Journal Article

Phytophthora methylomes are modulated by 6mA methyltransferases and associated with adaptive genome regions

Gu, Tingting, Jiang, Lubin, Mao, Fei, Ma, Hongyu, Zhang, Fan, Li, Xi, Dong, Suomeng, Kamoun, Sophien, Wu, Yufeng, Ye, Wenwu, Wang, Liyuan, Ochola, Sylvans Ochieng, Shu, Haidong, Chen, Han, Wang, Yuanchao

2018

Overview

Background Filamentous plant pathogen genomes often display a bipartite architecture with gene-sparse, repeat-rich compartments serving as a cradle for adaptive evolution. The extent to which this two-speed genome architecture is associated with genome-wide DNA modifications is unknown. Results We show that the oomycetes Phytophthora infestans and Phytophthora sojae possess functional adenine N6-methylation (6mA) methyltransferases that modulate patterns of 6mA marks across the genome. In contrast, 5-methylcytosine could not be detected in these species. Methylated DNA IP sequencing (MeDIP-seq) of each species reveals 6mA is depleted around the transcription start sites (TSSs) and is associated with lowly expressed genes, particularly transposable elements. Genes occupying the gene-sparse regions have higher levels of 6mA in both genomes, possibly implicating the methylome in adaptive evolution. All six putative adenine methyltransferases from P . infestans and P . sojae , except PsDAMT2, display robust enzymatic activities. Surprisingly, single knockouts in P . sojae significantly reduce in vivo 6mA levels, indicating that the three enzymes are not fully redundant. MeDIP-seq of the psdamt3 mutant reveals uneven 6mA methylation reduction across genes, suggesting that PsDAMT3 may have a preference for gene body methylation after the TSS. Furthermore, transposable elements such as DNA elements are more active in the psdamt3 mutant. A large number of genes, particularly those from the adaptive genomic compartment, are differentially expressed. Conclusions Our findings provide evidence that 6mA modification is potentially an epigenetic mark in Phytophthora genomes, and complex patterns of 6mA methylation may be associated with adaptive evolution in these important plant pathogens.

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: 5-methylcytosine / Adaptive genome / Adenine / Animal Genetics and Genomics / Bioinformatics / Biomedical and Life Sciences / Chromatography / Deoxyribonucleic acid / DNA / DNA Methylation / DNA sequencing / Enzymatic activity / Enzymes / Epigenetics / Evolution / Evolution & development / evolutionary adaptation / Evolutionary Biology / Famine / Fungi / Gene expression / Gene Expression Regulation / genes / Genome / Genomes / Genomics / Glycine max - parasitology / Human Genetics / Insects / Life Sciences / Localization / Mammals / Methyltransferases / Methyltransferases - metabolism / Microbial Genetics and Genomics / mutants / N6-methyladenosine / Nematodes / Pathogens / Phylogeny / Phytophthora / Phytophthora - classification / Phytophthora - enzymology / Phytophthora - genetics / Phytophthora infestans / Phytophthora sojae / Plant Genetics and Genomics / plant pathogens / Prokaryotes / Proteins / Stem cells / Transcription / Virulence