88 and ATCC 1015), which allowed us to consider cluster synteny, which approached 100%, between these strains in addition to the orthology between Aspergillus species. Figure

3 Conserved cluster synteny between the gliotoxin cluster of A. fumigatus and the orthologous cluster of Neosartorya fischeri . The predicted gene cluster is indicated with a red bar. The left border of the Afu6g09650 cluster shows a small increase in intergenic distance while the right border shows a large change in intergenic distance. Both borders are examples of interspecies cluster synteny. find more Red bar indicates experimentally determined cluster boundary (Afu6g09630 – Afu6g09740). Blue bar indicates SMURF boundary prediction (Afu6g09580 – Afu6g09740) and green bar indicates the antiSMASH-predicted boundary (Afu6g09520 – Afu6g09745). AspGD displays and provides sequence resources for 15 Aspergillus genomes and related species. A given genome is typically particularly closely related to that of one or two of the other species; the A. fumigatus genome best matches that of Neosartorya fischeri (see Sybil syntenic genomic context

in Additional file 3), A. niger best matches A. acidus and A. brasiliensis (Additional file 4) and A. oryzae best matches A. flavus (Additional file 5). Unlike A. fumigatus, selleck screening library A. niger and A. oryzae, A. nidulans lacks such a closely related species in AspGD with sufficient synteny to enable routine use of cluster orthology in boundary determination. Therefore, we used other nearly criteria such as published gene expression patterns [16], increases in intergenic distance and changes from secondary metabolism-related gene annotations to non-secondary metabolism-related gene annotations (described below) for making these predictions in A. nidulans (Figure 1). The numbers of manually predicted gene clusters in each of these additional

species, determined by observing breaks in gene cluster synteny (see Methods), are summarized in Table 9. In some cases, the functional annotation of the putative gene cluster members was informative in predicting cluster boundaries, especially for A. nidulans, which often lacked cluster synteny with other species present in AspGD. In addition to genes encoding the core backbone enzymes, clusters typically include one or more acyl transferase, oxidoreductase, hydrolase, cytochrome P450, transmembrane transporter and a transcription factor. We manually inspected each cluster and the genomic region surrounding it; changes in functional annotations from typical secondary metabolism annotations to annotations atypical of secondary metabolic processes were frequently BIBF 1120 ic50 observed upon traversing a cluster boundary (Additional files 2, 3, 4, 5) and this was used as an additional criterion for boundary prediction, especially in cases where inter- or intra-species clustering or published gene expression data were not available.