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. 2019 Jun 15:6:78.
doi: 10.1038/s41438-019-0160-4. eCollection 2019.

MDR: an integrative DNA N6-methyladenine and N4-methylcytosine modification database for Rosaceae

Zhao-Yu Liu #  1 , Jian-Feng Xing #  1   2 , Wei Chen #  1 , Mei-Wei Luan  1 , Rui Xie  3 , Jing Huang  4 , Shang-Qian Xie  1 , Chuan-Le Xiao  2
Affiliations

MDR: an integrative DNA N6-methyladenine and N4-methylcytosine modification database for Rosaceae

Zhao-Yu Liu et al. Hortic Res. .

Abstract

Eukaryotic DNA methylation has been receiving increasing attention for its crucial epigenetic regulatory function. The recently developed single-molecule real-time (SMRT) sequencing technology provides an efficient way to detect DNA N6-methyladenine (6mA) and N4-methylcytosine (4mC) modifications at a single-nucleotide resolution. The family Rosaceae contains horticultural plants with a wide range of economic importance. However, little is currently known regarding the genome-wide distribution patterns and functions of 6mA and 4mC modifications in the Rosaceae. In this study, we present an integrated DNA 6mA and 4mC modification database for the Rosaceae (MDR, http://mdr.xieslab.org). MDR, the first repository for displaying and storing DNA 6mA and 4mC methylomes from SMRT sequencing data sets for Rosaceae, includes meta and statistical information, methylation densities, Gene Ontology enrichment analyses, and genome search and browse for methylated sites in NCBI. MDR provides important information regarding DNA 6mA and 4mC methylation and may help users better understand epigenetic modifications in the family Rosaceae.

Keywords: DNA methylation; DNA sequencing; Plant genetics.

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Conflict of interest statement

Conflict of interestThe authors declare that they have no conflict of interest.

Figures

Fig. 1
Fig. 1
Structure and contents of MDR
Fig. 2
Fig. 2. Output of query and visualization of methylation sites.
(a) Output of query by gene, (b) output of query by genomic region, (c) visualization of methylation sites in genome browser
Fig. 3
Fig. 3. Comparison of 6mA and 4mC modifications in F. vesca and R. chinensis.
a Percentage of methylation density at 6mA and 4mC in F. vesca and R. chinensis, (b) 6mA motif (ADSYA) and 4mC motif (CWSBA) in F. vesca, (c) 6mA motif (ADGYA) and 4mC motif (CDSSA) in R. chinensis. Sequence logos represent the consensus motifs containing methylation sites. Motif sequence numbers relative to the total number of methylation sites and the corresponding P-values (generated by MEME) are shown under the logos
Fig. 4
Fig. 4
Analysis pipeline in MDR
See this image and copyright information in PMC

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