Whole-Genome gene expression and gene family analyses of Phycomyces blakesleeanus, a model photoresponsive zygomycete
The photoresponsive zygomycete Phycomyces blakesleeanus is an experimentally tractable model system for elucidating the signalling pathways underlying photoregulation. Our recent sequencing, assembly, and annotation of the P. blakesleeanus genome allows us to complement classical molecular biological studies with genome-wide analyses of gene expression. We sequenced cDNAs from mycelia grown with and without light. The resulting 23410 'light' ESTs and 24437 'dark' ESTs were aligned with the genome and used to identify which of the 14792 genes could be described as transcriptionally active under either condition. We tagged 1538 genes (10%) as potentially light-specific, 1558 genes (11%) as potentially dark-specific, and 2431 genes (16%) as transcribed under both light and dark. In addition to its value as a model organism, P. blakesleeanus is one of only 2 zygomycetes with a sequenced genome, providing an opportunity to discover genes that are specific to or missing from zygomycetes, and gene families that are expanded or contracted in zygomycetes relative to the much better-sampled ascomycetes and basidiomycetes. We clustered P. blakesleeanus proteins with those of 13 other fungi and so far find 2 zygomycete-specific families of Zn-finger proteins, and a zygomycete-specific expansion of protein kinases. We also confirm the existence of a Phycomyces-specific family of F-box domain proteins.