List of Current Databases and Bioinformatics Tools for Comparative Fungal Genomics Studies_
| Tools | Type | Link to Website |
|---|---|---|
| FastQC | QC tool for high throughput sequence data | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| Cytoscape | Network Visualization Tool | https://cytoscape.org/ |
| VisANT | Biological Network Analysis Tool | http://www.visantnet.org |
| Pathway Studio | Navigation and Analysis of Biological Pathways, Gene Regulation Networks and Protein Interaction Maps | https://ariadnegenomics.com/products/pathway-studio |
| Patika | Integrated Visual Environment for Collaborative Construction and Analysis of Cellular Pathways | https://www.patika.org/ |
| BLAST+ | Sequence Homology Search Tool | https://blast.ncbi.nlm.nih.gov/blast/Blast.cgi |
| ClustalW | Multiple Sequence Alignment Tool | http://www.clustal.org/clustal2/ |
| MAFFT | Multiple Sequence Alignment Tool | https://mafft.cbrc.jp/alignment/server/index.html |
| MUSCLE | Multiple Sequence Alignment Tool | https://www. drive5.com/muscle/ |
| PHYLIP | Phylogenetics Tree Building Tool | https://phylipweb.github.io/phylip/ |
| MEGA | Molecular Evolutionary Genetics Analysis Tool | https://www. megasoftware.net/ |
| Unipro UGENE | Integrated Bioinformatics Tool | https://ugene.net/ |
| EDGAR | Software Platform for Comparative Genomics | https://edgar3.computational.bio.uni-giessen.de/cgi-bin/ edgar_login.cgi?cookie_test= 1 |
| PHI-base | Pathogen Host Interactions Database | http://www.phi-base.org/ |
| CAZy | Carbohydrate-Active enZYmes Database | http://www.cazy.org/Home.html |
| DFVF | Database of Virulence Factors in Fungal Pathogens | http://sysbio.unl.edu/DFVF/ |
| FungiDB | Database | https://fungidb.org/fungidb/app |
| GenBank | Genetic Sequence Database | https://www.ncbi.nlm.nih.gov/genbank/ |
| DDBJ | Genetic Sequence Database | https://www.ddbj.nig.ac.jp/index-e.html |
| EMBL | Genetic Sequence Database | https://www.ebi.ac.uk/ |
| Fungal Genome Initiatives | Fungal Genome Database | https://www.broadinstitute.org/scientific-community/science/ projects/fungal-genome-initiative/status-fungal-genome-projects |
| EnsemblFungi | Genome Portal for Selected Fungal Species | https://fungi.ensembl.org/index.html |
| ARFbase | Database on protein mutations responsible for antifungal resistance | http://proteininformatics.org/mkumar/afrbase/ |
| FunResDB | Web source for genotyping susceptibility testing of Aspergillus fumigatus | https://elbe.hki-jena.de/FunResDb/index.php |
| MARDy | Mycology Antifungal Resistance Database | http://mardy.net |
Enzyme Classes and Associated Modules that are involved in Breakdown, Biosynthesis or Modification of Carbohydrates and Glycoconjugates
| Family | Description |
|---|---|
| Glycoside Hydrolases (GHs) | Involves in hydrolysis and/or rearrangement of glycosidic bonds |
| Glycosyl Transferases (GTs) | Involves in the formation of glycosidic bonds |
| Polysaccharide Lyases (PLs) | Involves in non-hydrolytic cleavage of glycosidic bonds |
| Carbohydrate Esterases (CEs) | Involves in hydrolysis of carbohydrate esters |
| Auxiliary Activities (AAs) | Involves in redox enzymes that act in conjunction with CAZymes |
| Carbohydrate-Binding Modules (CBM) | Involves in adhesion to carbohydrates |
Top 10 fungal plant pathogens (Dean et al_ 2012)_
| Rank | Fungal pathogen | Author of fungal description |
|---|---|---|
| 1 | Magnaporthe oryzae | Ralph Dean |
| 2 | Botrytis cinerea | Jan A.L. van Kan |
| 3 | Puccinia spp. | Zacharias A. Pretorius |
| 4 | Fusarium graminearum | Kim Hammond-Kosack |
| 5 | Fusarium oxysporum | Antonio Di Pietro |
| 6 | Blumeria graminis | Pietro Spanu |
| 7 | Mycoshaerella graminicola | Jason J. Rudd |
| 8 | Colletotrichum spp. | Marty Dickman |
| 9 | Usitlago maydis | Regine Kahmann |
| 10 | Melampsora lini | Jeff Ellis |
Ranking of Human Fungal Priority Pathogen according to World Health Organization (World Health Organization 2022)_
| Grouping | Fungal pathogen |
|---|---|
| Critical Group | Cryptococcus neoformans |
| Candida auris | |
| Aspergillus fumigatus | |
| Candida albicans | |
| High Group | Nakaseomyces glabrata |
| Histoplasma spp. | |
| Eumycetoma causative agents | |
| Mucorales | |
| Fusarium spp. | |
| Candida tropicalis | |
| Candida parapsilosis | |
| Medium Group | Scedosporium spp. |
| Lomentospora prolificans | |
| Coccidioides spp. | |
| Pichia kudriavzeveii (Candida krusei) | |
| Cryptococcus gattii | |
| Talaromyces marneffei | |
| Pneumocystis jirovecii | |
| Paracoccidioides spp. |