We sequenced and annotated the genome of the filamentous fungus Fusarium graminearum, a major pathogen of cultivated cereals. Very few repetitive sequences were detected, and the process of repeat-induced point mutation, in which duplicated sequences are subject to extensive mutation, may partially account for the reduced repeat content and apparent low number of paralogous (ancestrally duplicated) genes. A second strain of F. graminearum contained more than 10,000 single-nucleotide polymorphisms, which were frequently located near telomeres and within other discrete chromosomal segments. Many highly polymorphic regions contained sets of genes implicated in plant-fungus interactions and were unusually divergent, with higher rates of recombination. These regions of genome innovation may result from selection due to interactions of F. graminearum with its plant hosts.

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of interfaces to genomic data across the tree of life, including reference genome sequence, gene models, transcriptional data, genetic variation and comparative analysis. Data may be accessed via our website, online tools platform and programmatic interfaces, with updates made four times per year (in synchrony with Ensembl). Here, we provide an overview of Ensembl Genomes, with a focus on recent developments. These include the continued growth, more robust and reproducible sets of orthologues and paralogues, and enriched views of gene expression and gene function in plants. Finally, we report on our continued deeper integration with the Ensembl project, which forms a key part of our future strategy for dealing with the increasing quantity of available genome-scale data across the tree of life.

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including genome sequence, gene models, transcript sequence, genetic variation, and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments and expansions. These include the incorporation of almost 20 000 additional genome sequences and over 35 000 tracks of RNA-Seq data, which have been aligned to genomic sequence and made available for visualization. Other advances since 2015 include the release of the database in Resource Description Framework (RDF) format, a large increase in community-derived curation, a new high-performance protein sequence search, additional cross-references, improved annotation of non-protein-coding genes, and the launch of pre-release and archival sites. Collectively, these changes are part of a continuing response to the increasing quantity of publicly-available genome-scale data, and the consequent need to archive, integrate, annotate and disseminate these using automated, scalable methods.

The a mating type locus of the phytopathogenic fungus U. maydis controls fusion of haploid cells and filamentous growth of the dikaryotic mycelium. The a locus exists in two alleles, termed a1 and a2, which are defined by nonhomologous DNA regions comprising 4.5 kb for a1 and 8 kb for a2, flanked by identical sequences. Based on functional assays, mutants, and sequencing, we demonstrate that the mating type in each allele is determined by a set of two genes. One encodes a precursor for a lipopeptide mating factor, and the other specifies the receptor for the pheromone secreted by cells of opposite mating type. Thus, U. maydis employs a novel strategy to determine its mating type by providing the primary determinants of cell-cell recognition directly from the mating type locus.

The rice blast fungus Magnaporthe grisea uses appressoria to penetrate into plant cells. Appressorium formation occurs following conidial germination on hydrophobic surfaces and may involve a cyclic AMP (cAMP)-dependent signaling mechanism. Recently, gene replacement mutants of CPKA, a gene encoding a proposed catalytic subunit of cAMP-dependent protein kinase A, were shown to be defective in appressorium formation, cAMP responsiveness, and lesion formation (T. K. Mitchell and R. A. Dean, Plant Cell, 7:1869–1878, 1995). Here we report a detailed phenotypic characterization of three cpkA mutants. cpkA mutants are dramatically reduced in pathogenicity toward healthy plants. However, the reduced pathogenicity does not appear to be due to a loss of appressorium formation. cpkA mutants are delayed in appressorium formation but form appressoria at the same level as wild-type strains over a 24-h period. Appressoria formed by cpkA mutants are fully melanized but are smaller than wild type and are defective in penetrating plant cells. cpkA mutants can produce infectious hyphae and cause lesion formation when inoculated through wounds. Finally, cpkA mutants are still responsive to exogenous cAMP for appressorium formation. These findings indicate an additional role for cAMP signaling involved in appressorial penetration and suggest the presence of additional cAMP-dependent protein kinase(s) involved in surface sensing in M. grisea.

To utilize effectively the growing number of verified genes that mediate an organism's ability to cause disease and/or to trigger host responses, we have developed PHI-base. This is a web-accessible database that currently catalogs 405 experimentally verified pathogenicity, virulence and effector genes from 54 fungal and Oomycete pathogens, of which 176 are from animal pathogens, 227 from plant pathogens and 3 from pathogens with a fungal host. PHI-base is the first on-line resource devoted to the identification and presentation of information on fungal and Oomycete pathogenicity genes and their host interactions. As such, PHI-base is a valuable resource for the discovery of candidate targets in medically and agronomically important fungal and Oomycete pathogens for intervention with synthetic chemistries and natural products. Each entry in PHI-base is curated by domain experts and supported by strong experimental evidence (gene/transcript disruption experiments) as well as literature references in which the experiments are described. Each gene in PHI-base is presented with its nucleotide and deduced amino acid sequence as well as a detailed description of the predicted protein's function during the host infection process. To facilitate data interoperability, we have annotated genes using controlled vocabularies (Gene Ontology terms, Enzyme Commission Numbers and so on), and provide links to other external data sources (e.g. NCBI taxonomy and EMBL). We welcome new data for inclusion in PHI-base, which is freely accessed at .

The a mating type locus of Ustilago maydis contains the structural genes for a pheromone-based cell recognition system that governs fusion of haploid cells. Binding of pheromone to its cognate receptor includes mating competence in haploid cells and stimulates filamentous growth of the dikaryon. We have analyzed transcription of genes located in the a locus and demonstrate that all genes are induced by pheromone. Transcriptional stimulation is mediated by a 9 bp DNA element (ACAAAGGGA) that occurs in multiple copies in both alleles of the a locus. By fusing multimers containing this 9 bp sequence to the pheromone gene promoter and to a heterologous promoter we demonstrate that this sequence acts as a pheromone response element. In addition, we show that expression of the b genes, which regulate pathogenic development of the dikaryon, is also stimulated by pheromone. Pheromone-inducible genes can be divided into three classes depending on whether their expression is reduced, maintained, or increased after cell fusion. These differences may suggest some regulatory cross-talk between the a and b loci.

Background: Accurate genome assembly and gene model annotation are critical for comparative species and gene functional analyses. Here we present the completed genome sequence and annotation of the reference strain PH-1 of Fusarium graminearum, the causal agent of head scab disease of small grain cereals which threatens global food security. Completion was achieved by combining (a) the BROAD Sanger sequenced draft, with (b) the gene predictions from Munich Information Services for Protein Sequences (MIPS) v3.2, with (c) de novo whole-genome shotgun re-sequencing, (d) re-annotation of the gene models using RNA-seq evidence and Fgenesh, Snap, GeneMark and Augustus prediction algorithms, followed by (e) manual curation.