Table 2.
List of websites/databases useful for Rosaceae research.
| Database name | URL | Species | Information provided | Reference |
|---|---|---|---|---|
| ROSACEAE DATABASES | ||||
| GDR (Genome Database for Rosaceae) | https://www.rosaceae.org | Rosaceae | Genomic | Jung et al., 2019 |
| MDR (Methylation Database for Rosaceae) | http://mdr.xieslab.org | Rosaceae | Methylation | Liu et al., 2019 |
| AppleMDO | http://bioinformatics.cau.edu.cn/AppleMDO | Malus domestica | Co-expression | Da et al., 2019 |
| Fragaria vesca co-expression network explorer | http://159.203.72.198:3838/fvesca | Fragaria vesca | Co-expression | Shahan et al., 2018 |
| SGR (Strawberry Genome Resources) | http://bioinformatics.towson.edu/strawberry | Fragaria vesca | Transcriptome | Darwish et al., 2013 |
| SGD (Strawberry Genome Database) | http://www.strawberryblast.ml:8080/strawberry/viroblast.php | Fragaria x ananassa | Genomic | Liu et al., 2021 |
| TRANSNAP | http://plantomics.mind.meiji.ac.jp/nashi | Pyrus pyrifolia | Transcriptome | Koshimizu et al., 2019 |
| GENERAL PLANT DATABASES | ||||
| NCBI Genome | https://www.ncbi.nlm.nih.gov/genome | General | Genomic | Tatusova et al., 1999 |
| PLAZA | https://bioinformatics.psb.ugent.be/plaza | Plant | Genomic | Van Bel et al., 2018 |
| Phytozome | https://phytozome-next.jgi.doe.gov | Plant | Genomic | Goodstein et al., 2012 |
| EnsemblPlants | https://plants.ensembl.org/index.html | Plant | Genomic | Bolser et al., 2017 |
| PMN (Plant Metabolic Network) | https://plantcyc.org | Plant | Functional (Pathway) | Schläpfer et al., 2017 |
| Plant Reactome | https://plantreactome.gramene.org/index.php?lang=en | Plant | Functional (Pathway) | Naithani et al., 2020 |
| PlantTFDB (Transcription Factor Database) | http://planttfdb.gao-lab.org | Plant | Functional (TF Regulation) | Jin et al., 2017 |
| PlantRegMap (Plant Transcriptional Regulatory Map) | http://plantregmap.gao-lab.org | Plant | Functional (TF Regulation) | Tian et al., 2020 |
| Next-Gen Sequence Databases and sRNA Tools | https://mpss.danforthcenter.org | Plant | ncRNA (small RNA) | Nakano et al., 2020 |
| CANTATAdb | http://cantata.amu.edu.pl | Plant | ncRNA (lncRNA) | Szcześniak et al., 2016 |
| RPTEdb (Rosaceae Plant Transposable Element Database) | http://genedenovoweb.ticp.net:81/RPTEdb/index.php | Rosaceae | TE | Ma et al., 2018 |
| PlantRGDB (Plant Retrocopied Gene DataBase) | https://probes.pw.usda.gov/plantrgdb/index.php | Plant | Retrocopied Gene | Wang, 2017 |