Fig. 3
Pangenome characteristics. a The distribution of orthogroups in the core, softcore, shell, and cloud genome of Penicillium. The x-axis lists the different orthogroups whereas the y-axis lists the different assemblies. Purple and grey list whether the orthogroup is present or absent, respectively. The number under each panel lists the number of orthogroups in the different part of the pangenome. The panels were scaled after the number of orthogroups. Thus, softcore genome is approximately two and half times larger than core genome, whereas shell genome is approximately four times larger than softcore genome. The exception is the cloud genome that should be four times larger than shell genome, but instead is four times smaller. b The distribution of lengths of all protein sequences in the pangenome. The y-axis is discontinuous. All distributions were significantly different from each other (two-sided Mann–Whitney U-test) as indicated by stars. c The cumulative size of the Penicillium gene pool. The analysis was performed ten times with random addition of genomes. d The distribution of the median dN/dS value for each orthogroup. The y-axis is discontinuous. The two distributions are significantly different from each other as indicated by stars corresponding to a p value of < 2 × 10−16 using two-sided Mann–Whitney U-test. e KOG functional classification of the pangenome. Only the best hit from each orthogroup was included and if this hit had multiple categories, all of them are plotted. The R and S category were discarded in the plot. A, RNA processing and modification; B, chromatin structure and dynamics; C, energy production and conversion; D, cell cycle control, cell division and chromosome partitioning; E, amino-acid transport and metabolism; F, nucleotide transport and metabolism; G, carbohydrate transport and metabolism; H, coenzyme transport and metabolism; I, lipid transport and metabolism; J, translation, ribosomal structure, and biogenesis; K, transcription; L, replication, recombination, and repair; M, cell wall/membrane/envelope biogenesis; N, cell motility; O, post-translational modification, protein turnover, and chaperones; P, inorganic ion transport and metabolism; Q, secondary metabolites biosynthesis, transport, and catabolism; T, signal transduction mechanisms; U, intracellular trafficking, secretion, and vesicular transport; V, defense mechanisms; W, extracellular structures; Y, nuclear structure; and Z, cytoskeleton