Table 1.
Database resources of plants in the CNCB-NGDC
| Type | Database | Web link | Functionality | Data volume |
|---|---|---|---|---|
| Repositories | Genome Sequence Archive (GSA) | https://ngdc.cncb.ac.cn/gsa | Data repository for collecting, archiving, managing and sharing raw sequence data generated from different platforms |
1850 plant species 154,749 experiments 173,258 runs ~ 4500 TB volume |
| Genome Warehouse (GWH) | https://ngdc.cncb.ac.cn/gwh | Centralized resource housing genome-scale data for a wide range of species and delivering a series of web services for genome data submission, storage, release and sharing |
1423 plant species 10,594 assemblies |
|
| GenBase | https://ngdc.cncb.ac.cn/genbase | Accepts user submissions (mRNA, genomic DNAs, ncRNA, or small genomes such as organelles, viruses, plasmids, phages from any organism) and integrates data from INSDC |
1085 proteins sequences 1024 nucleotide sequences |
|
| Chloroplast Genome Information Resource (CGIR) | https://ngdc.cncb.ac.cn/cgir | Provides curated resource of chloroplast genome information, dedicating to the integration, annotation and standardization of chloroplast genomes, genes, simple sequence repeats (SSR), and DNA signature sequences (DSS) |
16,435 plant species 5918 featured plants 29,069 genomes |
|
| Genome Variation Map (GVM) | https://ngdc.cncb.ac.cn/gvm | Public repository of genome variations, providing single nucleotide polymorphisms (SNPs) and small insertions & deletions (InDels) presentation and variome data archiving |
30 plant species 72 projects 34,643 samples |
|
| Gene Expression Nebulas (GEN) | https://ngdc.cncb.ac.cn/gen | Provide data portal of transcriptomic profiles under various conditions derived entirely from bulk and single-cell RNA-Seq data analysis in multiple species |
10 plant species 1867 samples 22,215 single-cells |
|
| Methylation Bank (MethBank) | https://ngdc.cncb.ac.cn/methbank | Banks of integrated DNA methylomes across a variety of species. Providing whole genome single-base methylome and manually curate knowledge of both featured differentially methylated genes |
7 plant species 236 tissues/cell lines 1449 single-base resolution methylomes |
|
| Plant pan-genome (PlantPan) | https://ngdc.cncb.ac.cn/plantpan | Encompasses pan-genome analysis results from multiple plant species, provides gene-based and graph-based pan-genome for each species, along with detailed gene functions, 13 types of genomic variations, and genome synteny |
11 plant species 195 genomes 9,127,208 genes 413,000,124 genomic variations 3,345,098 genome synteny |
|
| Open Plant Image Archive (OPIA) | https://ngdc.cncb.ac.cn/opia | An archive database of plant images and related phenotypic data from high-throughput phenotyping platforms for a diversity of species |
11 plant species 56 datasets 566,225 images 56 i-traits |
|
| Knowledge databases | GWAS Atlas | https://ngdc.cncb.ac.cn/gwas/ | Manually curated resource of genome-wide genotype-phenotype (G2P) associations for a wide range of species |
10 plant species 269,138 association 630 publications |
| Plant Editosome Database (PED) | https://ngdc.cncb.ac.cn/ped | Provides RNA editing factors, RNA editing events of targeted organelle genes, interactions between editing factors and events in multiple species, biological functional effects of editing factors in regulating plant phenotypes and the corresponding experimental detailed information |
1618 plant species 144 editing factors 203 edited genes 25,164 editing evens 137 publications |
|
| Internal Control Genes (ICG) | https://ngdc.cncb.ac.cn/icg | Provides a comprehensive collection of high-quality experimentally verified internal control genes and their application scenarios for both model and non-model organisms |
278 plant species 340 studies 1216 genes |
|
| Leaf Senescence Database (LSD) | https://ngdc.cncb.ac.cn/lsd/ | Provides senescence associated genes, mutants, phenotypes and literature references |
86 plant species 31,214 genes 1037 mutants |
|
| Species-specific resources | Information Commons for Rice (IC4R) | http://ic4r.org/ | A curated database providing rice genome sequences, updating rice gene annotations and integrating multiple omics data through community-contributed modules |
56,221 protein-coding genes 80,038 protein-coding transcripts 6259 long non-coding RNAs 4373 circular RNAs 1503 RNA-Seq datasets |
| Rice Expression Database (RED) | http://expression.ic4r.org | Provides gene expression profiles derived entirely from RNA-Seq data analysis on tissues spanning an entire range of rice growth stages and covering a wide variety of biotic and abiotic treatments |
9 tissues 24 projects 284 experiments |
|
| SoyOmics | https://ngdc.cncb.ac.cn/soyomics | Provides a wide variety of soybean multi-omics data, encompassing assembled genomes, graph pan-genomes, resequencing data, phenotypic information from representative germplasms, transcriptomic and epigenomic data from different tissues, organs, and accessions, as well as knowledge of quantitative trait locus and genome-wide association study |
Genome of 27 cultivars variome of ~ 3000 soybean germplasms transcriptome of 28 tissues phenome of 115 traits homology and synteny of 28 genomes |
|
| SorgSD | https://ngdc.cncb.ac.cn/sorgsd | Provides a wealth of sorghum-related information, including genome, variations, phenotypes, panicle images, online resources and critical references |
289 sorghum accessions 39,547,621 variations 289 phenotypes |
|
| Tropical Crop Omics Database (TCOD) | https://ngdc.cncb.ac.cn/tcod | Provides genome sequences, gene function annotations, cross-species homology relationships, genome variations, gene expression and germplasm resource descriptions for 15 tropical crops |
15 plant species 34 genome assemblies 1,255,044 genes 282,436,992 variants 88 expressions 13,381 cultivars |