The Coriander Genome Database (CGDB) mainly contained the Genome, transcriptome and metabolome of Coriandrum sativum. Here, we statistics the data output and the related analyses.
Genomic Data:
Table 1. Kmer=17 Statistics of the genomic characteristics of coriander obtained by genome survey analysis.
| K-mer | K-mer number | K-mer Depth | Genome Size(Mb) | Revised Genome Size (Mb) | Heterozygous Ratio(%) | Repeat (%) |
|---|---|---|---|---|---|---|
| 17 | 109,724,893,392 | 51 | 2,151.47 | 2,130.29 | 0.47 | 80.58 |
Table 2. Statistics on the sequencing data of the coriander genome.
| Pair-end libraries | Insert size | Total data (G) | Read length (bp) | Coverage (X) |
|---|---|---|---|---|
| Illumina reads | 350bp | 139.87 | 150 | 65.66 |
| Pacbio reads | - | 197.45 | - | 92.69 |
| 10X Genomics | - | 240.56 | 150 | 112.92 |
| Total | - | 577.88 | - | 271.27 |
Table 3. The results of the Hi-C auxiliary assembly of the C. sativum genome (**Assembled scaffolds > 100bp).
| Sample ID | Length | Number | ||
|---|---|---|---|---|
| Contig**(bp) | Scaffold (bp) | Contig** | Scaffold | |
| Total | 2,118,309,730 | 2,118,684,730 | 9,936 | 6,186 |
| Max | 3,580,399 | 184,508,978 | - | - |
| Number>=2000 | - | - | 9711 | 5961 |
| N50 | 604,128 | 160,995,510 | 1,031 | 7 |
| N60 | 464,580 | 156,618,565 | 1,432 | 8 |
| N70 | 345,039 | 149,113,063 | 1,957 | 9 |
| N80 | 233,760 | 132,297,589 | 2,696 | 11 |
| N90 | 115,576 | 176,899 | 3,961 | 238 |
Table 4. Coriander genome genome length distribution results.
| Chr_id | Length(bp) |
|---|---|
| Chr01 | 175,015,798 |
| Chr02 | 149,113,063 |
| Chr03 | 138,218,460 |
| Chr04 | 184,508,978 |
| Chr05 | 169,111,100 |
| Chr06 | 166,461,324 |
| Chr07 | 176,067,867 |
| Chr08 | 156,618,565 |
| Chr09 | 166,053,162 |
| Chr10 | 160,995,510 |
| Chr11 | 132,297,589 |
| TOTAL | 1,774,461,416(83.77%) |
Table 5. Statistics of the sequence classification results.
| Denovo+Repbase | TE Proteins | Combined TEs | ||||
|---|---|---|---|---|---|---|
| Length(bp) | %in Genome | Length(bp) | % in Genome | Length(bp) | % in Genome | |
| DNA | 13,129,775 | 0.62 | 15,944,501 | 0.75 | 27,580,681 | 1.3 |
| LINE | 5,038,419 | 0.24 | 11,351,841 | 0.53 | 14,638,836 | 0.7 |
| SINE | 91,099 | 0 | 0 | 0 | 91,099 | 0 |
| LTR | 1,348,029,047 | 62.63 | 593,165,832 | 27.99 | 1,413,525,086 | 66.71 |
| Other | 0 | 0 | 0 | 0 | 0 | 0 |
| Unknown | 13,338,918 | 0.63 | 1143 | 0 | 13,340,061 | 0.63 |
| Total | 1,379,493,248 | 65.11 | 619,863,920 | 29.25 | 1,465,499,528 | 69.17 |
Table 6. Statistical results of gene functional annotations.
| Database | Annotated Num | Annotated Percent(%) | |
|---|---|---|---|
| NR | 37595 | 92.3 | |
| Swiss-Prot | 30357 | 74.5 | |
| KEGG | 28,684 | 70.4 | |
| InterPro | All | 32,031 | 78.6 |
| Pfam | 29,707 | 72.9 | |
| GO | 22,149 | 54.4 | |
| Annotated | 37,772 | 92.7 | |
| Total | 40747 | - | |
RNA-seq Data:
Table 1. The summary of data quality for four different tissues of RNA-Seq in Coriandrum sativum.
| Sample name | Raw reads | Clean reads | Clean bases (Gb) | Error rate(%) | Q20(%) | Q30(%) |
|---|---|---|---|---|---|---|
| R_1 | 50142480 | 48894458 | 7.33 | 0.02 | 95.85 | 92.98 |
| R_2 | 46898322 | 46029694 | 6.9 | 0.02 | 96.31 | 93.57 |
| R_3 | 51761854 | 50317882 | 7.55 | 0.02 | 96.26 | 93.51 |
| S_1 | 35565340 | 34944462 | 5.24 | 0.02 | 97.45 | 95.25 |
| S_2 | 44976948 | 44151812 | 6.62 | 0.02 | 95.88 | 92.98 |
| S_3 | 41122924 | 40139718 | 6.02 | 0.02 | 97.31 | 95.07 |
| L_1 | 42501062 | 41894922 | 6.28 | 0.02 | 97.36 | 95.12 |
| L_2 | 42672852 | 41990884 | 6.3 | 0.02 | 95.84 | 92.92 |
| L_3 | 42879590 | 42158930 | 6.32 | 0.02 | 96.1 | 93.29 |
| F_1 | 47131806 | 46068070 | 6.91 | 0.02 | 96.16 | 93.35 |
| F_2 | 44549078 | 43806294 | 6.57 | 0.02 | 96.33 | 93.58 |
| F_3 | 50034336 | 48815268 | 7.32 | 0.02 | 96.26 | 93.48 |
Table 2. The summary of data quality for three different periods of RNA-Seq in Coriandrum sativum and Daucus carota.
| Species | Sample name | Raw reads | Clean reads | Clean bases (Gb) | Error rate(%) | Q20(%) | Q30(%) | GC content(%) |
|---|---|---|---|---|---|---|---|---|
| Coriandrum sativum | D30_1 | 50133324 | 48840010 | 7.33 | 0.02 | 97.75 | 93.44 | 43.63 |
| D30_2 | 55934278 | 54589410 | 8.19 | 0.02 | 97.94 | 93.86 | 43.69 | |
| D30_3 | 55363982 | 54344384 | 8.15 | 0.02 | 96.63 | 91.43 | 43.71 | |
| D60_1 | 52469706 | 51405112 | 7.71 | 0.02 | 96.62 | 91.41 | 42.76 | |
| D60_2 | 50038720 | 48735548 | 7.31 | 0.02 | 96.47 | 91.07 | 42.84 | |
| D60_3 | 48405258 | 47172870 | 7.08 | 0.02 | 96.51 | 91.15 | 43.23 | |
| D90_1 | 57211690 | 55882290 | 8.38 | 0.02 | 97.95 | 93.87 | 43.11 | |
| D90_2 | 56393850 | 53965884 | 8.09 | 0.02 | 97.94 | 93.89 | 43.46 | |
| D90_3 | 47877452 | 46519956 | 6.98 | 0.02 | 97.96 | 93.92 | 43.56 | |
| Daucus carota | D30_1 | 47041712 | 45598900 | 6.84 | 0.02 | 97.88 | 93.76 | 44.9 |
| D30_2 | 51174356 | 49391044 | 7.41 | 0.02 | 97.8 | 93.61 | 44.83 | |
| D30_3 | 50240452 | 48713538 | 7.31 | 0.02 | 98.05 | 94.18 | 44.91 | |
| D60_1 | 57488220 | 55613984 | 8.34 | 0.02 | 97.87 | 93.73 | 44.67 | |
| D60_2 | 49308210 | 47242220 | 7.09 | 0.02 | 97.56 | 92.98 | 44.41 | |
| D60_3 | 55447744 | 52949686 | 7.94 | 0.02 | 97.84 | 93.7 | 44.92 | |
| D90_1 | 50467774 | 48988858 | 7.35 | 0.02 | 97.99 | 94 | 44.36 | |
| D90_2 | 58196876 | 55942734 | 8.39 | 0.02 | 97.53 | 92.89 | 44.09 | |
| D90_3 | 55044610 | 53551586 | 8.03 | 0.02 | 96.5 | 91.17 | 44.06 |
Metaboic Data:
Table 1. The metabolic data for 30, 60, and 90 days after sowing of Coriandrum sativum and Daucus carota (partial).
| Formula | Molecular Weight | Coriandrum sativum | Daucus carota | ||||
|---|---|---|---|---|---|---|---|
| D30 | D60 | D90 | D30 | D60 | D90 | ||
| C22 H36 N2 O7 P2 | 502.20 | 24684.45 | 63947.23 | 59172.35 | 1975.77 | 3256.40 | 4205.56 |
| C30 H30 O11 | 566.18 | 70072.80 | 13010.63 | 5946.26 | 11044.18 | 13718.50 | 7525.37 |
| C40 H57 N5 O7 | 719.43 | 25193.98 | 28665.26 | 36225.72 | 17786.61 | 19458.43 | 21526.83 |
| C10 H16 O S3 | 248.04 | 1160758.44 | 482469.43 | 416082.87 | 9889195.52 | 852813.68 | 122707.96 |
| C19 H30 O4 | 322.21 | 97775.85 | 58926.75 | 49617.06 | 96614.58 | 55004.33 | 44431.33 |
| C5 H13 N O2 | 119.09 | 52972.06 | 55336.20 | 65917.99 | 34214.54 | 64696.35 | 46639.58 |
| C4 H10 N O P S2 | 183.00 | 47891.87 | 25150.10 | 28557.65 | 58285.41 | 36323.70 | 38035.47 |
| C15 H20 N2 O P2 S | 338.08 | 31647.38 | 46929.91 | 48396.10 | 35089.77 | 74933.07 | 86780.78 |
| C24 H32 O5 S | 432.20 | 140264.98 | 95705.12 | 65957.84 | 120148.97 | 115856.54 | 85299.82 |
| C7 H10 O P2 S3 | 267.94 | 11566237.39 | 243410.27 | 140559.83 | 2106285.92 | 462016.30 | 307778.83 |
| C20 H27 N O7 | 393.18 | 75088.86 | 47786.30 | 41827.58 | 82446.98 | 50463.68 | 36316.18 |