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Abstract
BackgroundOomycetes are a group of fungus-like eukaryotes with diverse microorganisms living in marine, freshwater and terrestrial environments. Many of them are important pathogens of plants and animals, causing severe economic losses. Based on previous study, gene expression in eukaryotic cells is regulated by epigenetic mechanisms such as DNA methylation and histone modification. However, little is known about epigenetic mechanisms of oomycetes.ResultsIn this study, we investigated the candidate genes in regulating histone acetylation in oomycetes genomes through bioinformatics approaches and identified a group of diverse histone acetyltransferases (HATs) and histone deacetylases (HDACs), along with three putative novel HATs. Phylogenetic analyses suggested that most of these oomycetes HATs and HDACs derived from distinct evolutionary ancestors. Phylogenetic based analysis revealed the complex and distinct patterns of duplications and losses of HATs and HDACs in oomycetes. Moreover, gene expression analysis unveiled the specific expression patterns of the 33 HATs and 11 HDACs of Phytophthora infestans during the stages of development, infection and stress response.ConclusionsIn this study, we reveal the structure, diversity and the phylogeny of HATs and HDACs of oomycetes. By analyzing the expression data, we provide an overview of the specific biological stages of these genes involved. Our datasets provide useful inputs to help explore the epigenetic mechanisms and the relationship between genomes and phenotypes of oomycetes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3285-y) contains supplementary material, which is available to authorized users.
Highlights
Oomycetes are a group of fungus-like eukaryotes with diverse microorganisms living in marine, freshwater and terrestrial environments
Histone acetyltransferases in oomycetes Both Type A and Type B histone acetyltransferases (HATs) were found in oomycetes in five families, comprising HAGs, HAFs, HACs, HAMs, and Hat1s (Fig. 1)
HATs and histone deacetylases (HDACs) of P. infestans are expressed in stages of development, infection and responsive to stress In order to gain insight into the possible role of oomycetes HATs and HDACs, we examined the expression of predicted HATs and HDACs in ten developmental stages of P. infestans
Summary
Oomycetes are a group of fungus-like eukaryotes with diverse microorganisms living in marine, freshwater and terrestrial environments. Gene expression in eukaryotic cells is regulated by epigenetic mechanisms such as DNA methylation and histone modification. Gene expression and physiological function can be regulated by epigenetic mechanisms. Epigenetic modifications of chromatin can cause heritable changes that are not encoded by the underlying DNA sequences. The mechanisms involved mainly include DNA methylation and histone modification [1]. DNA methylation mostly occurs at CpG dinucleotides through adding methyl groups and converting cytosine to 5-methylcytosine by DNA methyltransferases (DNMTs) [2, 3]. DNMT1, DNMT2, DNMT3A, DNMT3B, and DNMT3L are C(5)-cytosine-specific DNA methyltransferases [4,5,6].
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