Table 2.
Genome characteristics
| R. commune UK7 | R. secalis | R. agropyri | R. ortho-sporum | M. brunnea | |
|---|---|---|---|---|---|
| Assembly statistics | |||||
| Total scaffold length (Mb) | 55.59 | 56,80 | 52.18 | 58.16 | 51.95 |
| N50 contig (kb) | 49.6 | 47.5 | 61.6 | ||
| N50 scaffold (kb) | 800.5 | 113.7 | 303.4 | 104.3 | |
| Scaffolds/Chromosomes | 163 | 2129 | 508 | 29183 | 89 |
| GC-content (%) | 42.33 | 43.91 | 42.9 | 41.1 | 42.72 |
| - coding (%) | 49.86 | 49.85 | 49.75 | 54.12 | |
| - non-coding (%) | 39.09 | 40.87 | 39.52 | 38.12 | |
| Coding sequence | |||||
| Percent coding (%) | 30.06 | 33.84 | 33.08 | 28.78 | |
| Average gene size (bp) | 1367.7 | 1271.6 | 1269.4 | 1491 | |
| Average gene density (gene/kb) | 0.22 | 0.27 | 0.26 | 0.19 | |
| Protein-coding genes | 12212 | 13151 | 13674 | 10027 | |
| Exons | 38363 | 39806 | 41720 | 33423 | |
| Average exon size | 434.4 | 419.1 | 415.1 | 394.6 | |
| Exons/gene | 3.1 | 3 | 3.1 | 3.9 | |
| tRNA genes | 113 (29 mta) | 117 (30 mta) | 107 (29 mta) | nd | |
| Validation of prediction | |||||
| SCPCH (246) | 246 | 246 | 246 | 246 | |
| CEGMAS (248) | 248 | 248 | 247 | 247 | |
| Secretome | |||||
| Secreted proteins ≥300aa | 711 | 690 | 724 | 509 | |
| Small secreted proteins <300aa | 457 | 574 | 655 | 429 | |
| Non-classical secreted proteins ≥300aa | 77 | 90 | 89 | 61 | |
| Small non-classical secr. proteins <300aa | 63 | 167 | 196 | 63 | |
| non-secreted protein | 10904 | 11630 | 12010 | 8965 | |
| All proteins | 12212 | 13151 | 13674 | 10027 | |
| Non-coding sequence | |||||
| Introns | 26151 | 26655 | 28046 | 24747 | |
| Introns/gene | 2.6 | 2.5 | 2.5 | 2.9 | |
| Average intron length (base) | 80.5 | 82.4 | 83.1 | 118.5 | |
| Average intergenic distance (bp) | 3013 | 2319 | 2398 | 3398 | |
| Repeat sequences | |||||
| DNA Transposon | 8.04% | 4.27% | 6.89% | 7.64% | |
| LINE | 0.39% | 0.97% | 0.44% | 1.56% | |
| SINE | 0.07% | 0.11% | 0.07% | 0.15% | |
| LTR Retrotransposon | 17.06% | 7.84% | 10.56% | 27.41% | |
| Unclassified nonLTR-Retrotransposon | 0.02% | 0.03% | 0.00% | 0.07% | |
| Unclassified Retrotransposon | 2.56% | 3.35% | 2.69% | 2.54% | |
| Unclassfied | 0.22% | 0.60% | 0.42% | 1.36% | |
| Total TE class | 28.21% | 16.68% | 20.88% | 40.33% | |
| Simple sequence repeats | 0.90% | 1.03% | 0.94% | 2.57% | |
| Total excl. Tandem repeats | 29.16% | 17.79% | 21.89% | 43.07% | |
| Tandem repeats | 8.27% | 5.05% | 7.38% | 11.46% | |
| Total repeat coverage | 31.23% | 20.09% | 24.00% | 45.64% | |
a mitochondrial