Fig. 5

Divergence of gene expression and molecular functions between the two subgenomes of Pennisetum giganteum. a Boxplot showing expression levels of all the expressed genes (FPKM ≥ 0.1) across different tissues in the A and B subgenomes of P. giganteum. The numbers of expressed genes in the different tissues of subgenomes are given on the top. b Histogram showing distinct categories of all the expressed and highly expressed genes across different tissues in the A and B subgenomes. c Gene ontology (GO) enrichment of highly expressed genes in different tissues of the two subgenomes. Highly expressed genes in subgenome A were enriched in GO terms mainly related to protein synthesis, stress response and substance metabolism, and substance synthesis. Highly expressed genes in subgenome B were enriched in GO terms mainly associated with gene expression regulation, protein metabolism, and substance transport. d Histograms of genome-wide expression of homoeologous genes in six different tissues of P. giganteum. The numbers of dominant genes in the A and B subgenomes are displayed for each tissue. e Phylogeny of cellulose synthase-related gene family. The outermost tracks show the five gene types: CesA, CslD, CslE, CslF, and CslH. Red stars indicate the candidate cellulose synthase genes; Green triangles indicate multi-copy genes in the A and B subgenomes. The inner tracks show the cellulose synthase genes identified in the A and B subgenomes and in S. viridis. The middle tracks show the expression level of cellulose synthase-related genes across different tissues in the two subgenomes. I, Apt; II, Int; III, Root; IV, Seedling below; V, Seedling above; VI, Stem. The log2(FPKM + 0.001) level is indicated by the intensity of the color. S. viridis is in gray because of the lack of expression data. f Gene structures of homologous cellulose synthase-related genes spanning the gene body and 2-kb regions upstream and downstream in the A and B subgenomes and in S. viridis