Background: The number of sequenced fungal genomes is ever increasing, with about 200 genomes already fully sequenced or in progress. Only a small percentage of those genomes have been comprehensively studied, for example using techniques from functional genomics. Comparative analysis has proven to be a useful strategy for enhancing our understanding of evolutionary biology and of the less well understood genomes. However, the data required for these analyses tends to be distributed in various heterogeneous data sources, making systematic comparative studies a cumbersome task. Furthermore, comparative analyses benefit from close integration of derived data sets that cluster genes or organisms in a way that eases the expression of requests that clarify points of similarity or difference between species.
Description: To support systematic comparative analyses of fungal genomes we have developed the e-Fungi database, which integrates a variety of data for more than 30 fungal genomes. Publicly available genome data, functional annotations, and pathway information has been integrated into a single data repository and complemented with results of comparative analyses, such as MCL and OrthoMCL cluster analysis, and predictions of signaling proteins and the sub-cellular localisation of proteins. To access the data, a library of analysis tasks is available through a web interface. The analysis tasks are motivated by recent comparative genomics studies, and aim to support the study of evolutionary biology as well as community efforts for improving the annotation of genomes. Web services for each query are also available, enabling the tasks to be incorporated into workflows.
Conclusion: The e-Fungi database provides fungal biologists with a resource for comparative studies of a large range of fungal genomes. Its analysis library supports the comparative study of genome data, functional annotation, and results of large scale analyses over all the genomes stored in the database. The database is accessible at http://www.e-fungi.org.uk, as is the WSDL for the web services.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2242804 | PMC |
| http://dx.doi.org/10.1186/1471-2164-8-426 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Emergence of fungal hybrids - Potential threat to humans.
Microb Pathog
January 2025
Cell Biology and Molecular Genetics, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India. Electronic address:
Fungal hybrids arise through the interbreeding of distinct species. This hybridization process fosters increased genetic diversity and the emergence of new traits. Mechanisms driving hybridization include the loss of heterozygosity, copy number variations, and horizontal gene transfer.
View Article and Find Full Text PDFAligning genomes into common coordinates is central to pangenome analysis and construction, but it is also computationally expensive. Multi-sequence maximal unique matches (multi-MUMs) are guideposts for core genome alignments, helping to frame and solve the multiple alignment problem. We introduce Mumemto, a tool that computes multi-MUMs and other match types across large pangenomes.
View Article and Find Full Text PDF; unveiling the cause, spread, and molecular basis of a novel coriander leaf blight disease in Egypt.
Heliyon
January 2025
Microbial Activity Unit, Department of Microbiology, Soils, Water and Environment Research Institute, Agricultural Research Center (ARC), Giza, 12619, Egypt.
L. faced a new and previously undocumented leaf blight disease for the first time. This disease manifests initially as small, circular, or irregular brown spots on older leaves, which gradually expand and merge into dark brownish blotches over time.
View Article and Find Full Text PDFComparative genomic analysis of Fusarium oxysporum f. sp. lycopersici reveals telomeric duplications of a lineage-specific region carrying SIX8 and PSL1 and genome-wide expansion of Foxy transposable elements.
Int J Biol Macromol
January 2025
State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071000, China; Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Ministry of Education of China-Hebei Province Joint Innovation Center for Efficient Green Vegetable Industry, College of Horticulture, Hebei Agricultural University, Baoding 071000, China; Division of Plant Sciences, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia. Electronic address:
Fusarium oxysporum f. sp. lycopersici (Fol), the causal agent of tomato wilt disease, is a soil-borne, vascular-colonizing fungal pathogen that severely impacts tomato production in most growing regions worldwide.
View Article and Find Full Text PDFComparative Genomic Analysis Reveals Key Changes in the Genome of That Occurred During Classical Strain Improvement for Production of Antibiotic Cephalosporin C.
Int J Mol Sci
December 2024
Group of Fungal Genetic Engineering, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Leninsky Prosp. 33-2, 119071 Moscow, Russia.
From the 1950s to the present, the main tool for obtaining fungal industrial producers of secondary metabolites remains the so-called classical strain improvement (CSI) methods associated with multi-round random mutagenesis and screening for the level of target products. As a result of the application of such techniques, the yield of target secondary metabolites in high-yielding (HY) strains was increased hundreds of times compared to the wild-type (WT) parental strains. However, the events that occur at the molecular level during CSI programs are still unknown.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!