Table 2.
Principal genomic databases described according to their ability to discriminate fungal sequences
| Database | Ref. | Description | Taxonomic discriminative potential |
| AspGD | [100] | AspGD focuses on the genomes of Aspergillus species. It provides detailed genomic data, including gene annotations, functional information, and comparative genomics. Enables the identification of both the species and strain levels. | High within the genus Aspergillus |
| BOLD | [101] | BOLD is a comprehensive online platform primarily dedicated to DNA barcoding and biodiversity research. While it is a valuable resource, its primary focus is on animal barcoding. As a result, its fungal taxonomic discriminative potential is limited compared to databases specifically tailored for fungi. | Limited |
| Broad Insitute Database | http://www.broadinstitute.org/scientific-community/data/ | The Broad Institute has contributed extensively to fungal genomics. It offers genomic data for a variety of fungal species, with an emphasis on pathogenic fungi. | High |
| CGD | [102] | CGD is dedicated to Candida species, and it offers genomic sequences, gene annotations, and pathogenicity-related information, supporting research on the genus Candida. | High within the genus Candida |
| CYGD | [103] | CYGD offers comprehensive genome annotation and functional data primarily for Saccharomyces cerevisiae. While it provides essential information for yeast research, its taxonomic scope is restricted to this species. | Limited to species S. cerevisiae |
| Ensembl Fungi | https://fungi.ensembl.org | Ensembl Fungi is a component of the Ensembl project, offering genomic data and tools for various fungal species. While it covers a range of fungi, it may be more comprehensive for some taxa than others. | Moderate |
| FungiDB | [104] | FungiDB is a genomic database focused on fungal pathogens. It includes a diverse set of fungal genomes, with an emphasis on medically important species. | Moderate |
| FUNGIpath | [105] | FUNGIpath is a resource for fungal pathogen genomics. It provides genomic sequences and annotations for pathogenic fungi, with relevance to disease research. | Moderate |
| Fusarium-ID | [106] | Fusarium-ID is a specialized database for Fusarium species identification and classification. It provides detailed molecular and phenotypic data for various Fusarium species, including pathogenic strains. | High within the genus Fusarium |
| Fusarium MLST | [107] | Fusarium MLST is a database that focuses on sequence-based typing for Fusarium species. It allows researchers to differentiate between closely related Fusarium isolates by analyzing multiple gene loci. This database is particularly useful for studying genetic diversity within the genus. | High within the genus Fusarium |
| ISHAM-ITS | [108] | ISHAM-ITS database is designed to aid in the identification and classification of medically important fungi using the fungal Internal Transcribed Spacer (ITS) region of ribosomal DNA. Its taxonomic discriminative potential is high within the context of identifying and characterizing fungi relevant to human and animal health. | High within the medical mycology |
| ISHAM-MLST | http://mlst.mycologylab.org/ | ISHAM-MLST is dedicated to the Multilocus Sequence Typing of medically important fungi, particularly those associated with human and animal mycoses. It has a higher taxonomic discriminative potential for distinguishing between closely related strains within a species. | Very high within the medical mycology |
| JGI MycoCosm | [109] | MycoCosm, hosted by the JGI, provides access to a diverse collection of fungal genomes, including those from various taxonomic groups, making it suitable for discriminative research. | High |
| NCBI GenBank | https://www.ncbi.nlm.nih.gov/genbank/ | NCBI GenBank is a comprehensive and widely used repository for genomic data. It covers a wide taxonomic range, including fungi, but the level of detail and annotation quality can vary. | Moderate to high |
| NCBI RefSeq | http://www.ncbi.nlm.nih.gov/refseq/ | NCBI RefSeq offers high-quality genomic annotations and reference sequences, making it a preferred choice for researchers seeking accurate taxonomic and functional information for well-studied fungal species. | High |
| PomBase | [110] | PomBase is primarily focused on Schizosaccharomyces pombe. It provides detailed genomic and functional information for this species, making it an excellent resource for S. pombe research. However, its taxonomic scope is limited to this species. | Limited to species S. pombe |
| SGD | [111] | SGD is dedicated to Saccharomyces cerevisiae and is a comprehensive resource. While its primary focus is S. cerevisiae, it contains extensive genomic and functional data that can support the study of other Saccharomyces species as well. | High within the genus Saccharomyces |
| UNITE | [112] | UNITE provides a comprehensive collection of fungal ITS sequences, covering a broad range of fungal taxa, from common and well-studied species to rare and less-known fungi. | High |
AspGD: Aspergillus genome database; BOLD: barcode of life data systems; CGD: candida genome database; CYGD: comprehensive yeast genome database; ISHAM-ITS: international society for human and animal mycology-internal transcribed spacer; ISHAM-MLST: international society for human and animal mycology - multilocus sequence typing; JGI: joint genome institute; MLST: multilocus sequence typing; SGD: saccharomyces genome database.