Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative proteincoding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter-and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.DNA barcoding | fungal biodiversity T he absence of a universally accepted DNA barcode for Fungi, the second most speciose eukaryotic kingdom (1, 2), is a serious limitation for multitaxon ecological and biodiversity studies. DNA barcoding uses standardized 500-to 800-bp sequences to identify species of all eukaryotic kingdoms using primers that are applicable for the broadest possible taxonomic group. Reference barcodes must be derived from expertly identified vouchers deposited in biological collections with online metadata and validated by available online sequence chromatograms. Interspecific variation should exceed intraspecific variation (the barcode gap), and barcoding is optimal when a sequence is constant and unique to one species (3, 4). Ideally, the barcode locus would be the same for all kingdoms. A region of the mitochondrial gene encoding the cytochrome c oxidase subunit 1 (CO1) is the barcode for animals (3, 4) and the default marker adopted by the Consortium for the Barcode of Life for all groups of organisms, including fungi (5). In Oomycota, part of the kingdom Stramenopila historically studied by mycologists, the de facto barcode internal transcribed spacer (ITS) region is suitable for identification, but the default CO1 marker is more reliable in a few clades of closely related species (6)...

We examined phylogenetic relationships among species of the mycoparasite genus Syncephalis using sequences from three nuclear ribsosomal DNA genes (18S, 5.8S, and 28S nuc rDNA) and a gene encoding the largest subunit of RNA polymerase II (RPB1). Our data set included 88 Syncephalis isolates comprising 23 named species and several unnamed taxa. We also revived a culturing technique using beef liver and cellophane to grow several Syncephalis isolates without their host fungi to obtain pure parasite DNA. Most isolates, however, were grown in co-cultures with their host fungi, so we designed Syncephalis-specific primers to obtain sequence data. Individual and combined data sets were analyzed by maximum likelihood (ML) and Bayesian methods. We recovered 20 well-supported lineages and 38 operational taxonomic units (OTUs). Most major clades contained isolates from distant localities on multiple continents. There were taxonomic and nomenclature issues within several clades, probably due to high phenotypic plasticity or species dimorphism. We also conducted an analysis of Syncephalis nuc rDNA internal transcribed spacer (ITS) sequences for 31 phylogenetically diverse isolates, and we determined that most Syncephalis species have long ITS sequences relative to other fungi. Although commonly employed eukaryotic and fungal primers are compatible with diverse Syncephalis species, the ITS sequences of Syncepahlis are nonetheless rarely recovered in environmental molecular diversity surveys.

Improved sequencing technologies have profoundly altered global views of fungal diversity and evolution. High throughput sequencing methods are critical for studying fungi due to the cryptic, symbiotic nature of many species, particularly those that are difficult to culture. However, the low coverage genome sequencing (LCGS) approach to phylogenomic inference has not been widely applied to fungi. Here we analyzed 171 Kickxellomycotina fungi using LCGS methods to obtain hundreds of marker genes for robust phylogenomic reconstruction. Additionally, we mined our LCGS data for a set of nine rDNA and protein coding genes to enable analyses across species for which no LCGS data were obtained. The main goals of this study were to: 1) evaluate the quality and utility of LCGS data for both phylogenetic reconstruction and functional annotation, 2) test relationships among clades of Kickxellomycotina, and 3) perform comparative functional analyses between clades to gain insight into putative trophic modes. In opposition to previous studies, our nine-gene analyses support two clades of arthropod gut dwelling species and suggest a possible single evolutionary event leading to this symbiotic lifestyle. Furthermore, we resolve the mycoparasitic Dimargaritales as the earliest diverging clade in the subphylum and find four major clades of Coemansia species. Finally, functional analyses illustrate clear variation in predicted carbohydrate active enzymes and secondary metabolites (SM) based on ecology, i.e., biotroph vs. saprotroph. Saprotrophic Kickxellales broadly lack many known pectinase families compared to saprotrophic Mucoromycota and are depauperate for SM but are enriched for chitinases compared to biotrophic taxa in Zoopagomycota.

No abstract

Four new species of Coemansia from Taiwan are described. Three produce spirally twisted sporangiophores, and these new taxa increase the number of species in the Coemansia spiralis complex from three to six. Each new taxon is morphologically unique. Coemansia biformis, sp. nov., has two different asexual reproductive types on the same thallus; one is straight and the other has a spiral fertile region. Coemansia helicoidea, sp. nov., has stoloniferous sporangiophores with a helicoid fertile region. Coemansia pennisetoides, sp. nov., has a sporangiophore with a fertile region that resembles the inflorescence of the plant genus Pennisetum. Coemansia umbellata, sp. nov., has an umbellate sporangiophore branching pattern and a spirally twisted fertile region on the lowest branches. A dichotomous key was provided to identify the 23 accepted Coemansia species. Phylogenetic analysis based on a combined data set of D1-D2 domains of nuc 28S ribosomal RNA (rDNA) and partial nuc 18S rDNA identifies several independent evolutionary lineages within Coemansia and suggests that Spirodactylon aureum and Kickxella alabastrina may be nested within the genus Coemansia. Sequences of nuc rDNA ITS1-5.8S-ITS2 (internal transcribed spacer [ITS] barcode) are also used to support the description of these new species of Coemansia.