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Francois Lutzoni - One of the best experts on this subject based on the ideXlab platform.
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Multi-locus phylogeny supports the placement of Endocarpon pulvinatum within Staurothele s. str. (lichenised ascomycetes, Eurotiomycetes, Verrucariaceae)
Phytotaxa, 2017Co-Authors: Starri Heiðmarsson, Jolanta Miadlikowska, Cecile Gueidan, Francois LutzoniAbstract:Within the lichen family Verrucariaceae, the genera Endocarpon , Willeya and Staurothele are characterised by muriform ascospores and the presence of algal cells in the hymenium. Endocarpon thalli are squamulose to subfruticose, whereas Willeya and Staurothele include only crustose species. Endocarpon pulvinatum , an arctic-alpine species newly reported for Iceland, is one of the few Endocarpon with a subfruticose thallus formed by long and narrow erected squamules. Molecular phylogenetic analyses of four loci (ITS, nrLSU, mtSSU, and mcm 7) newly obtained from E. pulvinatum specimens from Iceland, Finland and North America does not confirm its current classification within the mostly squamulose genus Endocarpon , but instead supports its placement within the crustose genus Staurothele . The new combination Staurothele pulvinata is therefore proposed here. It includes also E. tortuosum , which was confirmed as a synonym of E. pulvinatum based on a single sequence.
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phylogenetic analyses of eurotiomycetous endophytes reveal their close affinities to chaetothyriales eurotiales and a new order phaeomoniellales
Molecular Phylogenetics and Evolution, 2015Co-Authors: Ko Hsuan Chen, Katalin Molnar, Ester Gaya, Jana M Uren, Elizabeth A Arnold, Cecile Gueidan, Jolanta Miadlikowska, Francois LutzoniAbstract:Abstract Symbiotic fungi living in plants as endophytes, and in lichens as endolichenic fungi, cause no apparent symptoms to their hosts. They are ubiquitous, ecologically important, hyperdiverse, and represent a rich source of secondary compounds for new pharmaceutical and biocontrol products. Due in part to the lack of visible reproductive structures and other distinctive phenotypic traits for many species, the diversity and phylogenetic affiliations of these cryptic fungi are often poorly known. The goal of this study was to determine the phylogenetic placement of representative endophytes within the Eurotiomycetes (Pezizomycotina, Ascomycota), one of the most diverse and evolutionarily dynamic fungal classes, and to use that information to infer processes of macroevolution in trophic modes. Sequences of a single locus marker spanning the nuclear ribosomal internal transcribed spacer region (nrITS) and 600 base pairs at the 5′ end of the nuclear ribosomal large subunit (nrLSU) were obtained from previous studies of >6000 endophytic and endolichenic fungi from diverse biogeographic locations and hosts. We conducted phylum-wide phylogenetic searches using this marker to determine which fungal strains belonged to Eurotiomycetes and the results were used as the basis for a class-wide, seven-locus phylogenetic study focusing on endophytic and endolichenic Eurotiomycetes. Our cumulative supermatrix-based analyses revealed that representative endophytes within Eurotiomycetes are distributed in three main clades: Eurotiales, Chaetothyriales and Phaeomoniellales ord. nov., a clade that had not yet been described formally. This new order, described herein, is sister to the clade including Verrucariales and Chaetothyriales. It appears to consist mainly of endophytes and plant pathogens. Morphological characters of endophytic Phaeomoniellales resemble those of the pathogenic genus Phaeomoniella. This study highlights the capacity of endophytic and endolichenic fungi to expand our understanding of the ecological modes associated with particular clades, and provides a first estimation of their phylogenetic relationships in the Eurotiomycetes.
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Phylogenetic analyses of eurotiomycetous endophytes reveal their close affinities to Chaetothyriales, Eurotiales, and a new order – Phaeomoniellales
Molecular Phylogenetics and Evolution, 2015Co-Authors: Ko Hsuan Chen, Katalin Molnar, Ester Gaya, Cecile Gueidan, Jolanta Miadlikowska, A. Elizabeth Arnold, Jana M. U'ren, Francois LutzoniAbstract:Abstract Symbiotic fungi living in plants as endophytes, and in lichens as endolichenic fungi, cause no apparent symptoms to their hosts. They are ubiquitous, ecologically important, hyperdiverse, and represent a rich source of secondary compounds for new pharmaceutical and biocontrol products. Due in part to the lack of visible reproductive structures and other distinctive phenotypic traits for many species, the diversity and phylogenetic affiliations of these cryptic fungi are often poorly known. The goal of this study was to determine the phylogenetic placement of representative endophytes within the Eurotiomycetes (Pezizomycotina, Ascomycota), one of the most diverse and evolutionarily dynamic fungal classes, and to use that information to infer processes of macroevolution in trophic modes. Sequences of a single locus marker spanning the nuclear ribosomal internal transcribed spacer region (nrITS) and 600 base pairs at the 5′ end of the nuclear ribosomal large subunit (nrLSU) were obtained from previous studies of >6000 endophytic and endolichenic fungi from diverse biogeographic locations and hosts. We conducted phylum-wide phylogenetic searches using this marker to determine which fungal strains belonged to Eurotiomycetes and the results were used as the basis for a class-wide, seven-locus phylogenetic study focusing on endophytic and endolichenic Eurotiomycetes. Our cumulative supermatrix-based analyses revealed that representative endophytes within Eurotiomycetes are distributed in three main clades: Eurotiales, Chaetothyriales and Phaeomoniellales ord. nov., a clade that had not yet been described formally. This new order, described herein, is sister to the clade including Verrucariales and Chaetothyriales. It appears to consist mainly of endophytes and plant pathogens. Morphological characters of endophytic Phaeomoniellales resemble those of the pathogenic genus Phaeomoniella. This study highlights the capacity of endophytic and endolichenic fungi to expand our understanding of the ecological modes associated with particular clades, and provides a first estimation of their phylogenetic relationships in the Eurotiomycetes.
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Molecular phylogeny and systematics of Polyblastia (Verrucariaceae, Eurotiomycetes) and allied genera.
Fungal Biology, 2008Co-Authors: Sanja Savić, Leif Tibell, Cecile Gueidan, Francois LutzoniAbstract:Phylogenetic relationships of the lichen genus Polyblastia and closely related taxa in the family Verrucariaceae (Verrucariales, Chaetothyriomycetidae) were studied. A total of 130 sets of sequences (nuLSU rDNA, nuITS rDNA and RPB1 region A–D), including 129 newly generated sequences, were analysed. Phylogenetic relationships were inferred using a Bayesian approach based on two datasets. A first analysis of a larger, two-locus dataset (nuLSU and RPB1) for 128 members of the Verrucariaceae, confirmed the polyphyly of Polyblastia, Thelidium, Staurothele, and Verrucaria, as currently construed. The second analysis focused on 56 Polyblastia and allied taxa, but using an additional locus (nuITS rDNA) and two closely related outgroup taxa. The latter analysis revealed strongly supported groups, such as Polyblastia s. str., the Thelidium group (a mixture of Polyblastia, Thelidium, Staurothele and Verrucaria species). The genus Sporodictyon, which is here accepted, also accommodates Sporodictyon terrestre comb. nov. Morphological features traditionally used for characterizing Polyblastia, Thelidium, Staurothele and Verrucaria, such as spore septation and colour, occurrence of hymenial photobiont, involucrellum structure, and substrate preference, were found to be only partially consistent within the strongly supported clades, and thus are not always reliable features for characterizing natural groups.
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Eurotiomycetes : Eurotiomycetidae and Chaetothyriomycetidae
Mycologia, 2006Co-Authors: David M. Geiser, Francois Lutzoni, Cecile Gueidan, Jolanta Miadlikowska, Frank Kauff, Valérie Hofstetter, Emily Fraker, Conrad L. Schoch, Leif Tibell, Wendy A. UntereinerAbstract:The class Eurotiomycetes (Ascomycota, Pezizomycotina) is a monophyletic group comprising two major clades of very different ascomycetous fungi: (i) the subclass Eurotiomycetidae, a clade that conta ...
Allan K. Bertram - One of the best experts on this subject based on the ideXlab platform.
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ice nucleation by fungal spores from the classes agaricomycetes ustilaginomycetes and Eurotiomycetes and the effect on the atmospheric transport of these spores
Atmospheric Chemistry and Physics, 2014Co-Authors: D I Haga, M. J. Wheeler, Ryan H Mason, Susannah M Burrows, Elena Polishchuk, Jing M. Chen, Raffaele Iannone, Ulrich Poschl, Allan K. BertramAbstract:Abstract. We studied the ice nucleation properties of 12 different species of fungal spores chosen from three classes: Agaricomycetes , Ustilaginomycetes , and Eurotiomycetes . Agaricomycetes include many types of mushroom species and are widely distributed over the globe. Ustilaginomycetes are agricultural pathogens and have caused widespread damage to crops. Eurotiomycetes are found on all types of decaying material and include important human allergens. We focused on these classes because they are thought to be abundant in the atmosphere and because there is very little information on the ice nucleation ability of these classes of spores in the literature. All of the fungal spores investigated contained some fraction of spores that serve as ice nuclei at temperatures warmer than homogeneous freezing. The cumulative number of ice nuclei per spore was 0.001 at temperatures between −19 °C and −29 °C, 0.01 between −25.5 °C and −31 °C, and 0.1 between −26 °C and −31.5 °C. On average, the order of ice nucleating ability for these spores is Ustilaginomycetes > Agaricomycetes ≃ Eurotiomycetes . The freezing data also suggests that, at temperatures ranging from −20 °C to −25 °C, all of the fungal spores studied here are less efficient ice nuclei compared to Asian mineral dust on a per surface area basis. We used our new freezing results together with data in the literature to compare the freezing temperatures of spores from the phyla Basidiomycota and Ascomycota , which together make up 98% of known fungal species found on Earth. The data show that within both phyla ( Ascomycota and Basidiomycota ), there is a wide range of freezing properties, and also that the variation within a phylum is greater than the variation between the average freezing properties of the phyla. Using a global chemistry–climate transport model, we investigated whether ice nucleation on the studied spores, followed by precipitation, can influence the transport and global distributions of these spores in the atmosphere. Simulations suggest that inclusion of ice nucleation scavenging of these fungal spores in mixed-phase clouds can decrease the annual mean concentrations of fungal spores in near-surface air over the oceans and polar regions, and decrease annual mean concentrations in the upper troposphere.
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Ice nucleation and its effect on the atmospheric transport of fungal spores from the classes Agaricomycetes, Ustilaginomycetes, and Eurotiomycetes
Atmospheric Chemistry and Physics, 2014Co-Authors: D I Haga, M. J. Wheeler, Ryan H Mason, Susannah M Burrows, Elena Polishchuk, Jing M. Chen, Raffaele Iannone, Ulrich Poschl, Allan K. BertramAbstract:Abstract. Ice nucleation on fungal spores may affect the frequency and properties of ice and mixed-phase clouds. We studied the ice nucleation properties of 12 different species of fungal spores chosen from three classes: Agaricomycetes, Ustilaginomycetes, and Eurotiomycetes. Agaricomycetes include many types of mushroom species and are cosmopolitan. Ustilaginomycetes are agricultural pathogens and have caused widespread damage to crops. Eurotiomycetes are found on all types of decaying material and include important human allergens. We focused on these classes since they are thought to be abundant in the atmosphere and because there is very little information on the ice nucleation ability of these classes of spores in the literature. All of the fungal spores investigated were found to cause freezing of water droplets at temperatures warmer than homogeneous freezing. The cumulative number of ice nuclei per spore was 0.001 at temperatures between −19 °C and −29 °C, 0.01 between −25.5 °C and −31 °C, and 0.1 between −26 °C and −36 °C. On average, the order of ice nucleating ability for these spores is Ustilaginomycetes > Agaricomycetes ≃ Eurotiomycetes. We show that at temperatures below −20 °C, all of the fungal spores studied here are less efficient ice nuclei compared to Asian mineral dust on a per surface area basis. We used our new freezing results together with data in the literature to compare the freezing temperatures of spores from the phyla Basidiomycota and Ascomycota, which together make up 98% of known fungal species found on Earth. The data show that within both phyla (Ascomycota and Basidiomycota) there is a wide range of freezing properties, and also that the variation within a phylum is greater than the variation between the average freezing properties of the phyla. Using a global chemistry–climate transport model, we investigated whether ice nucleation on the studied spores, followed by precipitation, can influence the atmospheric transport and global distributions of these spores in the atmosphere. Simulations show that inclusion of ice nucleation scavenging of these fungal spores in mixed-phase clouds can decrease the annual mean concentrations of fungal spores in near-surface air over the oceans and polar regions and decrease annual mean mixing ratios in the upper troposphere.
Souwalak Phongpaichit - One of the best experts on this subject based on the ideXlab platform.
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Phylogenetic diversity of endophyte assemblages associated with the tropical seagrass Enhalus acoroides in Thailand
Fungal Diversity, 2010Co-Authors: Jariya Sakayaroj, O. Supaphon, Sita Preedanon, E.b.g. Jones, Souwalak PhongpaichitAbstract:Seagrasses are flowering plants inhabiting coastal and marine environments, with a worldwide distribution. They serve as feeding, breeding and nursery grounds for economically important marine organisms including endangered species. The tropical seagrass Enhalus acoroides was collected from Had Khanom-Mu Ko Thale Tai National Park, southern Thailand. The objectives of this study were to investigate for the presence of endophyte assemblages in E. acoroides , as well as to describe the diversity of endophytes based on LSU, ITS1, 2, 5.8S rDNA sequence analyses. Forty-two fungal assemblages were isolated and identified through molecular data. This resulted in a diversity of fungal groups of Ascomycota (98%) and Basidiomycota (2%). Three major Ascomycota classes including the Sordariomycetes (36%), Eurotiomycetes (33%) and Dothideomycetes (24%) were determined. The predominant ascomycete orders were the Hypocreales, followed by the Eurotiales and the Capnodiales , respectively. Additionally one taxon belonged to the Russulales , Basidiomycota and was possibly mycorrhiza. This study confirms that E. acoroides harbors a wide diversity of fungal endophytes, and provides a baseline for further studies on fungal-host plant interactions.
Cecile Gueidan - One of the best experts on this subject based on the ideXlab platform.
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Multi-locus phylogeny supports the placement of Endocarpon pulvinatum within Staurothele s. str. (lichenised ascomycetes, Eurotiomycetes, Verrucariaceae)
Phytotaxa, 2017Co-Authors: Starri Heiðmarsson, Jolanta Miadlikowska, Cecile Gueidan, Francois LutzoniAbstract:Within the lichen family Verrucariaceae, the genera Endocarpon , Willeya and Staurothele are characterised by muriform ascospores and the presence of algal cells in the hymenium. Endocarpon thalli are squamulose to subfruticose, whereas Willeya and Staurothele include only crustose species. Endocarpon pulvinatum , an arctic-alpine species newly reported for Iceland, is one of the few Endocarpon with a subfruticose thallus formed by long and narrow erected squamules. Molecular phylogenetic analyses of four loci (ITS, nrLSU, mtSSU, and mcm 7) newly obtained from E. pulvinatum specimens from Iceland, Finland and North America does not confirm its current classification within the mostly squamulose genus Endocarpon , but instead supports its placement within the crustose genus Staurothele . The new combination Staurothele pulvinata is therefore proposed here. It includes also E. tortuosum , which was confirmed as a synonym of E. pulvinatum based on a single sequence.
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phylogenetic analyses of eurotiomycetous endophytes reveal their close affinities to chaetothyriales eurotiales and a new order phaeomoniellales
Molecular Phylogenetics and Evolution, 2015Co-Authors: Ko Hsuan Chen, Katalin Molnar, Ester Gaya, Jana M Uren, Elizabeth A Arnold, Cecile Gueidan, Jolanta Miadlikowska, Francois LutzoniAbstract:Abstract Symbiotic fungi living in plants as endophytes, and in lichens as endolichenic fungi, cause no apparent symptoms to their hosts. They are ubiquitous, ecologically important, hyperdiverse, and represent a rich source of secondary compounds for new pharmaceutical and biocontrol products. Due in part to the lack of visible reproductive structures and other distinctive phenotypic traits for many species, the diversity and phylogenetic affiliations of these cryptic fungi are often poorly known. The goal of this study was to determine the phylogenetic placement of representative endophytes within the Eurotiomycetes (Pezizomycotina, Ascomycota), one of the most diverse and evolutionarily dynamic fungal classes, and to use that information to infer processes of macroevolution in trophic modes. Sequences of a single locus marker spanning the nuclear ribosomal internal transcribed spacer region (nrITS) and 600 base pairs at the 5′ end of the nuclear ribosomal large subunit (nrLSU) were obtained from previous studies of >6000 endophytic and endolichenic fungi from diverse biogeographic locations and hosts. We conducted phylum-wide phylogenetic searches using this marker to determine which fungal strains belonged to Eurotiomycetes and the results were used as the basis for a class-wide, seven-locus phylogenetic study focusing on endophytic and endolichenic Eurotiomycetes. Our cumulative supermatrix-based analyses revealed that representative endophytes within Eurotiomycetes are distributed in three main clades: Eurotiales, Chaetothyriales and Phaeomoniellales ord. nov., a clade that had not yet been described formally. This new order, described herein, is sister to the clade including Verrucariales and Chaetothyriales. It appears to consist mainly of endophytes and plant pathogens. Morphological characters of endophytic Phaeomoniellales resemble those of the pathogenic genus Phaeomoniella. This study highlights the capacity of endophytic and endolichenic fungi to expand our understanding of the ecological modes associated with particular clades, and provides a first estimation of their phylogenetic relationships in the Eurotiomycetes.
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Phylogenetic analyses of eurotiomycetous endophytes reveal their close affinities to Chaetothyriales, Eurotiales, and a new order – Phaeomoniellales
Molecular Phylogenetics and Evolution, 2015Co-Authors: Ko Hsuan Chen, Katalin Molnar, Ester Gaya, Cecile Gueidan, Jolanta Miadlikowska, A. Elizabeth Arnold, Jana M. U'ren, Francois LutzoniAbstract:Abstract Symbiotic fungi living in plants as endophytes, and in lichens as endolichenic fungi, cause no apparent symptoms to their hosts. They are ubiquitous, ecologically important, hyperdiverse, and represent a rich source of secondary compounds for new pharmaceutical and biocontrol products. Due in part to the lack of visible reproductive structures and other distinctive phenotypic traits for many species, the diversity and phylogenetic affiliations of these cryptic fungi are often poorly known. The goal of this study was to determine the phylogenetic placement of representative endophytes within the Eurotiomycetes (Pezizomycotina, Ascomycota), one of the most diverse and evolutionarily dynamic fungal classes, and to use that information to infer processes of macroevolution in trophic modes. Sequences of a single locus marker spanning the nuclear ribosomal internal transcribed spacer region (nrITS) and 600 base pairs at the 5′ end of the nuclear ribosomal large subunit (nrLSU) were obtained from previous studies of >6000 endophytic and endolichenic fungi from diverse biogeographic locations and hosts. We conducted phylum-wide phylogenetic searches using this marker to determine which fungal strains belonged to Eurotiomycetes and the results were used as the basis for a class-wide, seven-locus phylogenetic study focusing on endophytic and endolichenic Eurotiomycetes. Our cumulative supermatrix-based analyses revealed that representative endophytes within Eurotiomycetes are distributed in three main clades: Eurotiales, Chaetothyriales and Phaeomoniellales ord. nov., a clade that had not yet been described formally. This new order, described herein, is sister to the clade including Verrucariales and Chaetothyriales. It appears to consist mainly of endophytes and plant pathogens. Morphological characters of endophytic Phaeomoniellales resemble those of the pathogenic genus Phaeomoniella. This study highlights the capacity of endophytic and endolichenic fungi to expand our understanding of the ecological modes associated with particular clades, and provides a first estimation of their phylogenetic relationships in the Eurotiomycetes.
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5 Pezizomycotina: Eurotiomycetes
Systematics and Evolution, 2015Co-Authors: David M. Geiser, Katherine F. Lobuglio, Cecile GueidanAbstract:The class Eurotiomycetes is a morphologically and ecologically diverse clade of filamentous ascomycetes (Ascomycota; Pezizomycotina). Based on a series of molecular phylogenetic discoveries, the taxonomic concept has expanded significantly in the past decade. While our phylogenetic knowledge has advanced greatly, we still lack a satisfactorily comprehensive multilocus phylogeny for the group. Eurotiomycetes comprises at least nine orders distributed in three subclasses (Eurotiomycetidae, Chaetothyriomycetidae, Mycocaliciomycetidae), as well as the unresolved coelomycetous taxon Cirrosporium. This chapter will summarize current knowledge of the morphological, ecological, and biological diversity of Eurotiomycetes and place it in an evolutionary and taxonomic context.
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A reappraisal of orders and families within the subclass Chaetothyriomycetidae (Eurotiomycetes, Ascomycota)
Mycological Progress, 2014Co-Authors: Cecile Gueidan, André Aptroot, Marcela Eugenia Da Silva Cáceres, Hamid Badali, Soili StenroosAbstract:The subclass Chaetothyriomycetidae (Eurotiomycetes, Ascomycota) is an assemblage of ecologically diverse species, ranging from mutualistic lichenised fungi to human opportunistic pathogens. Recent contributions from molecular studies have changed our understanding of the composition of this subclass. Among others, ant-associated fungi, deep-sea fungi and bryophilous fungi were also shown to belong to this group of ascomycetes. The delimitation of orders and families within this subclass has not previously been re-assessed using a broad phylogenetic study and the phylogenetic position of some taxa such as the lichenised family Celotheliaceae or the Chaetothyrialean bryophilous fungi is still unclear. In our study, we assemble new and published sequences from 132 taxa and reconstruct phylogenetic relationships using four markers (nuLSU, nuSSU, mtSSU and RPB1). Results highlight several shortfalls in the current classification of this subclass, mainly due to un-assigned paraphyletic taxa. The family Epibryaceae is therefore described to circumscribe a previously un-assigned lineage. Celotheliales ad int. is suggested for the lineage including the lichen genus Celothelium and various plant pathogens. The delimitation of the family Trichomeriaceae is also broadened to include the genus Knufia and some anamorphic taxa. As defined here, Chaetothyriomycetidae includes four orders (Celotheliales ad int., Chaetothyriales, Pyrenulales, and Verrucariales) and ten families (Adelococcaceae, Celotheliaceae, Chaetothyriaceae, Cyphellophoraceae, Epibryaceae fam. nov., Herpotrichiellaceae, Pyrenulaceae, Requienellaceae, Trichomeriaceae, and Verrucariaceae).
Emmanuel Serusiaux - One of the best experts on this subject based on the ideXlab platform.
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conserved genomic collinearity as a source of broadly applicable fast evolving markers to resolve species complexes a case study using the lichen forming genus peltigera section polydactylon
Molecular Phylogenetics and Evolution, 2017Co-Authors: Nicolas Magain, Jolanta Miadlikowska, Olaf Mueller, Michael Gajdeczka, Camille Truong, Asaf Salamov, Inna Dubchak, Igor V Grigoriev, Bernard Goffinet, Emmanuel SerusiauxAbstract:Abstract Synteny can be maintained for certain genomic regions across broad phylogenetic groups. In these homologous genomic regions, sites that are under relaxed purifying selection, such as intergenic regions, could be used broadly as markers for population genetic and phylogenetic studies on species complexes. To explore the potential of this approach, we found 125 Collinear Orthologous Regions (COR) ranging from 1 to >10 kb across nine genomes representing the Lecanoromycetes and Eurotiomycetes (Pezizomycotina, Ascomycota). Twenty-six of these COR were found in all 24 eurotiomycete genomes surveyed for this study. Given the high abundance and availability of fungal genomes we believe this approach could be adopted for other large groups of fungi outside the Pezizomycotina. As a proof of concept, we selected three Collinear Orthologous Regions (COR1b, COR3, and COR16), based on synteny analyses of several genomes representing three classes of Ascomycota: Eurotiomycetes, Lecanoromycetes, and Lichinomycetes. COR16, for example, was found across these three classes of fungi. Here we compare the resolving power of these three new markers with five loci commonly used in phylogenetic studies of fungi, using section Polydactylon of the cyanolichen-forming genus Peltigera (Lecanoromycetes) – a clade with several challenging species complexes. Sequence data were subjected to three species discovery and two validating methods. COR markers substantially increased phylogenetic resolution and confidence, and highly contributed to species delimitation. The level of phylogenetic signal provided by each of the COR markers was higher than the commonly used fungal barcode ITS. High cryptic diversity was revealed by all methods. As redefined here, most species represent lineages that have relatively narrower, and more homogeneous biogeographical ranges than previously understood. The scabrosoid clade consists of ten species, seven of which are new. For the dolichorhizoid clade, twenty-two new species were discovered for a total of twenty-nine species in this clade.
