Fig. 2

Comparative genomics analysis between Pennisetum giganteum and other grass species. a Phylogenetic relationship of P. giganteum with 11 other plant species. C3 species are shaded in blue; C4 species are shaded in yellow. Species divergence times were estimated using r8s based on one calibration time point obtained from the TimeTree website. Estimated divergence times are shown in gray. The number of expanded and contracted gene families obtained using CAFE based on the orthologous groups of each species assigned by OrthoFinder are given below the species names in green and red, respectively. Distribution of different categories of protein-coding genes across all the species is shown on the right. b Venn diagram of gene families among five species. A total of 13,737 common gene families were identified among these species, and the number of unique gene families is listed for each species. c Gene ontology (GO) and Kyoto Encyclopedia of Genes and Gnomes (KEGG) enrichment analysis of genes that were commonly and uniquely expanded in the A and B subgenomes of P. giganteum. d Classification of gene duplicates in the A and B subgenomes of P. giganteum. The origins of duplicated genes were categorized into five types: whole genome/segmental duplication, tandem duplication, proximal duplication, dispersed duplication, and singleton. Statistical significance was determined using Fisher’s exact test. e Distribution of genes encoding proteins containing the N-terminal domain of chalcone and stilbene synthases (CHS/STS) in two subgenomes of P. giganteum and four other related species. f Phylogeny of the chalcone synthase (CHS) gene family. The inner tracks show CHS genes identified in the A and B subgenomes of P. giganteum and S. viridis. The outer six tracks show the expression level of CHS genes in different tissues in the two subgenomes of P. giganteum. I, Apt; II, Int; III, Root; IV, Seedling below; V, Seedling above; VI, Stem. The log2(FPKM + 0.01) level is indicated by the intensity of the color. S. viridis is in gray because of the lack of expression data