FungiDB (fungidb.org) is a free online resource for data mining and functional genomics analysis for fungal and oomycete species. FungiDB is part of the Eukaryotic Pathogen Genomics Database Resource (EuPathDB, eupathdb.org) platform that integrates genomic, transcriptomic, proteomic, and phenotypic datasets, and other types of data for pathogenic and nonpathogenic, free-living and parasitic organisms. FungiDB is one of the largest EuPathDB databases containing nearly 100 genomes obtained from GenBank, Aspergillus Genome Database (AspGD), The Broad Institute, Joint Genome Institute (JGI), Ensembl, and other sources. FungiDB offers a user-friendly web interface with embedded bioinformatics tools that support custom in silico experiments that leverage FungiDB-integrated data. In addition, a Galaxy-based workspace enables users to generate custom pipelines for large-scale data analysis (e.g., RNA-Seq, variant calling, etc.). This review provides an introduction to the FungiDB resources and focuses on available features, tools, and queries and how they can be used to mine data across a diverse range of integrated FungiDB datasets and records.

Symbiotic associations of cellulolytic eukaryotic protists and diverse bacteria are common in the gut microbial communities of termites. Besides cellulose degradation by the gut protists, reductive acetogenesis from H₂plus CO₂and nitrogen fixation by gut bacteria play crucial roles in the host termites’ nutrition by contributing to the energy demand of termites and supplying nitrogen poor in their diet, respectively. Fractionation of these activities and the identification of key genes from the gut community of the wood-feeding termiteHodotermopsis sjoestedtirevealed that substantial activities in the gut—nearly 60% of reductive acetogenesis and almost exclusively for nitrogen fixation—were uniquely attributed to the endosymbiotic bacteria of the cellulolytic protist in the genusEucomonympha. The rod-shaped endosymbionts were surprisingly identified as a spirochete species in the genusTreponema, which usually exhibits a characteristic spiral morphology. The endosymbionts likely use H₂produced by the protist for these dual functions. Although H₂is known to inhibit nitrogen fixation in some bacteria, it seemed to rather stimulate this important mutualistic process. In addition, the single-cell genome analyses revealed the endosymbiont's potentials of the utilization of sugars for its energy requirement, and of the biosynthesis of valuable nutrients such as amino acids from the fixed nitrogen. These metabolic interactions are suitable for the dual functions of the endosymbiont and reconcile its substantial contributions in the gut.

FungiDB (https://fungidb.org) serves as a valuable online resource that seamlessly integrates genomic and related large-scale data for a wide range of fungal and oomycete species. As an integral part of the VEuPathDB Bioinformatics Resource Center (https://veupathdb.org), FungiDB continually integrates both published and unpublished data addressing various aspects of fungal biology. Established in early 2011, the database has evolved to support 674 datasets. The datasets include over 300 genomes spanning various taxa (e.g. Ascomycota, Basidiomycota, Blastocladiomycota, Chytridiomycota, Mucoromycota, as well as Albuginales, Peronosporales, Pythiales, and Saprolegniales). In addition to genomic assemblies and annotation, over 300 extra datasets encompassing diverse information, such as expression and variation data, are also available. The resource also provides an intuitive web-based interface, facilitating comprehensive approaches to data mining and visualization. Users can test their hypotheses and navigate through omics-scale datasets using a built-in search strategy system. Moreover, FungiDB offers capabilities for private data analysis via the integrated VEuPathDB Galaxy platform. FungiDB also permits genome improvements by capturing expert knowledge through the User Comments system and the Apollo genome annotation editor for structural and functional gene curation. FungiDB facilitates data exploration and analysis and contributes to advancing research efforts by capturing expert knowledge for fungal and oomycete species.

“ Candidatus Erwinia dacicola” is a Gammaproteobacterium that forms a symbiotic association with the agricultural pest Bactrocera oleae . Here, we present a 2.1-Mb draft hybrid genome assembly for “ Ca. Erwinia dacicola” generated from single-cell and metagenomic data.

Genome annotation is essential for understanding the functional elements within genomes. While automated methods are indispensable for processing large-scale genomic data, they often face challenges in accurately predicting gene structures and functions. Consequently, manual curation by domain experts remains crucial for validating and refining these predictions. These combined outcomes from automated tools and manual curation highlight the importance of integrating human expertise with artificial intelligence (AI) capabilities to improve both the accuracy and efficiency of genome annotation. However, the manual curation process is inherently labor-intensive and time-consuming, making it difficult to scale for large datasets. To address these challenges, we propose a conceptual framework, Human-AI Collaborative Genome Annotation (HAICoGA), that leverages the synergistic partnership between humans and AI to enhance human capabilities and accelerate the genome annotation process. Additionally, we explore the potential of integrating large language models into this framework to support and augment specific tasks. Finally, we discuss emerging challenges and outline open research questions to guide further exploration in this area.