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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.
Highlights
DNA methylation, which is the addition of a methyl group to a DNA nucleotide, plays an important role in biological processes due to the resulting changes in DNA structure and topology[1]
DNA 6mA and 4mC modifications have been detected by single-molecule real-time (SMRT) at a single-nucleotide resolution and single-molecule level based on variances in interpulse
For 6mA identification, SMRT sequencing has advantages compared with other methods[18,19], such as liquid chromatography coupled with tandem mass spectrometry (LC-MS/ MS)20, 6mA immunoprecipitation sequencing (6mAIPseq)[13], and certain restriction enzyme-based 6mA sequencing (6mA-REseq)[21]
Summary
DNA methylation, which is the addition of a methyl group to a DNA nucleotide, plays an important role in biological processes due to the resulting changes in DNA structure and topology[1]. Methylation on the fifth position of the cytosine pyrimidine ring (5-methylcytosine, 5mC) has been the focus of research on eukaryotic genome distribution and is an important epigenetic marker closely related to transcription[2,3,4,5]. Technology, a mainstream platform of third-generation sequencing, is prevalently applied due to the advantages of long-read sequencing and detectable DNA modification[15,16]. DNA 6mA and 4mC modifications have been detected by SMRT at a single-nucleotide resolution and single-molecule level based on variances in interpulse. SMRT sequencing has provided important information regarding the presence of 6mA and 4mC modifications and has greatly improved the genome-wide analysis of DNA modifications in eukaryotes
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