Fig. 2

Gene loss and duplication in Sapria himalayana genome. A UpSet Venn diagram showing the overview of orthogroups from Arabidopsis thaliana (Atha), Cuscuta australis (Caus), Manihot esculenta (Mesc), Populus trichocarpa (Ptri), S. himalayana (Shim), and Vitis vinifera (Vvin). The bar diagram (left) shows the number of orthogroups found in each species; the bar diagram (upper panel) and lattice diagram (lower panel) together show the number of overlapping and exclusive orthogroups found in the six species. The lost and species-specific orthogroups ib S. himalayana are represented by red and green dots, respectively. B Bar diagram showing the gene content in orthogroups in S. himalayana and other representative species. Orthogroups with exactly one gene in each species are indicated in orange. Orthogroups missing in S. himalayana but are present in each species (exactly 0:1, named: other species, pale green; 0:n (n > 1), green). Duplicated orthogroups were defined as having exactly 2:1 genes per species (wathet) or as having a ratio of at least 2n:n(n > 1) genes in each species (blue). C, D Functional enrichment analysis of genes either lost (ratio 0:1 or more, C) or duplicated (at least 2n:n, D) in S. himalayana. MapMan categories of significantly enriched genes are displayed using the logarithmic values of their P-values