MDR: an integrative DNA N6-methyladenine and N4-methylcytosine modification database for Rosaceae
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) modific...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Oxford University Press
2019-06-01
|
| Series: | Horticulture Research |
| Online Access: | https://doi.org/10.1038/s41438-019-0160-4 |
| _version_ | 1811230764682969088 |
|---|---|
| author | Zhao-Yu Liu Jian-Feng Xing Wei Chen Mei-Wei Luan Rui Xie Jing Huang Shang-Qian Xie Chuan-Le Xiao |
| author_facet | Zhao-Yu Liu Jian-Feng Xing Wei Chen Mei-Wei Luan Rui Xie Jing Huang Shang-Qian Xie Chuan-Le Xiao |
| author_sort | Zhao-Yu Liu |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-12T10:33:26Z |
| format | Article |
| id | doaj.art-38d03e78908b4f78949593dc6c7f2c0e |
| institution | Directory Open Access Journal |
| issn | 2052-7276 |
| language | English |
| last_indexed | 2024-04-12T10:33:26Z |
| publishDate | 2019-06-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | Horticulture Research |
| spelling | doaj.art-38d03e78908b4f78949593dc6c7f2c0e2022-12-22T03:36:47ZengOxford University PressHorticulture Research2052-72762019-06-01611710.1038/s41438-019-0160-4MDR: an integrative DNA N6-methyladenine and N4-methylcytosine modification database for RosaceaeZhao-Yu Liu0Jian-Feng Xing1Wei Chen2Mei-Wei Luan3Rui Xie4Jing Huang5Shang-Qian Xie6Chuan-Le Xiao7Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, Hainan UniversityHainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, Hainan UniversityHainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, Hainan UniversityHainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, Hainan UniversityInner Mongolia Academy of Agricultural and Animal Husbandry SciencesDepartment of Agronomy, College of Agriculture, Purdue UniversityHainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, Hainan UniversityState Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen UniversityAbstract 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.https://doi.org/10.1038/s41438-019-0160-4 |
| spellingShingle | Zhao-Yu Liu Jian-Feng Xing Wei Chen Mei-Wei Luan Rui Xie Jing Huang Shang-Qian Xie Chuan-Le Xiao MDR: an integrative DNA N6-methyladenine and N4-methylcytosine modification database for Rosaceae Horticulture Research |
| title | MDR: an integrative DNA N6-methyladenine and N4-methylcytosine modification database for Rosaceae |
| title_full | MDR: an integrative DNA N6-methyladenine and N4-methylcytosine modification database for Rosaceae |
| title_fullStr | MDR: an integrative DNA N6-methyladenine and N4-methylcytosine modification database for Rosaceae |
| title_full_unstemmed | MDR: an integrative DNA N6-methyladenine and N4-methylcytosine modification database for Rosaceae |
| title_short | MDR: an integrative DNA N6-methyladenine and N4-methylcytosine modification database for Rosaceae |
| title_sort | mdr an integrative dna n6 methyladenine and n4 methylcytosine modification database for rosaceae |
| url | https://doi.org/10.1038/s41438-019-0160-4 |
| work_keys_str_mv | AT zhaoyuliu mdranintegrativednan6methyladenineandn4methylcytosinemodificationdatabaseforrosaceae AT jianfengxing mdranintegrativednan6methyladenineandn4methylcytosinemodificationdatabaseforrosaceae AT weichen mdranintegrativednan6methyladenineandn4methylcytosinemodificationdatabaseforrosaceae AT meiweiluan mdranintegrativednan6methyladenineandn4methylcytosinemodificationdatabaseforrosaceae AT ruixie mdranintegrativednan6methyladenineandn4methylcytosinemodificationdatabaseforrosaceae AT jinghuang mdranintegrativednan6methyladenineandn4methylcytosinemodificationdatabaseforrosaceae AT shangqianxie mdranintegrativednan6methyladenineandn4methylcytosinemodificationdatabaseforrosaceae AT chuanlexiao mdranintegrativednan6methyladenineandn4methylcytosinemodificationdatabaseforrosaceae |