Table 1.
Item | Description | Cov. | Previous |
---|---|---|---|
Genome | High-quality assembly of the silkworm genome in chromosome level (7) | The same as Kawamoto et al. and Mita et al. (7, 16) | |
Gene models | 16 880 in total, with 12 752 correlated with old gene models (4, 28) | The same as Kawamoto et al. and Mita et al. (7, 16) | |
Gene function annotation | 15 594 genes are of function annotations | 92.4% | 80.3% in Kawamoto et al. and Mita et al. (7, 16) |
4937 gene feature annotations | 22.0% | NA | |
201 309 annotations from InterproScan | 93.9% | NA | |
8730 distinctive GO lists | 86.9% | 54.2% in Kawamoto et al. and Mita et al. (7, 16) | |
16 028 correlated KEGG Gene IDs | 96.4% | NA | |
138 KEGG pathways | 16.5% | NA | |
16 320 correlated Entrez IDs | 96.7% | NA | |
Biophysics and chemistry | 2487 EC numbers | 13.8% | NA |
329 biophysicochemical properties | 0.6% | NA | |
2445 catalytic activity annotations | 12.0% | NA | |
1743 cofactor information annotations | 7.5% | NA | |
Topology | 20 378 subcellular localization annotations | 99.9% | NA |
2878 genes with transmembrane regions | 17.0% | NA | |
1960 genes with signal peptides | 11.6% | NA | |
Proteomics and protein structure | 12 394 real peptides from experiments validated 2999 protein coding genes | 17.8% | NA |
9844 genes significantly correlated PDB protein structures | 58.3% | NA | |
1 730 892 correlated EMBL IDs | 92.3% | NA | |
17 762 correlated Gene3D IDs | 57.2% | NA | |
112 275 correlated Interpro IDs | 86.9% | NA | |
6257 CDD annotations | 29.0% | NA | |
TFs | 704 items | 4.2% | NA |
Repeat elements | 571 401 segments, with 28 519 DNA transposons, 190 316 LINE, 13763 LTR and 179 435 SINE | In accordance with Osanai-Futahashi et al. (53) | |
Transcriptomics | 306 samples from 41 projects | NA | |
Epigenomics | 187 samples from 38 projects | NA | |
Populations genetics | Sliding widow analysis results based on 158 silkworm genomes | NA |
‘Cov.’ denotes the coverage of genes with corresponding annotations in total genes. ‘Previous’ denotes the comparison of SGID and previous work. ‘NA’ denotes that related data is not available in previously built silkworm databases, such as SilkBase, Ensembl Silkworm and SilkDB.