zentrum für Infektionsforschung GmbH. Department of Microbial Drugs; Alemania. German Centre for Infection Research; AlemaniaFil: Lambert, Christopher. Helmholtz-Zentrum für Infektionsforschung GmbH. Department of Microbial Drugs; Alemania. German Centre for Infection Research; AlemaniaFil: Hladki, Adriana I.. Fundación Miguel Lillo. Dirección de Botánica. Instituto de Micologia; ArgentinaFil: Romero, Andrea Irene. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Micología y Botánica. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Micología y Botánica; ArgentinaFil: Luangsa-Ard, Janet Jennifer. National Center for Genetic Engineering and Biotechnology; TailandiaFil: Srikitikulchai, Prasert. National Center for Genetic Engineering and Biotechnology; TailandiaFil: Peršoh, Derek. Ruhr-Universität Bochum; AlemaniaFil: Stadler, Marc. Helmholtz-Zentrum für Infektionsforschung GmbH. Department of Microbial Drugs; Alemania. German Centre for Infection Research; Alemani

Finding needles in haystacks:Linking scientific names, reference specimens and molecular data for Fungi

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Reannotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.The Intramural Research Programs of the National Center for Biotechnology Information, National Library of Medicine and the National Human Genome Research Institute, both at the National Institutes of Health.http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353am201

Finding needles in haystacks : linking scientific names, reference specimens and molecular data for Fungi

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Reannotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.The Intramural Research Programs of the National Center for Biotechnology Information, National Library of Medicine and the National Human Genome Research Institute, both at the National Institutes of Health.http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353am201

Using High-Throughput Amplicon Sequencing to Evaluate Intragenomic Variation and Accuracy in Species Identification of Cordyceps Species

While recent sequencing technologies (third generation sequencing) can successfully sequence all copies of nuclear ribosomal DNA (rDNA) markers present within a genome and offer insights into the intragenomic variation of these markers, high intragenomic variation can be a source of confusion for high-throughput species identification using such technologies. High-throughput (HT) amplicon sequencing via PacBio SEQUEL I was used to evaluate the intragenomic variation of the ITS region and D1–D2 LSU domains in nine Cordyceps species, and the accuracy of such technology to identify these species based on molecular phylogenies was also assessed. PacBio sequences within strains showed variable level of intragenomic variation among the studied Cordyceps species with C. blackwelliae showing greater variation than the others. Some variants from a mix of species clustered together outside their respective species of origin, indicative of intragenomic variation that escaped concerted evolution shared between species. Proper selection of consensus sequences from HT amplicon sequencing is a challenge for interpretation of correct species identification. PacBio consensus sequences with the highest number of reads represent the major variants within a genome and gave the best results in terms of species identification

Discovery of novel biologically active secondary metabolites from Thai mycodiversity with anti-infective potential

This mini-review is dedicated to the summary of results of the EU-funded Project “Golden Mycological Triangle” (acronym GoMyTri), which was carried out in collaboration of three research infrastructures in Germany, the Netherlands and Thailand during the years 2014–2018. The cooperation explored the mycological and microbiological biodiversity of Europe and Southeast Asia with regard to the search for the badly needed new antibiotics and other biologically active secondary metabolites. The project was conducted to foster international collaboration networks, know-how exchange and interdisciplinary training of young scientists. The first two years of the project were mainly dedicated to field work, and several hundreds of fungal cultures have been isolated from material mostly collected in Thailand. These fungal strains were characterized by morphological and molecular phylogenetic methods and several new taxa were discovered. The cultures underwent screening for antimicrobial and nematicidal metabolites and a number of bioactive metabolites have already been found, isolated and characterized. Several large phylogenetic studies have already been published that resulted from the project work. The results were also brought to the attention of the scientific community as well as the general public through various dissemination events. Based on the tremendous success of this project, a follow-up project application including additional partners from Africa and further European countries has recently been filed and approved, and the international, interdisciplinary collaboration will now continue in the new RISE-MSCA-Project (acronym “Mycobiomics”).Alexander von Humboldt-Stiftun

Is Hyperdermium Congeneric with Ascopolyporus? Phylogenetic Relationships of Ascopolyporus spp. (Cordycipitaceae, Hypocreales) and a New Genus Neohyperdermium on Scale Insects in Thailand

During surveys of insect pathogenic fungi (IPF) in Thailand, fungi associated with scale insects and plants were found to represent five new species of the genus Ascopolyporus in Cordycipitaceae. Their macroscopic features resembled both Hyperdermium and Ascopolyporus. Morphological comparisons with the type and known Ascopolyporus and Hyperdermium species and phylogenetic evidence from a multigene dataset support the appointment of a new species of Ascopolyporus. Moreover, the data also revealed that the type species of Hyperdermium, H. caulium, is nested within Ascopolyporus, suggesting that Hyperdermium is congeneric with Ascopolyporus. The specimens investigated here differ from other Ascopolyporus species by phenotypic characters including size and color of stromata. Phylogenetic analyses of combined LSU, TEF1, RPB1 and RPB2 sequences strongly support the notion that these strains are distinct from known species of Ascopolyporus, and are proposed as Ascopolyporus albus, A. galloides, A. griseoperitheciatus, A. khaoyaiensis and A. purpuratus. Neohyperdermium gen. nov. is introduced for other species originally assigned to Hyperdermium and Cordyceps occurring on scale insects and host plants as epiphytes, accommodating two new combinations of Hyperdermium pulvinatum and Cordyceps piperis

Five Unprecedented Secondary Metabolites from the Spider Parasitic Fungus Akanthomyces novoguineensis.

Five new compounds including the glycosylated β-naphthol (1, akanthol), a glycosylated pyrazine (2, akanthozine), and three amide derivatives including a hydroxamic acid derivative (3-5) were isolated from the spider-associated fungus Akanthomyces novoguineensis (Cordycipitaceae, Ascomycota). Their structures were elucidated by using high resolution mass spectrometry (HRMS) and NMR spectroscopy. In this study, the antimicrobial, cytotoxic, anti-biofilm, and nematicidal activities of the new compounds were evaluated. The distribution pattern of secondary metabolites in the species was also revealed in which more isolates of A. novoguineensis were encountered and their secondary metabolite profiles were examined using analytical HPLC with diode array and mass spectrometric detection (HPLC-DAD/MS). Remarkably, all isolated compounds are specifically produced by A. novoguineensis