Genome sequencing and analysis of Aspergillus oryzae

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

“…The concentration of CAZyme genes (primarily GH genes) in syntenic gaps with F. graminearum and N. crassa further supports the notion that selective pressure can maintain the clustering of genes encoding proteins involved in biomass degradation. In comparison, previous studies [15][16][17] indicate that syntenic gaps in other genomes are enriched in genes that are important for species-specific attributes. Although it is possible that duplications may play a role in the loss of synteny, the CAZyme clusters in T. reesei show little evidence of expansion in comparison with the other fungi analyzed.…”

“…In many cases, these gaps are conserved between T. reesei and the other Sordariomycetes, suggesting that they are prone to frequent insertions, duplications or chromosomal breaks. Regions without synteny to other genomes often contain genes that are important for the adaptation of the organism [15][16][17] . Another noteworthy feature of the comparative map ( Fig.…”

Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum

“…Thirty-three of such genes were identified using SMURF software (http://www.tigr.org/software/) encoding for: 20 polyketide synthases (PKS), 10 nonribosomal peptide synthetases (NRPS), 2 hybrid NRPS-PKS enzymes and 1 dimethylallyltryptophan synthase (Supplementary Table 3 online). This is similar to the numbers found in Aspergilli 10,12,15,16 . The penicillin cluster is well known 17 , and the siderophore synthetases for ferrichrome (Pc13g05250) and triacetylfusarinine (Pc16g03850, Pc22g20400) were readily assigned by homology (Supplementary Table 4 online).…”

“…Almost 30% of the predicted P. chrysogenum proteins lack orthologs in other sequenced fungi. In the closely related genus Aspergillus, the origin of lineage-specific genes has been largely attributed to either gene acquisition through horizontal gene transfer 10,15 or to gene duplication followed by accelerated diversification and differential gene loss 13 . These genes tend to function in secondary metabolism and other accessory roles ( Supplementary Fig.…”

Diverse data supports the transition of filamentous fungal model organisms into the post-genomics era

“…This work showed the location of key genes including various amylases, nitrate reductase, tubulin, and ribonuclease T1 on various chromosomes and highlighted the low repeat content in the genome. A whole genome sequence for A. oryzae was published in 2005 (Machida et al 2005). …”