Dataset Information

Fungi.guru: Comparative genomic and transcriptomic resource for the fungi kingdom.

ABSTRACT: The fungi kingdom is composed of eukaryotic heterotrophs, which are responsible for balancing the ecosystem and play a major role as decomposers. They also produce a vast diversity of secondary metabolites, which have antibiotic or pharmacological properties. However, our lack of knowledge of gene function in fungi precludes us from tailoring them to our needs and tapping into their metabolic diversity. To help remedy this, we gathered genomic and gene expression data of 19 most widely-researched fungi to build an online tool, fungi.guru, which contains tools for cross-species identification of conserved pathways, functional gene modules, and gene families. We exemplify how our tool can elucidate the molecular function, biological process and cellular component of genes involved in various biological processes, by identifying a secondary metabolite pathway producing gliotoxin in Aspergillus fumigatus, the catabolic pathway of cellulose in Coprinopsis cinerea and the conserved DNA replication pathway in Fusarium graminearum and Pyricularia oryzae. The tool is available at www.fungi.guru.

SUBMITTER: Lim JJJ

PROVIDER: S-EPMC7718472 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Publications

Fungi.guru: Comparative genomic and transcriptomic resource for the fungi kingdom.

Lim Jolyn Jia Jia JJJ Koh Jace J Moo Jia Rong JR Villanueva Erielle Marie Fajardo EMF Putri Dhira Anindya DA Lim Yuen Shan YS Seetoh Wei Song WS Mulupuri Sriya S Ng Janice Wan Zhen JWZ Nguyen Nhi Le Uyen NLU Reji Rinta R Foo Herman H Zhao Margaret Xuan MX Chan Tong Ling TL Rodrigues Edbert Edric EE Kairon Ryanjit Singh RS Hee Ker Min KM Chee Natasha Cassandra NC Low Ann Don AD Chen Zoe Hui Xin ZHX Lim Shan Chun SC Lunardi Vanessa V Fong Tuck Choy TC Chua Cherlyn Xin'Er CX Koh Kenny Ting Sween KTS Julca Irene I Delli-Ponti Riccardo R Ng Jonathan Wei Xiong JWX Mutwil Marek M

Computational and structural biotechnology journal 20201120

The fungi kingdom is composed of eukaryotic heterotrophs, which are responsible for balancing the ecosystem and play a major role as decomposers. They also produce a vast diversity of secondary metabolites, which have antibiotic or pharmacological properties. However, our lack of knowledge of gene function in fungi precludes us from tailoring them to our needs and tapping into their metabolic diversity. To help remedy this, we gathered genomic and gene expression data of 19 most widely-researche ...[more]

PMID: 33304470

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Project description:BackgroundThe 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.DescriptionTo 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.ConclusionThe 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.

Dataset Information

Fungi.guru: Comparative genomic and transcriptomic resource for the fungi kingdom.

Publications

Fungi.guru: Comparative genomic and transcriptomic resource for the fungi kingdom.

Similar Datasets

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