Table 2.
Mapping characteristics of RNA‐sequencing (RNA‐seq) reads to the reference genomes of Brassica napus and Leptosphaeria maculans in the validation RNA‐seq experiment.
| Condition* | Replicate | Total no. of reads | Reads mapped on the B. napus genome (no./%) | Reads mapped on the L. maculans genome (no./%) | No. of B. napus expressed genes† | No. of L. maculans expressed genes† | ||
|---|---|---|---|---|---|---|---|---|
| Mycelium in vitro | 1 | 4.11E+07 | 4.29E+03 | (0.01%) | 4.00E+07 | (97.35%) | 4 | 10 775 |
| Mycelium in vitro | 2 | 4.57E+07 | 4.74E+03 | (0.01%) | 4.45E+07 | (97.36%) | 3 | 10 944 |
| Non‐inoculated cotyledons | 1 | 1.40E+08 | 1.27E+08 | (90.98%) | 1.52E+03 | (0.00%) | 52 288 | 0 |
| Non‐inoculated cotyledons | 2 | 1.77E+08 | 1.62E+08 | (91.31%) | 1.78E+04 | (0.01%) | 54 441 | 52 |
| Inoculated cotyledons | 1 | 1.56E+08 | 1.30E+08 | (83.36%) | 1.28E+07 | (8.16%) | 54 391 | 9315 |
| Inoculated cotyledons | 2 | 1.77E+08 | 1.38E+08 | (78.29%) | 2.41E+07 | (13.67%) | 54 591 | 9683 |
| Non‐inoculated stems | 1 | 1.88E+08 | 1.41E+08 | (75.23%) | 2.08E+03 | (0.00%) | 57 982 | 1 |
| Non‐inoculated stems | 2 | 1.38E+08 | 1.26E+08 | (91.68%) | 1.32E+03 | (0.00%) | 57 177 | 0 |
| Inoculated stems | 1 | 1.69E+08 | 1.55E+08 | (91.85%) | 8.72E+05 | (0.52%) | 58 997 | 5209 |
| Inoculated stems | 2 | 1.35E+08 | 1.23E+08 | (91.47%) | 4.21E+05 | (0.31%) | 58 259 | 3059 |
*Isolate JN2 was used in both in planta and in vitro conditions. In planta conditions correspond to cotyledons and stem tissue at 7 and 14 days post‐inoculation, respectively.
†Genes were considered to be expressed when more than 10 unique gene reads were mapped on a reference genome.