Explore the vast range of titles available.

Background The soil dwelling saprotrophic non-pathogenic fungus Fusarium venenatum , routinely used in the commercial fermentation industry, is phylogenetically closely related to the globally important cereal and non-cereal infecting pathogen F. graminearum . This study aimed to sequence, assemble and annotate the F. venenatum (strain A3/5) genome, and compare this genome with F. graminearum . Results Using shotgun sequencing, a 38,660,329 bp  F. venenatum genome was assembled into four chromosomes, and a 78,618 bp mitochondrial genome. In comparison to F. graminearum , the predicted gene count of 13,946 was slightly lower. The F. venenatum centromeres were found to be 25% smaller compared to F. graminearum . Chromosome length was 2.8% greater in F. venenatum, primarily due to an increased abundance of repetitive elements and transposons, but not transposon diversity. On chromosome 3 a major sequence rearrangement was found, but its overall gene content was relatively unchanged. Unlike homothallic F. graminearum , heterothallic F. venenatum possessed the MAT1–1 type locus, but lacked the MAT1–2 locus. The F. venenatum genome has the type A trichothecene mycotoxin TRI5 cluster, whereas F. graminearum has type B. From the F. venenatum gene set, 786 predicted proteins were species-specific versus NCBI. The annotated F. venenatum genome was predicted to possess more genes coding for hydrolytic enzymes and species - specific genes involved in the breakdown of polysaccharides than F. graminearum . Comparison of the two genomes reduced the previously defined F. graminearum- specific gene set from 741 to 692 genes. A comparison of the F. graminearum versus F. venenatum proteomes identified 15 putative secondary metabolite gene clusters (SMC), 109 secreted proteins and 38 candidate effectors not found in F. venenatum . Five of the 15 F. graminearum-specific SMCs that were either absent or highly divergent in the F. venenatum genome showed increased in planta expression. In addition, two predicted F. graminearum transcription factors previously shown to be required for fungal virulence on wheat plants were absent or exhibited high sequence divergence. Conclusions This study identifies differences between the F. venenatum and F. graminearum genomes that may contribute to contrasting lifestyles, and highlights the repertoire of F. graminearum -specific candidate genes and SMCs potentially required for pathogenesis.

The quantity and complexity of data being generated and published in biology has increased substantially, but few methods exist for capturing knowledge about phenotypes derived from molecular interactions between diverse groups of species, in such a way that is amenable to data-driven biology and research. To improve access to this knowledge, we have constructed a framework for the curation of the scientific literature studying interspecies interactions, using data curated for the Pathogen–Host Interactions database (PHI-base) as a case study. The framework provides a curation tool, phenotype ontology, and controlled vocabularies to curate pathogen–host interaction data, at the level of the host, pathogen, strain, gene, and genotype. The concept of a multispecies genotype, the ‘metagenotype,’ is introduced to facilitate capturing changes in the disease-causing abilities of pathogens, and host resistance or susceptibility, observed by gene alterations. We report on this framework and describe PHI-Canto, a community curation tool for use by publication authors. The increasingly vast amount of data being produced in research communities can be difficult to manage, making it challenging for both humans and computers to organise and connect information from different sources. Currently, software tools that allow authors to curate peer-reviewed life science publications are designed solely for single species, or closely related species that do not interact. Although most research communities are striving to make their data FAIR (Findable, Accessible, Interoperable and Reusable), it is particularly difficult to curate detailed information based on interactions between two or more species (interspecies), such as pathogen-host interactions. As a result, there was a lack of tools to support multi-species interaction databases, leading to a reliance on labour-intensive curation methods. To address this problem, Cuzick et al. used the Pathogen-Host Interactions database (PHI-base), which curates knowledge from the text, tables and figures published in over 200 journals, as a case study. A framework was developed that could capture the many observable traits (phenotype annotations) for interactions and link them directly to the combination of genotypes involved in those interactions across multiple scales – ranging from microscopic to macroscopic. This demonstrated that it was possible to build a framework of software tools to enable curation of interactions between species in more detail than had been done before. Cuzick et al. developed an online tool called PHI-Canto that allows any researcher to curate published pathogen-host interactions between almost any known species. An ontology – a collection of concepts and their relations – was created to describe the outcomes of pathogen-host interactions in a standardised way. Additionally, a new concept called the ‘metagenotype’ was developed which represents the combination of a pathogen and a host genotype and can be easily annotated with the phenotypes arising from each interaction. The newly curated multi-species FAIR data on pathogen-host interactions will enable researchers in different disciplines to compare and contrast interactions across species and scales. Ultimately, this will assist the development of new approaches to reduce the impact of pathogens on humans, livestock, crops and ecosystems with the aim of decreasing disease while increasing food security and biodiversity. The framework is potentially adoptable by any research community investigating interactions between species and could be adapted to explore other harmful and beneficial interspecies interactions.

Background: The entomopathogenic fungus Metarhizium brunneum (M. brunneum) is an effective biocontrol agent against various vector arthropods such as ticks, mosquitoes, and flies. However, its virulence mechanisms remain poorly understood, which hinders its broader application. This study aims to establish an integrative framework for prioritizing virulence-related pathways in M. brunneum to aid in the development of more effective biocontrol strategies. Methods: A multidimensional virulence pathway scoring framework was developed using publicly available protein annotation data of M. brunneum. This approach integrates protein pathway enrichment, Gene Ontology (GO) functional analysis, PHI-base virulence factor mapping, and literature-derived evidence. A total of 20 pathways were evaluated, and a scoring system was applied based on protein coverage, Gene Ontology Biological Process (GO-BP) support, PHI-base hits, and literature support. Results: Among the 20 pathways evaluated, five pathways, including MAPK signaling, apoptosis, endocytosis, carbon metabolism, and biosynthesis of secondary metabolites received the highest priority scores. These pathways were identified as key virulence-related candidates, supported by both functional annotation and existing biological evidence. Conclusions: The proposed framework provides a reliable and scalable strategy for prioritizing virulence pathways in entomopathogenic fungi. It offers a solid foundation for subsequent transcriptomic validation, target screening, and functional characterization. This framework can also be applied to other fungi, contributing to the development of optimized biocontrol formulations.

The Rhizoctonia solani species complex is comprised of strains belonging to different anastomosis groups and causes diseases in several economically important crops, including rice. However, individuals within same anastomosis group exhibit distinct morphological and pathological differences on the same host. In this study, we have sequenced the genome of two aggressive Indian strains (BRS11 and BRS13) belonging to AG1-IA anastomosis group and compared them with the available genome of R. solani AG1-IA. We identified several SNPs and Indels in both of these genomes, in comparison to the AG1-IA genome. Furthermore, we observed expansion and emergence of orthogroups in these Indian strains and identified those potentially associated with pathogenesis. Amongst them, transposable elements, cell wall degrading enzymes, transcription factors, and oxalate decarboxylase were noteworthy. The current study unravels genetic variations and identifies genes that might account for pathogenicity variations amongst R. solani strains.