Table 1 Summary of genome assembly metrics for the five new assemblies reported in this study and previous assemblies of the same accession (B. rapa) or different accessions of the same morphotype (B. oleracea).
Quality metric | Brassica rapa | Brassica oleracea | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ssp. trilocularis | ssp. narinosa | ssp. acephala | ssp. botrytis | ssp. oleracea | |||||||||||||
R500 (this study) | R500 (ref. 20) | Wutacai (this study) | Wutacai (ref. 4) | C102 (this study) | 07-DH-33 (ref. 26) | T18 (ref. 48) | Nd125 (this study) | T21 (ref. 48) | T25 (ref. 48) | Korso (ref. 47) | C-8 (ref. 46) | Bos01 (this study) | T09 (ref. 48) | T10 (ref. 48) | W03 (ref. 49) | W1701 (ref. 26) | |
Cumulative size (bp) | 373,325,180 | 356, 000, 000 (a) | 404,489,077 | 466,502,319 | 563,329,934 | 588,360,242 | 553,363,182 | 567,916,392 | 534,419,652 | 547,890,678 | 552,847,295 | 568,515,523 | 646,170,971 | 576,023,240 | 580,974,251 | 630,729,510 | 634,424,806 |
Sequences | 33 | 1,753 (a) | 80 | 12,558 | 31 | 10 | 26 | 88 | 72 | 138 | 10 | 10 | 157 | 15 | 24 | 360 | 11 |
Pseudomolecules | 10 | 10 | 10 | 0 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 |
Pseudomolecule size (bp) (% of assembly) | 364,236,165 (97.6) | 280,850,083 (78.8) | 375,103,728 (92.7) | N/A | 555,962,841 (98.7) | 588,287,377 (99.9) | 550,420,920 (99.5) | 552,818,513 (97.3) | 526,630,535 (98.5) | 524,691,661 (95.8) | 547,555,460 (99.6) | 557,113,381 (98.0) | 594,003,544 (91.9) | 572,017,529 (99.3) | 570,456,620 (98.2) | 594,346,218 (94.2) | 618,795,957 (97.5) |
Scaffold N50 (bp) | 38,623,307 | N/A | 43,704,723 | 907,768 | 61,343,825 | 64,701,984 | 65,433,663 | 62,575,981 | 56,484,001 | 57,349,439 | 59,208,503 | 65,683,070 | 62,410,918 | 60,668,869 | 68,709,032 | 64,564,754 | 72,197,880 |
Scaffold N90 (bp) | 23,616,232 | N/A | 21,064,187 | 10,792 | 51,763,739 | 58,208,169 | 54,329,710 | 47,990,424 | 49,547,750 | 46,904,723 | 52,701,841 | 48,937,047 | 54,501,227 | 56,592,305 | 50,417,254 | 49,313,063 | 53,632,606 |
Longest scaffold (bp) | 62,577,379 | 24,500,000 (a) | 62,011,682 | 9,177,230 | 81,909,429 | 80,057,606 | 78,331,576 | 75,538,215 | 74,621,860 | 73,465,279 | 78,655,145 | 79,842,669 | 87,029,299 | 78,617,262 | 81,748,926 | 80,735,250 | 86,880,579 |
Contig N50 (bp) | 13,023,702 | NA | 11,339,266 | 793.238 | 28,762,279 | 11,430,835 | 20,808,756 | 12,119,172 | 5,552,566 | 11,427,368 | 8,222,774 | 21,552,297 | 7,307,935 | 2,5081,548 | 25,739,047 | 2,305,478 | 15,574,327 |
GC content (%) | 36.757 | 29.205 | 37.417 | 38.353 | 36.802 | 36.995 | 36.737 | 36.702 | 36.635 | 36.141 | 36.502 | 36.144 | 36.903 | 36.891 | 37.037 | 36.725 | 37.255 |
LTR Assembly Index | 12.13 | - | 10.19 | 5.91 | 14.74 | 6.98 | 6.95 | 14.79 | 7.90 | 6.52 | 13.91 | 5.85 | 12.81 | 5.77 | 6.95 | 14.0 | 4.16 |
BUSCO (6.0.0) scores brassicales odb12 (2025-07-01) (N = 4,311) | C:99.3% D:41.2% F:0.0% M:0.7% | C:97.3% D:39.3% F:0.0% M:2.7% | C:99.3% D:42.2% F:0.0% M:0.7% | C:99.4% D:47.2% F:0.0% M:0.6% | C:99.4% D:42.5% F:0.1% M:0.6% | C:99.3% D:42.5% F:0.1% M:0.6% | C:99.1% D:42.6% F:0.1% M:0.8% | C:99.4% D:44.3% F:0.0% M:0.6% | C:99.3% D:42.4% F:0.0% M:0.7% | C:99.2% D:42.5% F:0.0% M:0.7% | C:99.2% D:42.2% F:0.1% M:0.7% | C:99.4% D:42.5% F:0.1% M:0.6% | C:99.3% D:48.3% F:0.1% M:0.6% | C:99.3% D:42.4% F:0.1% M:0.7% | C:99.3% D:42.8% F:0.1% M:0.6% | C:99.3% D:49.8% F:0.0% M:0.7% | C:99.4% D:43.1% F:0.1% M:0.6% |
Protein-coding genes | 52,275 | 45,538 | 54,266 | 47,602 | 66,049 | 52,913 | 53,089 | 68,060 | 51,515 | 50,754 | 60,640 | 57,983 | 71,867 | 52,057 | 52,606 | 62,059 | 51,831 |
Genes within pseudo-molecules | 51,796 | 45,538 | 52,977 | N/A | 65,713 | 52,909 | 53,072 | 66,432 | 51,464 | 50,541 | 60,027 | 57,189 | 68,253 | 52,001 | 52,581 | 60,900 | 51,586 |
