FIG 2.

Pangenome members associated with the 58-MYA duplication event in the Papilionoids are actively transcribed in Glycine nodules. (A) A chronogram based on 20 single-copy genes with phylogenetic topology congruent with the phylogenomic species tree of test plants. The pangenome members of 24 Glycine max accessions and 4 Glycine soja accessions are divided into nine hierarchical subsets. The number of orthologous clusters for each subset is indicated. Subset 9 includes accessory genes of individual species. (B) Transcriptional levels of pangenome members in different tissues of G. max. (C) Transcriptional levels of single-copy genes or those with more than one copy in different pangenome subsets of G. max JD17 and G. soja WSD. Transcription levels are represented by reads per kilobase of transcript length per million reads (B) retrieved from RNA-seq data from https://soybase.org/soyseq or transcripts per million (C) obtained in this work. Proportions of DEGs belonging to individual pangenome subsets in all DEGs are shown in panel C. Confidence interval is shown for the average transcription levels in panels B and C. + and −, significant enrichment and depletion, respectively, of DEGs in individual pangenome subsets (Fisher’s exact test, alpha = 0.05).