cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14831196
title: Genetic diversity and gene flow amongst admixed populations of <i>Ganoderma boninense</i>, causal agent of basal stem rot in African oil palm (<i>Elaeis guineensis</i> Jacq.) in Sarawak (Malaysia), Peninsular Malaysia, and Sumatra (Indonesia)

description: In 1911 and 1917, the first commercial plantings of African oil palm (<i>Elaeis guineensis</i> Jacq.) were made in Indonesia and Malaysia in Southeast Asia. In less than 15 years, basal stem rot (BSR) was reported in Malaysia. It took nearly another seven decades to identify the main causal agent of BSR as the fungus, <i>Ganoderma boninense</i>. Since then, research efforts have focused on understanding <i>G. boninense</i> disease epidemiology, biology, and etiology, but limited progress was made to characterize pathogen genetic diversity, spatial structure, pathogenicity, and virulence. This study describes pathogen variability, gene flow, population differentiation, and genetic structure of <i>G. boninense</i> in Sarawak (Malaysia), Peninsular Malaysia, and Sumatra (Indonesia) inferred by 16 highly polymorphic cDNA-SSR (simple sequence repeat) markers. Marker-inferred genotypic diversity indicated a high level of pathogen variability among individuals within a population and among different populations. This genetic variability is clearly the result of outcrossing between basidiospores to produce recombinant genotypes. Although our results indicated high gene flow among the populations, there was no significant genetic differentiation among <i>G. boninense</i> populations on a regional scale. It suggested that <i>G. boninense</i> genetic makeup is similar across a wide region. Furthermore, our results revealed the existence of three admixed genetic clusters of <i>G. boninense</i> associated with BSR-diseased oil palms sampled throughout Sarawak, Peninsular Malaysia, and Sumatra. We postulate that the population structure is likely a reflection of the high genetic variability of <i>G. boninense</i> populations. This, in turn, could be explained by highly successful outcrossing between basidiospores of <i>G. boninense</i> from Southeast Asia and introduced genetic sources from various regions of the world, as well as regional adaptation of various pathogen genotypes to different palm hosts. Pathogen variability and population structure could be employed to deduce the epidemiology of <i>G. boninense</i>, as well as the implications of plantation cultural practices on BSR disease control in different regions.
DOI: 10.6084/m9.figshare.14935436
title: Thaxterogaster revisited: A phylogenetic and taxonomic overview of sequestrate Cortinarius from Patagonia

description: In the Patagonian region, <i>Cortinarius</i> is the most diverse and abundant genus of ectomycorrhizal fungi with at least 250 species. Sequestrate forms were until recently documented within the genus <i>Thaxterogaster</i>, a genus now known to be polyphyletic, and many were consequently transferred to <i>Cortinarius</i>. Original descriptions were mostly available in German and Spanish and interpretations of morphological structures outdated. Despite recent advances in <i>Cortinarius</i> systematics, the current classification, diversity, and ecology of sequestrate “cortinarioid” fungi in Patagonia remain unclear. The objective of this study was to provide an update on sequestrate <i>Cortinarius</i> of southern South America. We documented each species with morphological descriptions, photographs, basidiospore scanning electron microscopy (SEM) images, and molecular characterization using nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) and nuc 28S rDNA (28S) sequence data. Original descriptions of taxa were also translated to English and revised based on fresh collections. We documented 24 species from Patagonia based on molecular data and conducted morphological and phylogenetic analysis for 18 previously described species based on type and reference specimens. In addition, we formally described two new species. Four additional taxa were provisionally determined as new but require further study. New ITS sequence data were produced from eight type specimens. We also provide a new name, <i>Cortinarius gloiodes</i>, nom. nov., for the taxon previously described as <i>Thaxterogaster gliocyclus</i>. In addition to the species treated in detail, we provided additional reference information and discussion on six described species that remained incompletely known or for which no recent collections were found. Of the 24 taxa documented from Patagonia, 15 species were assigned to 12 current sections in the genus <i>Cortinarius</i>. Analysis of spore ultrastructure showed that sequestrate forms of Patagonian <i>Cortinarius</i> lack a true perisporium.
DOI: 10.6084/m9.figshare.14785684.v2
title: Three new species of <i>Trichoderma</i> in the Harzianum and Longibrachiatum lineages from Peruvian cacao crop soils based on an integrative approach

description: The hyperdiverse genus <i>Trichoderma</i> is one of most useful groups of microbes for a number of human activities, and their accurate identification is crucial. The structural simplicity and lack of distinctive phenotypic variation in this group enable the use of DNA-based species delimitation methods in combination with phylogenies (and morphology when feasible) to establish well-supported boundaries among species. Our study employed a multilocus phylogeny and four DNA-based methods (automated barcode gap discovery [ABGD], statistical parsimony [SPN], generalized mixed Yule coalescent [GMYC], and Bayesian phylogenetics and phylogeography [BPP]) for four molecular markers (<i>acl1, act, rpb2,</i> and <i>tef1</i>) to delimit species of two lineages of <i>Trichoderma</i>. Although incongruence among these methods was observed in our analyses, the genetic distance (ABGD) and coalescence (BPP) methods and the multilocus phylogeny strongly supported and confirmed recognition of 108 and 39 different species in the Harzianum and Longibrachiatum lineages, including three new species associated with cacao farms in northern Peru, namely, <i>T.</i><i>awajun</i>, sp. nov., <i>T.</i> <i>jaklitschii</i>, sp. nov., and <i>T.</i> <i>peruvianum</i>, sp. nov. Morphological distinctions between the new species and their close relatives are primarily related to growth rates, colony appearance, and size of phialides and conidia. This study confirmed that an integrative approach (DNA-based methods, multilocus phylogeny, and phenotype) is more likely to reliably verify supported species boundaries in <i>Trichoderma</i>.
DOI: 10.6084/m9.figshare.14935472.v2
title: The slippery nature of ectomycorrhizal host specificity: <i>Suillus</i> fungi associated with novel pinoid (<i>Picea</i>) and abietoid (<i>Abies</i>) hosts

description: <i>Suillus</i> is among the best-known examples of an ectomycorrhizal (ECM) fungal genus that demonstrates a high degree of host specificity. Currently recognized host genera of <i>Suillus</i> include <i>Larix, Pinus</i>, and <i>Pseudotsuga</i>, which all belong to the pinoid clade of the family Pinaceae. Intriguingly, <i>Suillus</i> sporocarps have been sporadically collected in forests in which known hosts from these genera are locally absent. To determine the capacity of <i>Suillus</i> to associate with alternative hosts in both the pinoid and abietoid clades of Pinaceae, we examined the host associations of two <i>Suillus</i> species (<i>S. punctatipes</i> and <i>S. glandulosus</i>) through field-based root tip sampling and seedling bioassays. Root tip collections underneath <i>Suillus</i> sporocarps were molecularly identified (fungi: nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 [ITS barcode]; plant: <i>trn</i>L) to assess the association with multiple hosts. The bioassays contained both single- and two-species treatments, including a primary (<i>Larix</i> or <i>Pseudotsuga</i>) and a secondary (<i>Picea, Pinus</i>, or <i>Abies</i>) host. For the <i>S. punctatipes</i> bioassay, an additional treatment in which the primary host was removed after 8 mo was included to assess the effect of primary host presence on longer-term ECM colonization. The field-based results confirmed that <i>Suillus</i> fungi were able to associate with <i>Abies</i> and <i>Tsuga</i> hosts, representing novel host genera for this genus. In the bioassays, colonization on the primary hosts was detected in both single- and two-species treatments, but no colonization was present when <i>Picea</i> and <i>Abies</i> hosts were grown alone. Removal of a primary host had no effect on percent ECM colonization, suggesting that primary hosts are not necessary for sustaining <i>Suillus</i> colonization once they are successfully established on secondary hosts. Collectively, our results indicate that host specificity is more flexible in this genus than previously acknowledged and help to explain the presence of <i>Suillus</i> in forests where recognized hosts are not present.
DOI: 10.6084/m9.figshare.14935472
title: The slippery nature of ectomycorrhizal host specificity: <i>Suillus</i> fungi associated with novel pinoid (<i>Picea</i>) and abietoid (<i>Abies</i>) hosts

description: <i>Suillus</i> is among the best-known examples of an ectomycorrhizal (ECM) fungal genus that demonstrates a high degree of host specificity. Currently recognized host genera of <i>Suillus</i> include <i>Larix, Pinus</i>, and <i>Pseudotsuga</i>, which all belong to the pinoid clade of the family Pinaceae. Intriguingly, <i>Suillus</i> sporocarps have been sporadically collected in forests in which known hosts from these genera are locally absent. To determine the capacity of <i>Suillus</i> to associate with alternative hosts in both the pinoid and abietoid clades of Pinaceae, we examined the host associations of two <i>Suillus</i> species (<i>S. punctatipes</i> and <i>S. glandulosus</i>) through field-based root tip sampling and seedling bioassays. Root tip collections underneath <i>Suillus</i> sporocarps were molecularly identified (fungi: nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 [ITS barcode]; plant: <i>trn</i>L) to assess the association with multiple hosts. The bioassays contained both single- and two-species treatments, including a primary (<i>Larix</i> or <i>Pseudotsuga</i>) and a secondary (<i>Picea, Pinus</i>, or <i>Abies</i>) host. For the <i>S. punctatipes</i> bioassay, an additional treatment in which the primary host was removed after 8 mo was included to assess the effect of primary host presence on longer-term ECM colonization. The field-based results confirmed that <i>Suillus</i> fungi were able to associate with <i>Abies</i> and <i>Tsuga</i> hosts, representing novel host genera for this genus. In the bioassays, colonization on the primary hosts was detected in both single- and two-species treatments, but no colonization was present when <i>Picea</i> and <i>Abies</i> hosts were grown alone. Removal of a primary host had no effect on percent ECM colonization, suggesting that primary hosts are not necessary for sustaining <i>Suillus</i> colonization once they are successfully established on secondary hosts. Collectively, our results indicate that host specificity is more flexible in this genus than previously acknowledged and help to explain the presence of <i>Suillus</i> in forests where recognized hosts are not present.
DOI: 10.6084/m9.figshare.14794110
title: <i>Gaeumannomyces nanograminis</i>, sp. nov., a hyphopodiate fungus identified from diseased roots of ultradwarf bermudagrass in the United States

description: The genus <i>Gaeumannomyces</i> (Magnaporthaceae, Magnaporthales, Sordariomycetes, Ascomycota) includes root-infecting pathogens, saprobes, and endophytes. Morphological, biological, and phylogenetic analyses were employed to identify fungal isolates derived from turfgrass roots colonized with ectotrophic, dark runner hyphae. Phylogenetic trees for partial sequences of the 18S nuc rDNA, ITS1-5.8S-ITS2 nuc rDNA internal transcribed spacer, and 28S nuc rDNA regions and of the minichromosome maintenance complex 7 (<i>MCM7</i>), largest subunit of RNA polymerase II (<i>RPB1</i>), and translation elongation factor 1-alpha (<i>TEF1</i>) genes were obtained via maximum likelihood and Bayesian methods. Our isolates consistently formed a distinct and highly supported clade within <i>Gaeumannomyces</i>. Common and distinctive biological and morphological characters reinforced these findings. Additionally, we conducted pathogenicity evaluations and demonstrated the ability of this fungus to colonize roots of ultradwarf bermudagrass (<i>Cynodon dactylon</i> (L.) Pers. × <i>C. transvaalensis</i> Burtt-Davey), its native host, via ectotrophic, dark runner hyphae, causing disease symptoms including root discoloration and reduced root and shoot mass. Altogether, our discoveries enabled recognition and description of a new species, <i>Gaeumannomyces nanograminis</i>, associated with rotted roots of ultradwarf bermudagrass.
DOI: 10.6084/m9.figshare.14794110.v1
title: <i>Gaeumannomyces nanograminis</i>, sp. nov., a hyphopodiate fungus identified from diseased roots of ultradwarf bermudagrass in the United States

description: The genus <i>Gaeumannomyces</i> (Magnaporthaceae, Magnaporthales, Sordariomycetes, Ascomycota) includes root-infecting pathogens, saprobes, and endophytes. Morphological, biological, and phylogenetic analyses were employed to identify fungal isolates derived from turfgrass roots colonized with ectotrophic, dark runner hyphae. Phylogenetic trees for partial sequences of the 18S nuc rDNA, ITS1-5.8S-ITS2 nuc rDNA internal transcribed spacer, and 28S nuc rDNA regions and of the minichromosome maintenance complex 7 (<i>MCM7</i>), largest subunit of RNA polymerase II (<i>RPB1</i>), and translation elongation factor 1-alpha (<i>TEF1</i>) genes were obtained via maximum likelihood and Bayesian methods. Our isolates consistently formed a distinct and highly supported clade within <i>Gaeumannomyces</i>. Common and distinctive biological and morphological characters reinforced these findings. Additionally, we conducted pathogenicity evaluations and demonstrated the ability of this fungus to colonize roots of ultradwarf bermudagrass (<i>Cynodon dactylon</i> (L.) Pers. × <i>C. transvaalensis</i> Burtt-Davey), its native host, via ectotrophic, dark runner hyphae, causing disease symptoms including root discoloration and reduced root and shoot mass. Altogether, our discoveries enabled recognition and description of a new species, <i>Gaeumannomyces nanograminis</i>, associated with rotted roots of ultradwarf bermudagrass.
DOI: 10.6084/m9.figshare.14963458
title: Secretome characterization of the lignocellulose-degrading fungi <i>Pycnoporus sanguineus</i> and <i>Ganoderma resinaceum</i> growing on <i>Panicum prionitis</i> biomass

description: C4 grasses are common species in rangelands around the world and represent an attractive option for second-generation biofuel production. Although they display high polysaccharide content and reach great levels of biomass accumulation, there is a major technical issue to be addressed before they can be used for bioethanol industrial production: lignin removal. Concerning this, <i>Pycnoporus</i> and <i>Ganoderma</i> fungal genera have been highlighted due to their ability to hydrolyze lignocellulose in biological pretreatments. Our goals here were to evaluate the pretreatment efficiency using the secretome of species from <i>Pycnoporus</i> and <i>Ganoderma</i> spp. harvested from a glucose-free inductive medium (using a C4 grass) and to identify the fungal enzymatic activities responsible for the lignin degradation and glucose release. Our results show that <i>P. sanguineus</i> secretome exhibits a higher activity of lignocellulolytic enzymes such as cellulases, xylanases, laccases, and manganese peroxidases compared with that from <i>G. resinaceum</i>. Interestingly, zymograms in the presence of 2 M glucose suggest that a β-glucosidase isoform from <i>P. sanguineus</i> could be glucose tolerant. The proteomic approach carried out allowed the identification of 73 and 180 different proteins in <i>G. resinaceum</i> and <i>P. sanguineus</i> secretomes, respectively, which were functionally classified in five main categories and a miscellaneous group. These results open new avenues for future experimental work that lead to a deeper comprehension and a greater application of the mechanisms underlying lignocellulosic biomass degradation.
DOI: 10.6084/m9.figshare.15091204
title: Seven new <i>Serendipita</i> species associated with Australian terrestrial orchids

description: <i>Serendipita</i> is one of the main fungal genera that form mutualistic associations with species of orchids (Orchidaceae). Here, seven new <i>Serendipita</i> species associated with various Australian orchid genera are described. These <i>Serendipita</i> species were originally characterized by multilocus DNA sequence species delimitation analyses (three mtDNA and four nuclear genes) and confirmed as distinct with addition of further isolates and reanalysis of nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) and nuc 28S rDNA (28S). Culture morphology and microscopic features are presented for each species, three of which are binucleate and four multinucleate. For the ITS region, the seven species have within-species sequence divergence between 1.07% and 4.31%, and all but one of the species pairs is separated by interspecific divergence of at least 4.35%. The newly described <i>Serendipita</i> species, <i>S. australiana, S. communis, S. occidentalis, S. rarihospitum, S. secunda, S. talbotii</i>, and <i>S. warcupii</i>, are shown to be separate species from <i>S. vermifera</i> on the basis of comparison against a sequence from the type. Isolates originally identified by Warcup as <i>Sebacina</i> “<i>vermifera</i>” from <i>Caladenia</i> orchids are revised and shown to belong to three of the species newly described here. Some non-<i>Caladenia</i> isolates identified by Warcup as <i>S</i>. “<i>vermifera</i>” are also shown to be non-conspecific with the type of <i>S. vermifera</i>. On the basis of ITS sequences, 346 isolates from 26 other studies, previously identified under provisional designations, are accommodated under the novel species. The species of <i>Serendipta</i> described here associate with the Australian orchid genera <i>Caladenia, Cyanicula, Elythranthera, Ericksonella, Eriochilus, Glossodia</i>, and <i>Pheladenia</i>. Most of the novel <i>Serendipita</i> species occur widely across Australia, often with widely distributed hosts, but one species, <i>Serendipita rarihospitum</i>, associates with narrowly distributed orchid species.
DOI: 10.6084/m9.figshare.14831196.v2
title: Genetic diversity and gene flow amongst admixed populations of <i>Ganoderma boninense</i>, causal agent of basal stem rot in African oil palm (<i>Elaeis guineensis</i> Jacq.) in Sarawak (Malaysia), Peninsular Malaysia, and Sumatra (Indonesia)

description: In 1911 and 1917, the first commercial plantings of African oil palm (<i>Elaeis guineensis</i> Jacq.) were made in Indonesia and Malaysia in Southeast Asia. In less than 15 years, basal stem rot (BSR) was reported in Malaysia. It took nearly another seven decades to identify the main causal agent of BSR as the fungus, <i>Ganoderma boninense</i>. Since then, research efforts have focused on understanding <i>G. boninense</i> disease epidemiology, biology, and etiology, but limited progress was made to characterize pathogen genetic diversity, spatial structure, pathogenicity, and virulence. This study describes pathogen variability, gene flow, population differentiation, and genetic structure of <i>G. boninense</i> in Sarawak (Malaysia), Peninsular Malaysia, and Sumatra (Indonesia) inferred by 16 highly polymorphic cDNA-SSR (simple sequence repeat) markers. Marker-inferred genotypic diversity indicated a high level of pathogen variability among individuals within a population and among different populations. This genetic variability is clearly the result of outcrossing between basidiospores to produce recombinant genotypes. Although our results indicated high gene flow among the populations, there was no significant genetic differentiation among <i>G. boninense</i> populations on a regional scale. It suggested that <i>G. boninense</i> genetic makeup is similar across a wide region. Furthermore, our results revealed the existence of three admixed genetic clusters of <i>G. boninense</i> associated with BSR-diseased oil palms sampled throughout Sarawak, Peninsular Malaysia, and Sumatra. We postulate that the population structure is likely a reflection of the high genetic variability of <i>G. boninense</i> populations. This, in turn, could be explained by highly successful outcrossing between basidiospores of <i>G. boninense</i> from Southeast Asia and introduced genetic sources from various regions of the world, as well as regional adaptation of various pathogen genotypes to different palm hosts. Pathogen variability and population structure could be employed to deduce the epidemiology of <i>G. boninense</i>, as well as the implications of plantation cultural practices on BSR disease control in different regions.
DOI: 10.6084/m9.figshare.15091080.v2
title: Novel species of <i>Alternaria</i> section <i>Nimbya</i> from Iran as revealed by morphological and molecular data

description: In this study, the diversity of <i>Alternaria</i> species in section <i>Nimbya</i> associated with symptomatic plants in the Cyperaceae and Juncaceae families was assessed. Multilocus sequence analyses of the rDNA internal transcribed spacer (ITS) region and parts of <i>Alternaria</i> major allergen (<i>Alt a 1</i>), glyceraldehyde-3-phosphate dehydrogenase (<i>GAPDH</i>), second largest subunit of RNA polymerase II (<i>RPB2</i>), and translation elongation factor 1-alpha (<i>TEF1</i>) genes revealed the presence of two previously known species, <i>A. scirpivora</i> and <i>A. caricicola</i>, and three new species, which are described here as <i>A. cypericola</i>, sp. nov., <i>A. heyranica</i>, sp. nov., and <i>A. junci-acuti</i>, sp. nov. These new species were characterized morphologically with respect to the dimensions of conidia, the number of pseudosepta in mature conidia, and the type of conidium apical beak. According to the results of phylogenetic analyses, the presence of long, filiform true beak is not a reliable morphological indicator for grouping species in sections <i>Alternantherae</i> and <i>Nimbya</i> and phylogenetic species recognition should be used. All identified species were described, illustrated, and their morphology and phylogenetic relationships with other species in <i>Alternaria</i> section <i>Nimbya</i> were discussed.