Table 2.
Comparison of the assembly and statistics among the Prunus genomes so far published
| Peach v2.0 | Peach v1.0 | P. mume | PAV_r1.0 (P. avium) | P. yedoensis | |
|---|---|---|---|---|---|
| Sequencing strategy | Sanger–NGS Illumina | Sanger | NGS Illumina | NGS Illumina | NGS Illumina–PacBio |
| Genome coverage | 8.47×–NGS 64× | Sanger 8.47× | 180× | 130.34× | 1265.6× (1192× + 73×) |
| Scaffold number total | 191 (241)a | 202 (234) | 1449 | 10,148 | 3185 |
| Contig number total | 2525 | 2730 | 10,894 | – | 4292 |
| Scaffold sequence total | 227.4 Mb | 227.3 | 237.1 Mb | 272.4 Mb | 323.8 Mb |
| Mapped scaffold sequence total | 225.7 Mb (99.2%) | 218.4 Mb (96%) | 198.9 (83.9%) | 191.7 Mb (70.4%) | 281.6 Mb (87.0%) |
| Oriented scaffold sequence | 223.3 Mb (98.2%) | 194.6 Mb (85.6%) | – | – | – |
| Contig sequence total | 224.6 Mb | 224.6 Mb | 219.9 Mb | – | 318.7 Mb |
| Scaffold N50/L50 | 10/7.3 Mb | 9/8.9 Mb | 120/577.8 kb | –/219.6 kb | 519/198.9 kb |
| Scaffold N50/L50 (chromosome-scale assembly) | 4/27.4 Mb | 4/26.8 Mb | – | – | – |
| Contig N50/L50 | 250/255.4 kb | 294/214.2 kb | 2009/31.8 kb | –/276 bp | 706/132.6 kb |
| Number of scaffolds >50 kb | 11 | 21 | – | – | – |
| % main genome in scaffolds >50 kb | 99.4% | 99.4 | – | – | – |
| Repetitive sequences | 79.38 Mb (35.34%) | 84.41 Mb (37.14%) | 106.8 Mb (44.9%) | 119.4 Mb (43.8%) | 150.8 Mb (47.2%) |
| Protein-coding genes | 26,873 | 27,852 | 31,390 | 43,673 | 41,294 |
| Protein-coding transcripts | 47,089 | 28,689 | – | – | 45,581 |
| Alternative transcripts | 20,216 | 837 | – | – | 4287 |
aIn brackets, assembled scaffolds prior the build of pseudomolecules