Table 1 Statistics of eight Hevea genome assemblies
From: Pan-genome and phylogenomic analyses highlight Hevea species delineation and rubber trait evolution
Item | RY73397 | Hbe | Hp | Hn | RY879 | RRIM600 | XJA868 | XJA968 |
|---|---|---|---|---|---|---|---|---|
Sequencing | ||||||||
Sequencing platform | ONT+ Hiseq+Hi-C | ONT+ Hiseq+Hi-C | ONT+ Hiseq+Hi-C | ONT+ Hiseq+Hi-C | ONT+ Hiseq | ONT+ Hiseq | ONT+ Hiseq | ONT+ Hiseq |
Estimated genome size (Gb) | 1.50 | 1.57 | 1.58 | 1.57 | 1.52 | 1.54 | 1.48 | 1.58 |
Genome sequencing depth (×) | 83 + 12 + 113 | 87 + 11 + 115 | 97 + 12 + 153 | 97 + 13 + 119 | 95 + 11 | 99 + 10 | 100 + 11 | 91 + 13 |
Assembly | ||||||||
Assembly size (Gb) | 1.49 | 1.58 | 1.55 | 1.55 | 1.52 | 1.54 | 1.56 | 1.54 |
% of estimated genome size | 98% | 100% | 98% | 99% | 100% | 100% | 101% | 97% |
Contig N50 (Mb) | 2.24 | 2.72 | 2.26 | 2.13 | 1.33 | 2.54 | 2.59 | 2.02 |
Contig N90 (Mb) | 0.59 | 0.70 | 0.70 | 0.63 | 0.47 | 0.80 | 0.80 | 0.67 |
No. of contigs | 1020 | 927 | 964 | 1082 | 1666 | 972 | 1003 | 1157 |
Scaffold N50 (Mb) | 87.73 | 90.86 | 93.08 | 92.10 | NA | NA | NA | NA |
No. of scaffolds | 346 | 327 | 139 | 296 | NA | NA | NA | NA |
Chromosome loading ratio (%) | 99.91 | 99.95 | 99.99 | 99.98 | NA | NA | NA | NA |
Repetitive content (%) | 81.80 | 81.01 | 82.06 | 82.04 | 81.88 | 82.05 | 81.85 | 82.06 |
Genome assessment | ||||||||
Reads mapping (%) | 99.65 | 99.73 | 99.75 | 99.61 | 99.63 | 99.66 | 99.64 | 99.65 |
CEGMA (%) | 96.51 | 97.82 | 96.72 | 97.16 | 96.94 | 97.16 | 96.94 | 97.16 |
BUSCO (%) | 92.71 | 95.21 | 94.10 | 94.58 | 95.12 | 94.65 | 93.19 | 94.51 |
Merqury (%) | 82.67 | 84.67 | 81.00 | 84.05 | 82.81 | 83.92 | 82.31 | 84.13 |
LAI | 12.05 | 11.11 | 11.40 | 10.40 | 13.38 | 15.21 | 16.67 | 15.71 |
Annotation | ||||||||
Gene number | 42897 | 46095 | 43481 | 44138 | 42386 | 43594 | 43994 | 43565 |
Average gene length (bp) | 4268.39 | 4192.64 | 4281.24 | 4277.56 | 4240.62 | 4289.5 | 4256.17 | 4214.77 |
Average coding sequence length (bp) | 1222.71 | 1223.89 | 1236.08 | 1227.83 | 1223.87 | 1231.41 | 1230.15 | 1224.54 |
Average exon number per gene | 5.34 | 5.25 | 5.33 | 5.33 | 5.33 | 5.34 | 5.33 | 5.31 |
