Systematics of the Ustilago-Sporisorium-Macalpinomyces complex of smut fungi

Smut fungi are important pathogens of grasses, including the cultivated crops maize, sorghum and sugarcane. Typically, smut fungi infect the inflorescence of their host plants. Three genera of smut fungi (Ustilago, Sporisorium and Macalpinomyces) form a complex with overlapping morphological characters, making species placement problematic. For example, the newly described Macalpinomyces mackinlayi possesses a combination of morphological characters such that it cannot be unambiguously accommodated in any of the three genera. Previous attempts to define Ustilago, Sporisorium and Macalpinomyces using morphology and molecular phylogenetics have highlighted the polyphyletic nature of the genera, but have failed to produce a satisfactory taxonomic resolution. A detailed systematic study of 137 smut species in the Ustilago-Sporisorium- Macalpinomyces complex was completed in the current work. Morphological and DNA sequence data from five loci were assessed with maximum likelihood and Bayesian inference to reconstruct a phylogeny of the complex. The phylogenetic hypotheses generated were used to identify morphological synapomorphies, some of which had previously been dismissed as a useful way to delimit the complex. These synapomorphic characters are the basis for a revised taxonomic classification of the Ustilago-Sporisorium-Macalpinomyces complex, which takes into account their morphological diversity and coevolution with their grass hosts. The new classification is based on a redescription of the type genus Sporisorium, and the establishment of four genera, described from newly recognised monophyletic groups, to accommodate species expelled from Sporisorium. Over 150 taxonomic combinations have been proposed as an outcome of this investigation, which makes a rigorous and objective contribution to the fungal systematics of these important plant pathogens.

CgDN24 : a gene involved in hyphal development in the fungal phytopathogen Colletotrichum gloeosporioides

A cDNA corresponding to a transcript induced in culture by N starvation, was identified in Colletotrichum gloeosporioides by a differential hybridisation strategy. The cDNA comprised 905 bp and predicted a 215 aa protein; the gene encoding the cDNA was termed CgDN24. No function for CgDN24 could be predicted by database homology searches using the cDNA sequence and no homologues were found in the sequenced fungal genomes. Transcripts of CgDN24 were detected in infected leaves of Stylosanthes guianensis at stages of infection that corresponded with symptom development. The CgDN24 gene was disrupted by homologous recombination and this led to reduced radial growth rates and the production of hyphae with a hyperbranching phenotype. Normal sporulation was observed, and following conidial inoculation of S. guianensis, normal disease development was obtained. These results demonstrate that CgDN24 is necessary for normal hyphal development in axenic culture but dispensable for phytopathogenicity. © 2005 Elsevier GmbH. All rights reserved.

High-resolution DNA melt curve analysis of the clustered, regularly interspaced short-palindromic-repeat locus of Campylobacter jejuni

A novel method for genotyping the clustered, regularly interspaced short-palindromic-repeat (CRISPR) locus of Campylobacter jejuni is described. Following real-time PCR, CRISPR products were subjected to high-resolution melt (HRM) analysis, a new technology that allows precise melt profile determination of amplicons. This investigation shows that the CRISPR HRM assay provides a powerful addition to existing C. jejuni genotyping methods and emphasizes the potential of HRM for genotyping short sequence repeats in other species

Geologically ancient DNA: fact or artefact?

Studies continue to report ancient DNA sequences and viable microbial cells that are many millions of years old. In this paper we evaluate some of the most extravagant claims of geologically ancient DNA. We conclude that although exciting, the reports suffer from inadequate experimental setup and insufficient authentication of results. Consequently, it remains doubtful whether amplifiable DNA sequences and viable bacteria can survive over geological timescales. To enhance the credibility of future studies and assist in discarding false-positive results, we propose a rigorous set of authentication criteria for work with geologically ancient DNA.

Combined mitochondrial and nuclear DNA sequences resolve the interrelations of the major Australasian marsupial radiations

Australasian marsupials include three major radiations, the insectivorous/carnivorous Dasyuromorphia, the omnivorous bandicoots (Peramelemorphia), and the largely herbivorous diprotodontians. Morphologists have generally considered the bandicoots and diprotodontians to be closely related, most prominently because they are both syndactylous (with the 2nd and 3rd pedal digits being fused). Molecular studies have been unable to confirm or reject this Syndactyla hypothesis. Here we present new mitochondrial (mt) genomes from a spiny bandicoot (Echymipera rufescens) and two dasyurids, a fat-tailed dunnart (Sminthopsis crassicaudata) and a northern quoll (Dasyurus hallucatus). By comparing trees derived from pairwise base-frequency differences between taxa with standard (absolute, uncorrected) distance trees, we infer that composition bias among mt protein-coding and RNA sequences is sufficient to mislead tree reconstruction. This can explain incongruence between trees obtained from mt and nuclear data sets. However, after excluding major sources of compositional heterogeneity, both the “reduced-bias” mt and nuclear data sets clearly favor a bandicoot plus dasyuromorphian association, as well as a grouping of kangaroos and possums (Phalangeriformes) among diprotodontians. Notably, alternatives to these groupings could only be confidently rejected by combining the mt and nuclear data. Elsewhere on the tree, Dromiciops appears to be sister to the monophyletic Australasian marsupials, whereas the placement of the marsupial mole (Notoryctes) remains problematic. More generally, we contend that it is desirable to combine mt genome and nuclear sequences for inferring vertebrate phylogeny, but as separately modeled process partitions. This strategy depends on detecting and excluding (or accounting for) major sources of nonhistorical signal, such as from compositional nonstationarity.