Data from: Prevalence of transcription factors in ascomycete and basidiomycete fungi

Background: Gene regulation underlies fungal physiology and therefore is a major factor in fungal biodiversity. Analysis of genome sequences has revealed a large number of putative transcription factors in most fungal genomes. The presence of fungal orthologs for individual regulators has been analysed and appears to be highly variable with some regulators widely conserved and others showing narrow distribution. Although genome-scale transcription factor surveys have been performed before, no global study into the prevalence of specific regulators across the fungal kingdom has been presented. Results: In this study we have analysed the number of members for 37 regulator classes in 77 ascomycete and 31 basidiomycete fungal genomes and revealed significant differences between ascomycetes and basidiomycetes. In addition, we determined the presence of 64 regulators characterised in ascomycetes across these 108 genomes. This demonstrated that overall the highest presence of orthologs is in the filamentous ascomycetes. A significant number of regulators lacked orthologs in the ascomycete yeasts and the basidiomycetes. Conversely, of seven basidiomycete regulators included in the study, only one had orthologs in ascomycetes. Conclusions: This study demonstrates a significant difference in the regulatory repertoire of ascomycete and basidiomycete fungi, at the level of both regulator class and individual regulator. This suggests that the current regulatory systems of these fungi have been mainly developed after the two phyla diverged. Most regulators detected in both phyla are involved in central functions of fungal physiology and therefore were likely already present in the ancestor of the two phyla.

背景：基因调控是真菌生理活动的核心基础，亦是影响真菌生物多样性的关键因素。基因组序列分析表明，多数真菌基因组中存在大量推定转录因子（putative transcription factors）。现有研究已针对单个调控因子的真菌同源基因（ortholog）分布情况展开分析，结果显示其差异显著：部分调控因子在真菌界广泛保守，而另一些则仅在狭窄类群中分布。尽管此前已有基因组规模的转录因子调研工作，但目前尚未有针对真菌界内特定调控因子分布普遍性的全域性研究发表。
结果：本研究对77个子囊菌（ascomycete）与31个担子菌（basidiomycete）的基因组中37类调控因子的成员数量进行了分析，结果显示子囊菌与担子菌间存在显著差异。此外，我们在这108个基因组中，检索了子囊菌中已鉴定的64个调控因子的同源基因存在情况，结果表明整体而言丝状子囊菌中的同源基因检出率最高。有相当数量的调控因子在子囊菌酵母与担子菌中未检出同源基因。与之相反，本研究纳入的7个担子菌调控因子中，仅1个在子囊菌中存在同源基因。
结论：本研究证实，子囊菌与担子菌的调控因子全套组成在调控因子类别与单个调控因子层面均存在显著差异。这表明两类真菌现有的调控系统主要是在两个门发生分化之后演化形成的。在两个门中均检出的多数调控因子参与真菌生理活动的核心功能，因此它们很可能已经存在于两个门的共同祖先中。