The fungus Fusarium fujikuroi causes “bakanae” disease of rice due to its ability to produce gibberellins (GAs), but it is also known for producing harmful mycotoxins. However, the genetic capacity for the whole arsenal of natural compounds and their role in the fungus' interaction with rice remained unknown. Here, we present a high-quality genome sequence of F. fujikuroi that was assembled into 12 scaffolds corresponding to the 12 chromosomes described for the fungus. We used the genome sequence along with ChIP-seq, transcriptome, proteome, and HPLC-FTMS-based metabolome analyses to identify the potential secondary metabolite biosynthetic gene clusters and to examine their regulation in response to nitrogen availability and plant signals. The results indicate that expression of most but not all gene clusters correlate with proteome and ChIP-seq data. Comparison of the F. fujikuroi genome to those of six other fusaria revealed that only a small number of gene clusters are conserved among these species, thus providing new insights into the divergence of secondary metabolism in the genus Fusarium. Noteworthy, GA biosynthetic genes are present in some related species, but GA biosynthesis is limited to F. fujikuroi, suggesting that this provides a selective advantage during infection of the preferred host plant rice. Among the genome sequences analyzed, one cluster that includes a polyketide synthase gene (PKS19) and another that includes a non-ribosomal peptide synthetase gene (NRPS31) are unique to F. fujikuroi. The metabolites derived from these clusters were identified by HPLC-FTMS-based analyses of engineered F. fujikuroi strains overexpressing cluster genes. In planta expression studies suggest a specific role for the PKS19-derived product during rice infection. Thus, our results indicate that combined comparative genomics and genome-wide experimental analyses identified novel genes and secondary metabolites that contribute to the evolutionary success of F. fujikuroi as a rice pathogen.

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Several key tree genera are used in planted forests worldwide, and these represent valuable global resources. Planted forests are increasingly threatened by insects and microbial pathogens, which are introduced accidentally and/or have adapted to new host trees. Globalization has hastened tree pest emergence, despite a growing awareness of the problem, improved understanding of the costs, and an increased focus on the importance of quarantine. To protect the value and potential of planted forests, innovative solutions and a better-coordinated global approach are needed. Mitigation strategies that are effective only in wealthy countries fail to contain invasions elsewhere in the world, ultimately leading to global impacts. Solutions to forest pest problems in the future should mainly focus on integrating management approaches globally, rather than single-country strategies. A global strategy to manage pest issues is vitally important and urgently needed.

The genus Ceratocystis was established in 1890 and accommodates many important fungi. These include serious plant pathogens, significant insect symbionts and agents of timber degradation that result in substantial economic losses. Virtually since its type was described from sweet potatoes, the taxonomy of Ceratocystis has been confused and vigorously debated. In recent years, particulary during the last two decades, it has become very obvious that this genus includes a wide diversity of very different fungi. These have been roughly lumped together due to their similar morphological structures that have clearly evolved through convergent evolution linked to an insect-associated ecology. As has been true for many other groups of fungi, the emergence of DNA-based sequence data and associated phylogenetic inferences, have made it possible to robustly support very distinct boundaries defined by morphological characters and ecological differences. In this study, DNA-sequence data for three carefully selected gene regions (60S, LSU, MCM7) were generated for 79 species residing in the aggregate genus Ceratocystis sensu lato and these data were subjected to rigorous phylogenetic analyses. The results made it possible to distinguish seven major groups for which generic names have been chosen and descriptions either provided or emended. The emended genera included Ceratocystis sensu stricto, Chalaropsis, Endoconidiophora, Thielaviopsis, and Ambrosiella, while two new genera, Davidsoniella and Huntiella, were described. In total, 30 new combinations have been made. This major revision of the generic boundaries in the Ceratocystidaceae will simplify future treatments and work with an important group of fungi including distantly related species illogically aggregated under a single name.

Species of Calonectria are important plant pathogens, several of which have a worldwide distribution. Contemporary taxonomic studies on these fungi have chiefly relied on DNA sequence comparisons of the β-tubulin gene region. Despite many new species being described, there has been no phylogenetic synthesis for the group since the last monographic study almost a decade ago. In the present study, the identity of a large collection of Calonectria isolates from various geographic regions was determined using morphological and DNA sequence comparisons. This resulted in the discovery of seven new species; Ca. densa, Ca. eucalypti, Ca. humicola, Ca. orientalis, Ca. pini, Ca. pseudoscoparia and Ca. sulawesiensis, bringing the total number of currently accepted Calonectria species to 68. A multigene phylogeny was subsequently constructed for all available Calonectria spp., employing seven gene regions, namely actin, β-tubulin, calmodulin, histone H3, the internal transcribed spacer regions 1 and 2 and the 5.8S gene of the ribosomal RNA, 28S large subunit RNA gene and translation elongation 1-alpha. Based on these data 13 phylogenetic groups could be distinguished within the genus Calonectria that correlated with morphological features. Dichotomous and synoptic keys to all Calonectria spp. currently recognised are also provided.