We constructed nine sets of oligonucleotide primers on the basis of the results of DNA hybridization of cloned genes from Neurospora crassa and Aspergillus nidulans to the genomes of select filamentous ascomycetes and deuteromycetes (with filamentous ascomycete affiliations). Nine sets of primers were designed to amplify segments of DNA that span one or more introns in conserved genes. PCR DNA amplification with the nine primer sets with genomic DNA from ascomycetes, deuteromycetes, basidiomycetes, and plants revealed that five of the primer sets amplified a product only from DNA of the filamentous ascomycetes and deuteromycetes. The five primer sets were constructed from the N. crassa genes for histone 3, histone 4, beta-tubulin, and the plasma membrane ATPase. With these five primer sets, polymorphisms were observed in both the size of and restriction enzyme sites in the amplified products from the filamentous ascomycetes. The primer sets described here may provide useful tools for phylogenetic studies and genome analyses in filamentous ascomycetes and deuteromycetes (with ascomycete affiliations), as well as for the rapid differentiation of fungal species by PCR.

Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous ascomycetes.

In the analysis of sequence-based data matrices, the use of different methods of treating gaps has been demonstrated to in? fluence the resulting phylogenetic hypothe? ses (e.g., Eernisse and Kluge, 1993; Vogler and DeSalle, 1994; Simons and Mayden, 1997). Despite this influence, a well-justi? fied, uniformly applied method of treating gaps is lacking in sequence-based phyloge? netic studies. Treatment of gaps varies widely from secondarily mapping gaps onto the tree inferred from base characters

/pdf/gaps-as-characters-in-sequence-based-phylogenetic-analyses-4hdlrw0k0r.pdf

Gaps as Characters in Sequence-Based Phylogenetic Analyses

The fungi comprise both members of the kingdom Fungi as we now recognize it (Ascomycota, Basidiomycota, Zygomycota, and Chytridiomycota) and fungal-like protists such as the Oomycota and the cellular and acellular slime molds (Myxomycota and Acrasiomycota). Treating this admittedly polyphyletic assemblage as a group is useful because these organisms often fill rather similar roles within ecosystems, and they have traditionally been studied almost exclusively by mycologists and plant pathologists. Throughout this review, Fungi will refer to the Kingdom, fungi to the organisms studied by mycologists. The fungi, as thus defined, are of great importance for the following reasons: (a) They are the primary decomposers in all terrestrial ecosystems; (b) they are important symbiotic associates of vascular plants both in mutualistic and parasitic relationships; (c) they constitute the overwhelming majority of plant pathogens and as such have a tremendous eco-

Fungal Molecular Systematics

Microbial sequencing of samples obtained from multiple skin sites in healthy human adults shows that core-body and arm sites are dominated by fungal species of the genus Malassezia, whereas foot sites show high fungal diversity, and that skin topography is associated with differential compositions of bacterial and fungal communities. As well as protecting against invasion by pathogens, our skin plays host to a varied population of microbes, some of which have important roles in human health and disease. The bacterial component of these communities is by now fairly well known, but our knowledge of the fungal members of the skin microbiota remains limited. Here Julia Segre and colleagues construct a map of the fungal species diversity at 14 different skin sites from 10 healthy adults, and compare this with the bacterial flora. They find that fungal richness varies across the body, and that bacterial and fungal communities are shaped by different factors. One finding with particular relevance to disease is that microbial communities around the feet that are commonly affected by fungal disease, such as athlete's foot, tend to be unstable. This instability may provide opportunities for harmful microbes to flourish. This finding highlights the need to develop new treatment strategies that specifically target microbial imbalances. Traditional culture-based methods have incompletely defined the microbial landscape of common recalcitrant human fungal skin diseases, including athlete’s foot and toenail infections. Skin protects humans from invasion by pathogenic microorganisms and provides a home for diverse commensal microbiota1. Bacterial genomic sequence data have generated novel hypotheses about species and community structures underlying human disorders2,3,4. However, microbial diversity is not limited to bacteria; microorganisms such as fungi also have major roles in microbial community stability, human health and disease5. Genomic methodologies to identify fungal species and communities have been limited compared with those that are available for bacteria6. Fungal evolution can be reconstructed with phylogenetic markers, including ribosomal RNA gene regions and other highly conserved genes7. Here we sequenced and analysed fungal communities of 14 skin sites in 10 healthy adults. Eleven core-body and arm sites were dominated by fungi of the genus Malassezia, with only species-level classifications revealing fungal-community composition differences between sites. By contrast, three foot sites—plantar heel, toenail and toe web—showed high fungal diversity. Concurrent analysis of bacterial and fungal communities demonstrated that physiologic attributes and topography of skin differentially shape these two microbial communities. These results provide a framework for future investigation of the contribution of interactions between pathogenic and commensal fungal and bacterial communities to the maintainenace of human health and to disease pathogenesis.

/pdf/topographic-diversity-of-fungal-and-bacterial-communities-in-39xqy6gj4t.pdf

Topographic diversity of fungal and bacterial communities in human skin

Molecular tools have now been applied for the past 5 years to dissect ectomycorrhizal (EM) community structure, and they have propelled a resurgence in interest in the field. Results from these studies have revealed that: (i) EM communities are impressively diverse and are patchily distributed at a fine scale below ground; (ii) there is a poor correspondence between fungi that appear dominant as sporocarps vs. those that appear dominant on roots; (iii) members of Russulaceae, Thelephoraceae, and/or non-thelephoroid resupinates are among the most abundant EM taxa in ecosystems sampled to date; (iv) dissimilar plants are associated with many of the same EM species when their roots intermingle — this occurs on a small enough spatial scale that fungal individuals are likely to be shared by dissimilar plants; and (v) mycoheterotrophic plants have highly specific fungal associations. Although, these results have been impressive, they have been tempered by sampling difficulties and limited by the taxonomic resolution of restriction fragment length polymorphism methods. Minor modifications of the sampling schemes, and more use of direct sequencing, has the potential to solve these problems. Use of additional methods, such as in situ hybridization to ribosomal RNA or hybridization coupled to microarrays, are necessary to open up the analysis of the mycelial component of community structure.

The molecular revolution in ectomycorrhizal ecology: peeking into the black-box.

Evolutionary relationships within the fungi: Analyses of nuclear small subunit rRNA sequences

(...) Isolates from anastomosis groups 3, 4, 7, 8, and BI all possess a single, invariant RFLP unique to each intraspecific group. A relatively low level of RFLP variation also was characteristic of isolates within AG-1-IB, AG-1-IC, AG-2-2, and AG-9. In contrast, a relatively high level of RFLP diversity was observed among isolates within AG-1-IA, AG-2-1, AG-5, and AG-6. We did not observe any obvious relationship between levels of RFLP within intraspecific groups and variation of other biological factors (host range, morphological variation, etc). Instead, we propose that the pattern of RFLP variation observed is most likely the result of genetic divergence within and among intraspecific groups

Ribosomal DNA restriction fragment length polymorphisms in Rhizoctonia solani

The plant pathogenic fungus Thanatephorus praticola (=Rhizoctonia solani AG4) was found to share a similar pattern of rDNA organization with other members of the Basidiomycotina. The 8.8 kb rDNA repeat unit from T. praticola contains coding regions for the 5S RNA as well as the major 17S–25S transcript. Major rDNA length variation between intraspecific strains was not observed. The number of rDNA repeat units in the genome was estimated to be 59.

Organization of ribosomal DNA in the basidiomycete Thanatephorus praticola

http://filogenetica.org/dolores_pdfs/MPE2006.pdf

Phylogenetic utility of indels within ribosomal DNA and β-tubulin sequences from fungi in the Rhizoctonia solani species complex

Classification of families of hypnobryalean mosses into the Hypnales, Leucodontales, and Hookeriales has been taxonomically difficult. Several researchers have sequenced different genes for independent phylogenetic studies of these three pleurocarp groups. Our goal is to summarize available molecular data and compile the largest data set to infer phylogenetic relationships among families as basis for classification at ordinal level. Sequences of rbcL, trnL-F, and rps4 loci for 38 exemplars of most families of Hypnales, Leucodontales, and Hookeriales were analyzed to evaluate whether or not each of the three orders is monophyletic. Cladistic analyses of combined sequences, using five taxa in the Bryales as outgroups, reveal a robust clade (decay > 5) including all hypnobryalean pleurocarps. Within this group, one clade (decay = 2) includes only taxa of the Hookeriales, and is sister to a large monophyletic group (Hypnales sensu lato) containing all other taxa (decay = 2) previously in the Leucodon...

http://filogenetica.org/deluna_pdfs/00ordinal%20phylogeny.pdf

Ordinal Phylogeny within the Hypnobryalean Pleurocarpous Mosses Inferred from Cladistic Analyses of Three Chloroplast DNA Sequence Data Sets: trnL-F, rps4, and rbcL

Dolores González

Papers

Evolutionary relationships within the fungi: Analyses of nuclear small subunit rRNA sequences

Ribosomal DNA restriction fragment length polymorphisms in Rhizoctonia solani

Organization of ribosomal DNA in the basidiomycete Thanatephorus praticola

Phylogenetic utility of indels within ribosomal DNA and β-tubulin sequences from fungi in the Rhizoctonia solani species complex

Ordinal Phylogeny within the Hypnobryalean Pleurocarpous Mosses Inferred from Cladistic Analyses of Three Chloroplast DNA Sequence Data Sets: trnL-F, rps4, and rbcL