Fig. 3

Construction and analysis of the Zymoseptoria tritici pangenome. a Proportions of core orthogroups (present in all isolates), accessory orthogroups (present ≥ 2 isolates but not all) and singletons (present in one isolate only) across the pangenome (upper-left). The proportions of core, accessory and singleton categories are shown for orthogroups coding for secreted proteins (upper-right), carbohydrate-active enzymes (CAZymes; lower-left) and effectors (lower-right). b Gene copy number variation in core orthogroups across the 19 genomes. c Pangenome gene count across six CAZyme families. Families are divided into glycoside hydrolase (GH), glycosyl transferase (GT), auxiliary activity (AA), carbohydrate esterase (CE), carbohydrate-binding modules (CBM) and polysaccharide lyase activity (PL) categories. d Pangenome categories of secondary metabolite gene clusters. e Synteny plot of succinate dehydrogenase (SDH) paralogs mediating fungicide resistance. The SDHC3 locus on chromosome 3 is shown for isolates 3D7 and Aus01 both carrying the paralog. IPO323 and 1A5 lack SDHC3. The position of the SDHC3 paralog is shown using dark arrows. Genes are coloured in grey and transposable elements in red