Aspergillus Genomics - Aspergillus fumigatus

1. Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. Fedorova et al. PLoS Genet. 2008 Apr 11;4(4):e1000046
   
   Supporting information
   
   
   1. Text S1: Allergens and sexual development genes
   2. Table S1: Growth rates of Af293, A1163, N. fischeri, and A. clavatus isolates at various temperatures
   3. Table S2: Resistance to antifungals among A. fumigatus clinical isolates
   4. Table S3: Divergent A. fumigatus Af293 genes with respect to Af294, Af71, and A1163
   5. Table S4: Distribution of polymorphic alleles among A. fumigatus isolates
   6. Table S5: Five A. fumigatus loci exhibiting trans-species polymorphism
   7. Table S6: A. fumigatus core and species-specific genes
   8. Table S7: Features of A. fumigatus-specific genes
   9. Table S8: Top biological processes overrepresented among four lineage specificity groups
   10. Table S9: Enzymes that control the first step in secondary metabolite biosynthesis
   11. Table S10: Top PFAM domains overrepresented among four lineage specificity groups
   12. Table S11: Lineage specificity and chromosomal location
   13. Table S12: Selective constraints operating on virulence-associated genes
   14. Table S13: Known A. fumigatus Af293 allergens
   15. Table S14: Predicted A. fumigatus Af293 allergens
   16. Table S15: Selective constraints operating on sex genes
   17. Table S16: Families of transposable elements identified in the Affc genomes
   18. Table S17: Fungal genomes used in phylogenetic analyses
   
   
   
2. A second strain of Aspergillus fumigatus has been sequenced. This is strain CEA10.
   
   The original strain to be sequenced was Af293, a clinical isolate from an individual who died of invasive aspergillosis. The strain is lodged with the Fungal Genetics Stock Center as acquisition A1100.
   
   Strain CEA10 is also a clinical isolate, obtained at a Paris hospital in 1989, and is the strain used in the laboratory of Dr Jean Paul Latgé at the Pasteur Institute, Paris. It is lodged with the FGSC as acquisition number A1163.
   
   
3. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature. 2005 Dec 22;438(7071):1151-6. Nierman WC et.al.
   
   

   Supplementary genomic material

   1. Figure S1. Aspergillus fumigatus chromosomes
   2. Figure S2. Clusters of cell-wall associated GPI-proteins.
   3. Supplementary Methods. Sequencing and Assembly.
   4. Supplementary Text: Secondary Metabolites
   5. Supplementary Text: Selfish Cluster Hypothesis.
   6. Supplementary Tables
      1. Table S1. Proteins implicated in A. fumigatus pathogenicity.
      2. Table S2. Clusters of genes with log2 ratios grouped by k-means in figure 1B.
      3. Table S3. Allergen homologs in A. fumigatus and other Aspergillus species.
      4. Table S4. Putative essential genes in the A. fumigatus genome.
      5. Table S5. Predicted gene clusters involved in secondary metabolism in Aspergillus fumigatus, and orthologous clusters in other Aspergilli.
      6. Table S6.Putative programmed cell death associated proteins in A. fumigatus.
      7. Table S7. Protein families putatively involved in cell wall construction in A. fumigatus and comparisons with genomes from yeasts, other filamentous fungi and other eukaryotes.
      8. Table S8. Partial listing of A. fumigatus specific genes as compared to A. oryzae and A. nidulans using BLASTp.
      9. Table S9. Arsenic metabolism genes in A. fumigatus.
      10. Table S10. Genes of the ergosterol biosynthesis pathway in Aspergillus spp and other fungal species.
      11. Table S11. Genes revealed by comparative genomic hybridization to be missing or diverged relative to A. fumigatus Af293.
          



4. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 2005 Dec 22;438(7071):1105-15 Galagan JE et.al.
   
   
5. Genome sequencing and analysis of Aspergillus oryzae Nature 2005 Dec 22;438(7071):1157-61 Machida M et.al.
   
   
6. Aspergillus fumigatus gene annotations
   
   
7. The Aspergillus fumigatus genome sequencing project
   
   
8. The Aspergillus fumigatus genome is nearly complete and is available as 19 contigs of finished sequence (consisting of Sanger and TIGR data). These data can be downloaded or searched using BLAST
   
   
9. The Aspergillus fumigatus Genome Sequencing Project at the Sanger Institute
   
   This site contains details of this project and includes BAC clone sequences, predicted genes and proteins and BAC end sequences which are searchable using Blast.
   
   
10. A. fumigatus codon usage table