Diversity, evolution and expression profiles of histone acetyltransferases and deacetylases in oomycetes

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.

A proper PiCAT2 level is critical for sporulation, sporangium function, and pathogenicity of Phytophthora infestans

“…Lesion samples were collected at 0 and 12 hr as well as at 1, 2, 3, 4, and 5 days, and immediately placed in liquid nitrogen. Total RNA was extracted and gene expression was analysed as previously described (Wang et al ., ). The gene of ubiquitin‐conjugating enzyme ( ubc, PITG_00505 ) in P. infestans was used as an internal control (Yan and Liou, ).…”

“…RNA was extracted and gene expression was analysed as previously described (Wang et al, 2016b). The gene of ubiquitin-conjugating enzyme (ubc, PITG_00505) in P. infestans was used as an internal control (Yan and Liou, 2006).…”

Genome-wide characterization deciphers distinct properties of major intrinsic proteins in six Phytophthora species

“…Recently, transcriptome data provided important clues about the involvement of MIPs in host-pathogen interactions (Galindo-Gonzàlez and Deyholos, 2016; Reeksting et al, 2016; Guo et al, 2017). Although there has been no study on PMIPs, in the present study, we identified and characterized a total of 126 MIP homologues from the genomes of six Phytophthora species, which cause severe economic losses because of devastating effects on numerous agriculturally and ornamentally important plants (Tyler et al, 2006; Haas et al, 2009; Lamour et al, 2012; Thines, 2014; Fawke et al, 2015; Derevnina et al, 2016; Wang et al, 2016). This study provided comparative information in context of genome-wide number, subclasses or groups, structural insight, and evolution of PMIPs relative to those in taxonomic groups.…”

“…MIPs in pathogenic fungi may act as attractive targets for antifungal drugs (Verma et al, 2014). However, no study has been conducted on the MIPs of oomycetes, a distinct lineage of fungus-like eukaryotes with diverse microorganisms that are related to organisms such as brown algae and diatoms (Beakes et al, 2012; Thines, 2014; Fawke et al, 2015; Wang et al, 2016). Oomycetes are globally distributed and ubiquitous in marine, freshwater, and terrestrial environments (Thines, 2014), and cause devastating diseases to both plants and animals (Derevnina et al, 2016).…”

“…Among oomycetes, the Phytophthora genus comprises more than 117 species, which are highly devastating to a wide range of agriculturally and ornamentally important plants, causing severe economic losses (Martin et al, 2012; Kroon et al, 2004; Tyler et al, 2006; Beakes et al, 2012; Thines, 2014; Fawke et al, 2015; Wang et al, 2016). P. infestans , the cause of late blight of potato and tomato, resulted the Irish Potato Famine in the mid-19th century (Haas et al, 2009; Yoshida et al, 2013; Thines, 2014; Wang et al, 2016), and P. sojae costs the soybean industry millions of dollars each year (Tyler et al, 2006; Sahoo et al, 2017). P. ramorum , the cause of death of oak trees in North America, has severe impact on natural ecosystem, and P. cinnamomi is a substantial threat to natural eucalyptus forests in Australia (Tyler et al, 2006; Lamour et al, 2012; Thines, 2014).…”