Fig. 1

Conditions and samples used for the RNA-Seq study of the Leptosphaeria maculans life cycle. Time-course studies are represented by an arrow and the sampling time points are indicated. a RNA was extracted from cotyledons infected with ascospores 1 or 2 days post inoculation (DPI). Another time-course study was conducted by inoculation with conidia, with RNA extraction at six time points, from 2 to 15 DPI. Young leaves from naturally infected fields were sampled 2 or 2.5 months post sowing (MPS). b Petiole colonization was achieved on petioles inoculated in controlled conditions, with RNA extraction at 7 and 14 DPI. c Stem colonization samples were obtained in controlled conditions, at 14 and 28 DPI. Stem base samples from naturally infected fields were collected and used for RNA extraction every 2 to 3 months over an entire growing season. d Leftover stem residues were sampled every 2 to 3 months for 1 year after harvest (dates expressed in months post harvest, MPH). e We used 10 sets of in vitro growth conditions, based on two different media (liquid or solid) and corresponding to different physiological states (mycelium, sporulation, germinating, and resting conidia, in vitro crossing conditions). The samples highlighted in bold red did not provide enough fungal RNA-Seq reads for statistical analysis. f Schematic representation of the colonization stages of oilseed rape by L. maculans. The plants are sown in mid-August/early September. During the early infection stage in autumn, the ascospores, generated on crop residues, produce hyphae that colonize the cotyledons/young leaves. Then, the fungus migrates asymptomatically in the petioles and the stems during the winter months. In early summer, L. maculans causes stem cankers. Then, L. maculans survives on crop residues and produces a new inoculum