Comparative genomics of Colletotrichum truncatum, C. plurivorum, C. musicola and C. sojae: Four Species Pathogenic to Soybean (Glycine max)

Figure S1. Phylogenetic tree of 23 Colletotrichum strains reconstructed from concatenated nucleotide alignments of the ACT, CHS, GAPDH. HIS3, ITS and TUB genes. Loci not retrieved from whole genome sequences are available in GenBank as reported in Marin-Felix et al. 2017. A Markov Chain Monte Carlo (MCMC) algorithm was used to generate phylogenetic trees with Bayesian probabilities using MrBayes 3.2.1. Thickened branches represent posterior probabilities higher than 0.9 while lower values are reported next to the nodes. Names in bold highlight the genome sequences produced in this work. Species complexes are reported in colored boxes on the right: yellow for the Orbiculare, orange for the Orchidearum and pink the Gloeosporioides.

* C. truncatum TYU genome sequences (AN: NOWE00000000) was incorrectly deposited as C. gloeosporioides.

Figure S2. Comparative genomic analysis of Colletotrichum species belonging to four complexes. Colors represent the species complexes: yellow for the Orbiculare, orange for the Orchidearum and pink the Gloeosporioides; species in bold highlight the genome sequences produced in this work. (A) Heatmap showing the percentage of overlapping proteins shared in pairwise comparisons (values plotted correspond to percentage of proteins encoded by the species reported in the y axis that show similarity with those reported by the species reported in the x axis). (B) UpsetR plot of the protein clustering analysis. Bars in the upper side represent the number of orthogroups shared by the species highlighted by the black dots reported in the bottom side. (C) Table reporting the information about the species used in the analysis. (D) Species phylogenetic tree reconstructed from concatenated nucleotide alignments of the ACT, CHS, and GAPDH genes. Thickened branches represent posterior probabilities equal to 1 while lower values are reported next to the nodes. The bars on the right of the tree represent the total proteome size and the number of genes not secreted and secreted encoded by each genome.

Literature cited

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