Bioinformatic prediction of stage-specific transcription factor binding of Plasmopara halstedii conserved in the downy mildew and Phytophthora species

Abstract

Abstract Oomycetes, a large group of fungi-like organisms, include some destructive plant pathogens causing enormous economic damage. Phylogenetically, oomycetes belong to the kingdom Straminipila and have diverse lifestyles, including saprotrophs and both general and specialized pathogens of various eukaryotic supergroups. A rapid increase in genomic studies and next generation sequencing technologies have led to significant progress in understanding oomycete lifestyles. However, their genetics, including transcriptional regulation, have been studied to a much lesser extent. Here we provide a cross-species analysis of oomycete promoter for providing a first step towards elucidating gene regulation networks related to pathogenicity and life cycle stages. To identify conserved regulatory sequences involved in this, clustered DNA sequences of Plasmopara halstedii transcriptome time-series expression levels dataset from a preliminary study, has been used as a core reference for cross-species comparisons. Using a computational pipeline, 46 potential TFBSs motifs in 25 clusters with functionally conserved downstream genes of downy mildew and two Phytophthora species, regardless of the gene expression levels of Phytophthora transcriptomes were found. This can now be followed up by knock-out experiments in oomycete species amenable for genetic modification.