Table 2 Summary of genome annotations for each haplotype.
From: Haplotype-resolved genome assembly of the tetraploid potato cultivar Désirée
Type | haplotype 1 | haplotype 2 | haplotype 3 | haplotype 4 |
|---|---|---|---|---|
Repeat elements | ||||
DNA | 46.6 Mbp (6.4%) | 54.1 Mbp (7.4%) | 44.6 Mbp (6.4%) | 45.9 Mbp (6.5%) |
Helitron | 36.1 Mbp (5.0%) | 38.0 Mbp (5.2%) | 33.6 Mbp (4.8%) | 42.3 Mbp (6.0%) |
LINE | 12.4 Mbp (1.7%) | 8.1 Mbp (1.1%) | 7.5 Mbp (1.1%) | 8.1 Mbp (1.1%) |
LTR | 176.5 Mbp (24.4%) | 188.0 Mbp (25.8%) | 165.9 Mbp (23.7%) | 193.6 Mbp (27.3%) |
LTR/Copia | 16.8 Mbp (2.3%) | 19.3 Mbp (2.6%) | 20.3 Mbp (2.9%) | 23.9 Mbp (3.4%) |
LTR/Gypsy | 136.2 Mbp (18.9%) | 133.6 Mbp (18.3%) | 130.0 Mbp (18.6%) | 102.8 Mbp (14.5%) |
MITE | 11.9 Mbp (1.6%) | 10.2 Mbp (1.4%) | 13.0 Mbp (1.9%) | 10.6 Mbp (1.5%) |
Other | 72.8 Mbp (10.1%) | 76.2 Mbp (10.4%) | 69.7 Mbp (10.0%) | 71.3 Mbp (10.1%) |
SINE | 5.1 Mbp (0.7%) | 6.6 Mbp (0.9%) | 4.7 Mbp (0.7%) | 4.9 Mbp (0.7%) |
Total | 514.2 Mbp (71.2%) | 534.1 Mbp (73.2%) | 489.3 Mbp (70.1%) | 503.6 Mbp (71.0%) |
Protein-coding genes | ||||
Total gene number | 44156 | 49598 | 43845 | 44330 |
Total transcript number | 67585 | 72597 | 66972 | 67185 |
Mean gene length (bp) | 1695.85 | 1610.97 | 1687.71 | 1677.79 |
Mean CDS length (bp) | 1062.59 | 1032.74 | 1060.23 | 1061.68 |
Mean exon number | 5.28 | 5.04 | 5.31 | 5.28 |
Mean intron number | 4.28 | 4.04 | 4.31 | 4.28 |
Complete BUSCO (%) | 94.1% | 93.3% | 95.4% | 93.7% |
Single Omark HOGs | 82.9% | 82.5% | 84.3% | 82.8% |
Duplicated Omark HOGs | 11.6% | 11.6% | 11.5% | 11.9% |
Missing Omark HOGs | 5.5% | 5.9% | 4.2% | 5.4% |
Mercator4 proteins annotated (%) | 93.5% | 93.5% | 93.7% | 93.5% |
Mercator4 proteins classified (%) | 50.5% | 46.5% | 50.7% | 50.0% |
Mercator4 bins occupied (%) | 94.2% | 93.9% | 94.6% | 94.3% |
