Figure 1.
Lifecycle of S. sclerotiorum and B. cinerea, with different stages of sexual and asexual development.
Figure 2.
Phylogeny of the Sclerotiniaceae (Ascomycota, Leotiomycetes, Helotiales), the sister group Rutstroemiaceae (represented by Lambertella species and “Sclerotinia” homoeocarpa), and the outgroup, Blumeria graminis (Leotiomycetes, Erysiphales).
The topology was estimated using Bayesian inference based on the combined sequence data of five genes. The tree was rooted using B. graminis. Bolded branches represent well-supported nodes with >90% support from 1000 maximum likelihood bootstrapped pseudoreplicates and >0.95 posterior probabilities. Support values for each node are listed in Table S29. Topologies recovered from single genes phylogenetic analyses were congruent with the concatenated gene tree topology. Top row Sclerotinia sclerotiorum, photos by H Lyon (left), LM Kohn (right). Left is apothecium emergent from sclerotium developed in vitro; right are apothecia associated with wild host, Ranunculus ficaria. Bottom row photos by AS Walker. Left is Botryotinia fuckeliana, sexual apothecia emergent from sclerotium developed in vitro; right, conidiophores bearing conidia produced by Botrytis cinerea on grapes.
Table 1.
Assembly and gene statistics.
Figure 3.
Genome organization of S. sclerotiorum.
For each putative chromosome of the optical map, alignment of supercontigs is shown in alternating color blocks of black and grey. Syntenic regions with B. cinerea T4 are shown in red. Frequency of repetitive sequences is shown in blue.
Figure 4.
Transposable element content of the genomes of S. sclerotiorum and B.cinerea.
Distribution of transposable elements in the genomes of S. sclerotiorum and B. cinerea (T4 and B05.10 isolates) according to the major clades: LTR retro-transposons, Line retro-transposons, TIR DNA transposons, MITE. UNK refers to unclassified transposable elements.
Figure 5.
Configuration of the MAT loci in S. sclerotiorum and B. cinerea (strains B05.10 and T4).
S. sclerotiorum is homothallic whereas B. cinerea strains are heterothallic. Strain B05.10 is of MAT1-1 identity whereas strain T4 is of MAT1-2 identity. Orthologous genes are displayed in the same colour and pattern. The entire MAT locus is contained between the genes APN2 (on the left, green) and SLA2 (on the right, yellow stippled). The MAT locus of S. sclerotiorum is displayed on the top line, whereas the MAT loci of both B. cinerea strains are displayed on the bottom line. The truncated fragments of the MAT1-1-2 gene in the MAT1-1 isolate and of the MAT1-1-1 gene in the MAT1-2 isolate are highlighted with a dotted circle. Possible ancestral loci are displayed in the middle. Gene names are indicated above the gene model, the presence of a conserved alpha domain or HMG domain is indicated below the gene model. Two hypothetical inversions are shown, which might convert one configuration into the other. Two separate deletions are shown which may have resulted in the evolution of the MAT1-1 or MAT1-2 locus in B. cinerea.
Table 2.
Comparison of the plant cell wall (PCW) degrading potential from CAZome analysis between S. sclerotiorum and B. cinerea and other Ascomycetes.
Table 3.
Secreted peptidases in S. sclerotiorum, B. cinerea, and other ascomycetes.
Figure 6.
Number of genes encoding secondary metabolism key enzymes, membrane transporters, and transcription factors in the genomes of S. sclerotiorum and B. cinerea.
S. sclerotiorum/B. cinerea orthologs were determined by BDBH. Secondary metabolism key enzymes (A), membrane transporters (B), and transcription factors (C). In panel C, the numbers in brackets indicate the number of genes lacking orthologs in other fungi.
Table 4.
Secondary metabolism key enzyme-encoding genes in fungal genomes.
Table 5.
Frequency of occurrence of predicted genes encoding membrane transporters.