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Open Access Research article

Prevalence of transcription factors in ascomycete and basidiomycete fungi

Richard B Todd1*, Miaomiao Zhou2, Robin A Ohm34, Hendrika ACF Leeggangers25, Loek Visser3 and Ronald P de Vries23

Author Affiliations

1 Department of Plant Pathology, Kansas State University, 4024 Throckmorton Plant Sciences Center, Manhattan, KS 66506, USA

2 Fungal Physiology, CBS-KNAW, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands

3 Microbiology & Kluyver Centre for Genomics of Industrial Fermentations, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands

4 Current address: US Department of Energy (DOE) Joint Genome Institute (JGI), 2800 Mitchell Drive, Walnut Creek, CA 94598, USA

5 Current address: Department of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PA, Wageningen, The Netherlands

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BMC Genomics 2014, 15:214  doi:10.1186/1471-2164-15-214

Published: 20 March 2014

Abstract

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.

Keywords:
Transcription factor; Ascomycete; Basidiomycete; Gene regulation; Fungal genomes; Evolution; Zinc binuclear cluster; Zinc finger; DNA binding domain; Aspergillus