Table 1.
Statistics based on the master transcriptomes. Mc = M. candidum; Ms = M. sanguineum; Hy = F1 hybrid; rep = replicate. aBased on EvidentialGene ‘okay’ transcripts. bFiltered reads to EvidentialGene ‘okay’ transcripts.
| Leaf | Flower petal | |
|---|---|---|
| No. of read pairs after normalization (% of total) | 15 389 729 (7.3 %) | 11 362 570 (5.6 %) |
| No. of contigs (Trinity output) | 209 516 | 196 293 |
| No. of contigs (EvidentialGene output, ‘okay’ transcripts) | 50 519 | 48 120 |
| Smallest contiga (bp) | 201 | 201 |
| Largest contiga (bp) | 16 762 | 16 810 |
| Total lengtha (bp) | 65 471 851 | 63 130 782 |
| Mean lengtha (bp) | 1295.99 | 1311.95 |
| % GCa | 48.1 | 48.1 |
| N50a (bp) | 1864 | 1885 |
| Mapping rateb (%) | ||
| Mc (rep 1; rep 2) | 88.3; 88.4 | 88.8; 89.5 |
| Ms (rep 1; rep 2) | 85.3; 84.6 | 89.7; 90.3 |
| Hy (rep 1; rep 2) | 88.4; 80.9 | 87.5; 89.6 |
| BUSCO assessmenta | ||
| Complete (%) | 92.8 | 92.6 |
| Single-copy (%) | 75.1 | 76.8 |
| Duplicated (%) | 17.7 | 15.8 |
| Fragmented (%) | 2.8 | 2.9 |
| Missing (%) | 4.4 | 4.5 |
| Transcript length assessmenta | ||
| No. of transcripts >90 % | 5404 | 5224 |
| No. of transcripts >70 % | 7558 | 7372 |
| No. of DE transcripts (logFC ≥ 2, FDR ≤ 0.001) | 3973 | 2116 |
| KOBAS annotation (Mc-Ms-Hy) | ||
| No. of transcripts annotated (% of total) | 34 640 (68.6 %) | 33579 (69.8 %) |
| No. of DE transcripts annotated (% of total) | 3165 (79.7 %) | 1545 (73.0 %) |
| No. of KEGG terms (corrected P ≤ 0.05) | 2 | 3 |
| No. of GO terms (corrected P ≤ 0.05) | 92 | 61 |
GC=the nucleotides Guanine and Cytosine.