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Dacrymyces flavobrunneus sp. nov. and two new combinations in Dacrymyces Nees based on morphological and phylogenetic data
Abstract
The class Dacrymycetes has two orders (Dacrymycetales and Unilacrymales), four families, and 13 genera, few of them with available molecular data and then usually of dubious delimitation. Dacrymyces Nees is a polyphyletic genus in Dacrymycetes and was introduced to accommodate one species, D. stillatus Nees, being characterized by a homogeneous composition of the intra-structure and an amphigenous or superior hymenium. In this study, neotropical specimens were added in the phylogeny of the Dacrymycetes, and as a result, Dacrymyces s.s. is emended to include species with resupinate basidiomata, unilateral hymenium, heterogeneous context, and absence of clamp connections. In this new delimitation, the new species Dacrymyces flavobrunneus sp. nov. is described using morphological and molecular data, two new combinations (D. maxidorii comb. nov. and D. spathularia comb. nov.) are proposed based on DNA analyses, and previous combinations and new species (Dacrymyces burdsallii, D. ceraceus, D. cereus, D. confluensunilateral, D. corticioides, D. grandii, D. grandinioides, D. lagerheimii, D. pulchrus, D. sobrius, and D. venustus) are formally included in the genus circumscription.
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A new genus named Dendrodacrys is proposed for a monophyletic group in Dacrymycetaceae, containing species with pulvinate to depressed basidiocarps, distinctly branched hymenial hyphidia, and up to 3-septate mature basidiospores. Four taxa in this group, occurring in Europe, are proposed as new species, viz. De. ciprense, De. concrescens, De. ellipsosporum, and De. oblongisporum, based both on morphological and DNA data (nrDNA, RPB1, RPB2, TEF-1α, 12S). These new species are all described in detail, illustrated, and compared with other published taxa that with which they can be confounded. The new combination De. paraphysatum is proposed after revising the type material of Dacrymyces paraphysatus, but other combinations or potentially new non-European species descriptions are postponed pending further studies of additional specimens.
Citation: Zamora JC, Savchenko A, González-Cruz Á, Prieto-García F, Olariaga I, Ekman S (2022). Dendrodacrys: a new genus for species with branched hyphidia in Dacrymyces s.l., with the description of four new species. Fungal Systematics and Evolution 9: 27–42. doi: 10.3114/fuse.2022.09.04
Cerinomyces (Dacrymycetes, Basidiomycota) is a genus traditionally defined by corticioid basidiocarps, in contrast to the rest of the class, which is characterized by gelatinous ones. In the traditional circumscription the genus is polyphyletic, and the monotypic family Cerinomycetaceae is paraphyletic. Aiming for a more concise delimitation, we revise Cerinomyces s.l. with a novel phylogeny based on sequences of nrDNA (SSU, ITS, LSU) and protein-coding genes (RPB1, RPB2, TEF1-α). We establish that monophyletic Cerinomyces s.s. is best characterized not by the corticioid morphology, but by a combination of traits: hyphal clamps, predominantly aseptate thin-walled basidiospores, and low content of carotenoid pigments. In our updated definition, Cerinomyces s.s. encompasses five well-supported phylogenetic clades divided into two morphological groups: (i-iii) taxa with arid corticioid basidiocarps, including the generic type C. pallidus; and (iv-v) newly introduced members with gelatinous basidiocarps, like Dacrymyces enatus and D. tortus. The remaining corticioid species of Cerinomyces s.l. are morphologically distinct and belong to the Dacrymycetaceae: our analysis places the carotenoid-rich Cerinomyces canadensis close to Femsjonia, and we transfer the clamps-lacking C. grandinioides group to Dacrymyces. In addition, we address genera related to Cerinomyces s.l. historically and morphologically, such as Ceracea, Dacryonaema and Unilacryma. Overall, we describe twenty-four new species and propose nine new combinations in both Cerinomycetaceae and Dacrymycetaceae.
A taxonomical revision of the Dacryopinax species in Mexico is presented in detail. Historically, only four species were known in the country: Dacryopinax elegans, D. lowyi, D. spathularia, and D. yungensis. Dacryopinax martinii is reported for the first time from Mexico. Taxonomical descriptions and remarks for all the species, based on macro- and micro-morphology, as well as geographical distribution are included, except for D. yungensis, as its record corresponded to a misidentification of D. spathularia. We propose a new phylogeny including the taxonomic position and relationships of all species, based on ITS and LSU sequence data. Finally, a dichotomous key to identify the four species in Mexico is provided.
We present a multilocus phylogeny of the class Dacrymycetes , based on data from the 18S, ITS, 28S, RPB1 , RPB2 , TEF-1α , 12S, and ATP6 DNA regions, with c. 90 species including the types of most currently accepted genera. A variety of methodological approaches was used to infer phylogenetic relationships among the Dacrymycetes , from a supermatrix strategy using maximum likelihood and Bayesian inference on a concatenated dataset, to coalescence-based calculations, such as quartet-based summary methods of independent single-locus trees, and Bayesian integration of single-locus trees into a species tree under the multispecies coalescent. We evaluate for the first time the taxonomic usefulness of some cytological phenotypic characters, i.e., vacuolar contents (vacuolar bodies and lipid bodies), number of nuclei of recently discharged basidiospores, and pigments, with especial emphasis on carotenoids. These characters, along with several others traditionally used for the taxonomy of this group (basidium shape, presence and morphology of clamp connections, morphology of the terminal cells of cortical/marginal hyphae, presence and degree of ramification of the hyphidia), are mapped on the resulting phylogenies and their evolution through the class Dacrymycetes discussed. Our analyses reveal five lineages that putatively represent five different families, four of which are accepted and named. Three out of these four lineages correspond to previously circumscribed and published families ( Cerinomycetaceae , Dacrymycetaceae , and Unilacrymaceae ), and one is proposed as the new family Dacryonaemataceae . Provisionally, only a single order, Dacrymycetales , is accepted within the class. Furthermore, the systematics of the two smallest families, Dacryonaemataceae and Unilacrymaceae , are investigated to the species level, using coalescence-based species delimitation on multilocus DNA data, and a detailed morphological study including morphometric analyses of the basidiospores. Three species are accepted in Dacryonaema , the type, Da. rufum , the newly combined Da. macnabbii (basionym Dacrymyces macnabbii ), and a new species named Da. macrosporum . Two species are accepted in Unilacryma ,the new U. bispora , and the type, U. unispora , the latter treated in a broad sense pending improved sampling across the Holarctic.
This article provides an outline of the classification of the kingdom Fungi (including fossil fungi. i.e. dispersed spores, mycelia, sporophores, mycorrhizas). We treat 19 phyla of fungi. These are Aphelidiomycota, Ascomycota, Basidiobolomycota, Basidiomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Entorrhizomycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota. The placement of all fungal genera is provided at the class-, order- and family-level. The described number of species per genus is also given. Notes are provided of taxa for which recent changes or disagreements have been presented. Fungus-like taxa that were traditionally treated as fungi are also incorporated in this outline (i.e. Eumycetozoa, Dictyosteliomycetes, Ceratiomyxomycetes and Myxomycetes). Four new taxa are introduced: Amblyosporida ord. nov. Neopereziida ord. nov. and Ovavesiculida ord. nov. in Rozellomycota, and Protosporangiaceae fam. nov. in Dictyosteliomycetes. Two different classifications (in outline section and in discussion) are provided for Glomeromycota and Leotiomycetes based on recent studies. The phylogenetic reconstruction of a four-gene dataset (18S and 28S rRNA, RPB1, RPB2) of 433 taxa is presented, including all currently described orders of fungi.
During the past few years, natural disasters, political or social unrest and institutional actions have imperiled herbaria. The question has been raised multiple times whether or not the data gathered about herbaria in Index Herbariorum could be used to predict which herbaria are at the greatest risk. Armed with such knowledge curators and the greater collections community might be in a better position to safeguard those herbaria. To explore the feasibility of using Index Herbariorum data in this way, we have identified a set of specific threats and then scored herbaria according to their susceptibility to those threats. These threats fall into two categories: Physical and Administrative. Physical threats are those that could lead to loss of collections through outright destruction due to catastrophic events (e.g., earthquake, flood) or loss of the protective controls (e.g., air conditioning, building security) that ensure a safe collections environment. Determination of these threats is based on location.
Administrative threats involve decisions made by the governing body to remove staff support, appropriate space or climate control measures for the collection. Physical threats were determined using GIS to plot the location of all herbaria, and then overlaying these with map layers indicating current earthquakes, floods, cyclones and landslides and potential future threats (sea level rise and civil unrest). We deduced Administrative threats from Index Herbariorum data elements. These include the status of the herbarium (active or inactive), whether or not the Index Herbariorum entry for an institution has been updated in the past 10 years, whether or not the herbarium has a designated curator, the ratio of staff to specimens, and whether or not the collection has been digitized. Each threat was assessed as absent or present, and assigned a value of 0 or 1 accordingly. Using this method, less than 4% face no identified threats; 65% face one to three threats and 35% face five or more threats. The criteria used in this study cannot alone predict the future security of a collection, or the lack thereof. The reasons for the loss of a collection are usually more complicated than Index Herbariorum data can convey. However, the large proportion of herbaria that face multiple threats suggests that all herbaria should be aware of the risk factors for their collection, perhaps conducting a self-evaluation using the criteria presented here or others, and where possible should incorporate responses to those threats into their strategic and disaster preparedness plans.
Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) (Drummond et al., 2002; Mau et al., 1999; Rannala and Yang, 1996) flourishes as a popular approach to uncover the evolutionary relationships among taxa, such as genes, genomes, individuals or species. MCMC approaches generate samples of model parameter values - including the phylogenetic tree -drawn from their posterior distribution given molecular sequence data and a selection of evolutionary models. Visualising, tabulating and marginalising these samples is critical for approximating the posterior quantities of interest that one reports as the outcome of a Bayesian phylogenetic analysis. To facilitate this task, we have developed the Tracer (version 1.7) software package to process MCMC trace files containing parameter samples and to interactively explore the high-dimensional posterior distribution. Tracer works automatically with sample output from BEAST (Drummond et al., 2012), BEAST2 (Bouckaert et al., 2014), LAMARC (Kuhner, 2006), Migrate (Beerli, 2006), MrBayes (Ronquist et al., 2012), RevBayes (Höhna et al., 2016) and possibly other MCMC programs from other domains.
The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches.
Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested datasets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.
This article describes several features in the MAFFT online service for multiple sequence alignment (MSA). As a result of recent advances in sequencing technologies, huge numbers of biological sequences are available and the need for MSAs with large numbers of sequences is increasing. To extract biologically relevant information from such data, sophistication of algorithms is necessary but not sufficient. Intuitive and interactive tools for experimental biologists to semiautomatically handle large data are becoming important. We are working on development of MAFFT toward these two directions. Here, we explain (i) the Web interface for recently developed options for large data and (ii) interactive usage to refine sequence data sets and MSAs.
The information about the distribution of 5 species of jelly fungi of Dacrymycetes, recorded in different locations of the Cerrado biome, is updated or expanded. Dacrymyces chrysospermus Berk. & M.A. Curtis, Dacryopinax elegans
(Berk. & M.A. Curtis) G.W. Martin, D. maxidorii Lowy and D. spathularia (Schwein.) G.W. Martin are the first records for the Cerrado and the Brazilian Midwest Region. Calocera cornea (Batsch) Fr. is being reported for the first time in Goiás state and newly reported for the Federal District, after 40 years.
The class Dacrymycetes has been considered a monophyletic group based on shared morphological characteristics and recent molecular studies, with bifurcate basidia and non perforate parenthosome as synapomorphies. In this review of the state of knowledge for Dacrymycetes (dacrymycetoid fungi) in Mexico, a detailed survey of the literature revealed 21 species in eight genera in Mexico; 20 belong to seven genera of Dacrymycetaceae and one species belongs to the Cerinomycetaceae. The best-represented genus is Dacrymyces, and the most-recorded species is Dacryopinax spathularia. Taxa of Dacrymycetes in Mexico have been recorded from 22 states, mainly those located in central Mexico. The members of this group recorded in Mexico are, apparently, wood-decomposers and have been most frequently collected during the wet season (end of May to beginning of October), but they can be found throughout the year. From the review, it is evident that systematic and biogeographic knowledge on the Dacrymycetes in Mexico is scarce. Thus, more extensive sampling and detailed systematic and molecular studies are needed.
Dacrymycetes, sister to Agaricomycetes, is a noteworthy lineage for studying the evolution of wooddecaying basidiomycetes; however, its species diversity and phylogeny are largely unknown. Species of Dacrymycetes previously used in molecular phylogenetic analyses are mainly derived from the Northern Hemisphere, thus insufficient knowledge exists concerning the Southern Hemisphere lineages. In this study, we investigated the species diversity of Dacrymycetes in New Zealand. We found 11 previously described species, and eight new species which were described here: Calocera pedicellata, Dacrymyces longistipitatus, D. pachysporus, D. stenosporus, D. parastenosporus, D. cylindricus, D. citrinus, and D. cyrtosporus. These eight newly described species and seven of the known ones, namely, Calocera fusca, C. cf. guepinioides, C. lutea, Dacrymyces flabelliformis, D. intermedius, D. subantarcticensis, and Heterotextus miltinus, have rarely or never been recorded from the Northern Hemisphere. In a molecular-based phylogeny, these New Zealand strains were scattered throughout the Dacrymycetaceae clade. Sequences obtained from specimens morphologically matching C. guepinioides were separated into three distant clades. Because no obvious morphological differences could be discerned between the specimens in each clade and no sequence exists from the type specimen, a C. guepinioides s.str. clade could not be determined. This survey of dacrymycetous species in the Southern Hemisphere has increased taxon sampling for phylogenetic analyses that can serve as a basis for the construction of a stable classification of Dacrymycetes.
A Dacryopinax species that was cultured in Costa Rica and fruited in the laboratory provided DNA for the first sequenced genome for the Dacrymycetes. Here we characterize the isolate morphologically and cytologically and name it D. primogenitus Molecular sequences from the nuclear large subunit gene and internal transcribed spacer indicated that it is closely related to the South American D. indacocheae with which it agrees structurally. Both species form conidia on the basidiocarp, and D primogenitus also forms them on the mycelium. Unlike previous reports for the Dacrymycetales postmeiotic nuclear division results in uninucleate basidiospores and six residual nuclei in the basidium after basidiospore discharge. Ultrastructural analysis shows the characteristic septal-pore apparatus for the class and endogenous origin of the epibasidia/sterigmata, which may be a common occurrence in Dacrymycetes and the early diverging orders of its sister class, the Agaricomycetes.
This article presents W-IQ-TREE, an intuitive and user-friendly web interface and server for IQ-TREE, an efficient phylogenetic
software for maximum likelihood analysis. W-IQ-TREE supports multiple sequence types (DNA, protein, codon, binary and morphology)
in common alignment formats and a wide range of evolutionary models including mixture and partition models. W-IQ-TREE performs
fast model selection, partition scheme finding, efficient tree reconstruction, ultrafast bootstrapping, branch tests, and
tree topology tests. All computations are conducted on a dedicated computer cluster and the users receive the results via
URL or email. W-IQ-TREE is available at http://iqtree.cibiv.univie.ac.at. It is free and open to all users and there is no login requirement.
Dacryopinax lowyi is described as new. The species can be differentiated from others in the genus by basidiome characteristics, a zone of subcortical vesicles and vesicular hyphae, basidiospores and basidia features, and substrate preference. A key to all known species of Dacryopinax is also provided.
Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast
programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus,
there is need for additional approaches that employ different search strategies to find ML trees and that are at the same
time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation
method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found
higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use
the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein
alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3–97.1%. IQ-TREE
is freely available at http://www.cibiv.at/software/iqtree.
Collections of macromycetes made in seven municipalities in southern Brazil, viz. six in Rio Grande do Sul and one in Santa Catarina, are listed. They belonged to the Myxomycota (6 spp.), Ascomycota (54 spp.) and Basidiomycota (189 spp.). First records for Brazil could be Battarrea phalloides, Amanita rubescens, Boletus edulis and Mycena filopes, the last three found under exotic Pinus.São listadas as coletas executadas pelo autor em sete municípios no sul do Brasil, sendo seis no estado de Rio Grande do Sul e um no estado de Santa Catarina. Pertencem à Myxomycota (6 espécies), Ascomycota (54 espécies) e Basidiomycota (189 espécies). Primeiros registros para o Brasil são aparentemente: Battarrea phalloides, Amanita rubescens, Boletus edulis e Mycena filopes, as últimas três encontradas sob espécies de Pinus.
We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements our RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.
The class Dacrymycetes is a rather small group of brown-rot wood-decaying jelly fungi characterised by forked basidia and an orange to yellow gelatinous to cartilaginous fruit body. In Japan, dacrymycetous fungi had not been investigated for a long time, justifying a taxonomic re-examination. In the present study we attempted an investigation of the dacrymycetous fungal flora of Japan, and recognised 28 taxonomic entities, including five new taxa, i.e. Dacrymyces ancyleus, D. aureosporus, D. pinacearum, D. subarcticus and Dacryopinax sphenocarpa, and nine new records. Due to the present survey, the total number of dacrymycetous species recorded from Japan increased from 28 to 42. Of the newly described species, Dacrymyces ancyleus is characterised by recurved, cylindrical basidiocarps and hyphae with clamp connections. Dacrymyces aureosporus resembles D. chrysospermus, but differs in wall thickness of its marginal hyphae. Dacrymyces pinacearum and D. subarcticus represent new coelomycetous anamorphic species. Dacryopinax sphenocarpa has sharp, spathulate basidiocarps, and hyphae with clamp connections. Descriptions, illustrations and photographs of fruit bodies are presented with some taxonomic notes. Molecular phylogenetic analyses were conducted to verify the species identification, and the remaining problems in Dacrymycetes taxonomy are discussed based on these data.
MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types—e.g. morphological, nucleotide, and protein—and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.
Availability: http://morphbank.ebc.uu.se/mrbayes
Contact: fredrik.ronquist@ebc.uu.se
*
To whom correspondence should be addressed.
The Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.
Thirty-two strains representing sixteen species in the Dacrymycetales were tested for ability to decay wood using the soil block test. Dacrymyces stillatus, D. capitatus, D. dictyosporus, D. spathularia, Cerinomyces ceraceus, Calocera cornea and C. lutea caused considerable decay of wood. Dacrymyces palmatus, D. minor, D. novae-zelandiae and Calocera viscosa decayed wood to a lesser but significant extent. Three distinct types of brown-rot were noted, and one type of white-rot. Some brown-rotting strains were unusual since they were able to remove considerable amounts of lignin.
Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.
Dacrymycetes, a morphologically, chemically, and ecologically well-defined monophyletic group of wood-decaying Basidiomycota, is reviewed in this article. The life cycle of Dacrymyces stillatus is considered as representative of all members of the class. Traditional taxonomy is based on morphological characters. This classification is compared with molecular phylogenies. The evolutionary trends of dacrymycetaceous fungi are discussed.
Concepts of relationships within the "jelly fungi" have undergone several revisions during the past several decades. While basidial morphology remains an important taxonomic consideration, ultrastructural studies, especially of the septal pore apparatus and the spindle pole body, as well as in vitro investigations, suggest that similar basidial types have evolved in divergent taxa. Among the taxa included by G. W. Martin in 1945 in the Tremellales s. l., the Ceratobasidiales, Tulasnellales, Dacrymycetales, and Auriculariales, as defined by R. J. Bandoni in 1984, form a coherent group. The Filobasidiaceae, Carcinomycetaceae, and Rhynchogastremaceae, i.e., the Filobasidiales, are possibly not monophyletic; therefore, the recognition of the Filobasidiales is questionable. Species concepts have also been refined due primarily to studies in culture, pairing tests, and improved microscopic studies utilizing phase optics. It seems obvious that neither one technique nor one definition of a species will suffice for continued refinements in the systematics of the "jelly fungi."
Dacrymyces Nees ex Fr. is divided into two subgenera, Dacrymyces and Turbinaster Kobay. Thirty species and one variety are described and illustrated: Dacrymyces ovisporus Bref., D. nigrescens Lowy, D. enatus (Berk. & Curt.) Mass., D. enatus var. macrosporus L. Kenn., D. paraphysalus L. Olive, D. adpressus Grogn., D. corlicioides Ell. & Everh., D. cokeri sp. nov., D. punctiformis Neuh., D. confluens P. Karst., D. microsporus P. Karst., D. dacryomitri-formis sp. nov., D. intermedius L. Olive, D. stillatus Nees ex Fr., D. lacrymalis ([Pers.] S. F. Gray) Sommer, D. minor Peck, D. capitatus Schw., D. cupularis Lloyd, D. dictyosporus Martin, D. falcatus Brasf., D. san-augustinil Kobay., D. coryneoides (P. Hcnn.) comb, nov., D. novae-zelandiae sp. nov., D. chryso-spermus Berk. & Curt., D. estonicus Raitv., D. minuius (L. Olive) comb, nov., D. marginatus nom. nov., D. pedunculatus (Berk. & Curt.) Cokcr, D. chrysocomus (Bull, ex Fr.) Tul., D. suecicus sp. nov., and D. variisporus sp. nov.Species Excludendae, Nomina Nuda, and Species Inquirendac sections follow.
We analyzed the DNA sequences of four gene regions, 28S and 18S rDNA, the ITS region, and rpb2, to obtain a high-resolution phylogenetic tree of Dacrymycetes. In addition, we comparatively studied micro- and macromorphological characteristics of representative species. The traditional generic classification based on morphological characteristics was not reflected by our molecular phylogenies. Ancestral state reconstructions indicated that the morphology of basidia and clamp-connections are evolutionarily stable. In contrast, basidiocarps and basidiospore septation patterns appear variable. Dacrymyces unisporus shares the typical dolipores with non-perforate parenthesomes with the other dacrymycetous taxa but is a unique species in having predominantly non-bifurcate basidia and subglobose to ovoid basidiospores with transverse and longitudinal septations. In molecular phylogenies this species is a member of Dacrymycetes but always occupies the sister group position to the rest of the Dacrymycetes. Based on our results we propose a new genus, Unilacryma, for D. unisporus. For proper accommodation of this taxon, we introduce the family Unilacrymaceae and the order Unilacrymales.
For several years we have been concentrating on developing methods for large-scale sequencing projects and the resulting software
is used in many major laboratories and genome centers. In the course of this work we devised a very powerful graphical user
interface for use in our sequence assembly and editing program GAP4 (1), and recently we have started to write replacements for our old analysis programs NIP (2) and SIP (3), and these entirely new programs have the same user interface as GAP4. The older programs were described in the previous
edition of this book (4), and are largely unchanged, but are still included in our package distribution. Here we give an overview of our methods
for sequencing projects and also of our new analytical programs, all of which are fully documented in our 500-page manual
which is available for printing or as an HTML document (http://www.mrc-lmb.cam.ac.uk/pubseq). This site also contains color versions of the figures used in this chapter and information about obtaining our package.
Typewritten. Thesis--University of London, November, 1961-
Detailed restriction analyses of many samples often require substantial amounts of time and effort for DNA extraction, restriction digests, Southern blotting, and hybridization. We describe a novel approach that uses the polymerase chain reaction (PCR) for rapid simplified restriction typing and mapping of DNA from many different isolates. DNA fragments up to 2 kilobase pairs in length were efficiently amplified from crude DNA samples of several pathogenic Cryptococcus species, including C. neoformans, C. albidus, C. laurentii, and C. uniguttulatus. Digestion and electrophoresis of the PCR products by using frequent-cutting restriction enzymes produced complex restriction phenotypes (fingerprints) that were often unique for each strain or species. We used the PCR to amplify and analyze restriction pattern variation within three major portions of the ribosomal DNA (rDNA) repeats from these fungi. Detailed mapping of many restriction sites within the rDNA locus was determined by fingerprint analysis of progressively larger PCR fragments sharing a common primer site at one end. As judged by PCR fingerprints, the rDNA of 19 C. neoformans isolates showed no variation for four restriction enzymes that we surveyed. Other Cryptococcus spp. showed varying levels of restriction pattern variation within their rDNAs and were shown to be genetically distinct from C. neoformans. The PCR primers used in this study have also been successfully applied for amplification of rDNAs from other pathogenic and nonpathogenic fungi, including Candida spp., and ought to have wide applicability for clinical detection and other studies.
A new species in Dacryopinax from Brazil
- B Lowy
Lowy B (1981) A new species in Dacryopinax from Brazil. Mycotaxon
13:428-430
New or noteworthy tropical fungi. IV
- GW Martin
Neotropical Polypores part 1
- L Ryvarden
Taxonomic studies in the Dacrymycetaceae I. Cerinomyces Martin
- Rfr Mcnabb
McNabb RFR (1964) Taxonomic studies in the Dacrymycetaceae I.
Cerinomyces Martin. N Z J Bot 2:415-424. https://doi.org/10.
1080/0028825x.1964.10428762
Taxonomic studies in the Dacrymycetaceae V. Heterotextus Lloyd
- Rfr Mcnabb
McNabb RFR (1965c) Taxonomic studies in the Dacrymycetaceae V.
Heterotextus Lloyd. N Z J Bot 3:215-222. https://doi.org/10.1080/
0028825x.1965.10428722
The Staden Package. Computer methods in molecular biology
- R Staden
- K F Beal
- J K Bonfield
Staden R, Beal KF, Bonfield JK (1998) The Staden Package. Computer
methods in molecular biology. Bioinform Methods Protocols 132:
115-130
- B Lowy
Lowy B (1971) Tremellales. Flora Neotropica, Monograph no. 6. Hafner,
New York 153 pp
- L Ryvarden
Ryvarden L (2004) Neotropical Polypores part 1. Synopsis Fungorum 19:
229p
Index Herbariorum: a global directory of public herbaria and associated staff
- B Thiers
Thiers B (2016 [continuously updated]) Index Herbariorum: a global
directory of public herbaria and associated staff. New York
Botanical Garden's Virtual Herbarium. Available from: http://
sweetgum.nybg.org/science/ih/ (accessed 20 September 2021)
https://doi.org/10.3897/biss.2.26440