Fig. 3. The origin and evolution of cell-surface receptor signalling component in plants.
a Schematic figure represents the simplified PTI signalling pathway in plants. Coloured hexagons on RLKs indicate activated kinases. For details, refer to Supplementary Fig. 6. b The top panel is a sequence similarity tree of multiple algal and plant lineages. Circles (○) and stars (☆) indicate the origins and expansion of receptor families, respectively. The timescale (in million years; MYA) of the sequence similarity tree was estimated by TIMETREE599. The bottom panel displays the presence or absence of receptor classes in different algal and plant lineages. *M/C/K represents Mesostigmatophyceae, Chlorokybophyceae, and Klebsormidiophyceae. The number of available species from each algal and plant lineage is indicated within the respective boxes. A grey box indicates the absence, while a green box indicates the presence of a given protein family in each lineage. Dark green indicates the presence of orthologs of immunity-related (PTI) signalling components within that protein family (see also Supplementary Fig. 8). The origin of a protein family is indicated with a circle (○), followed by another circle indicating the origin of the orthologs of PTI-signalling component. Expansion rates of PTI-signalling component families are indicated by boxplots. The percentages (%) of signalling components from each genome were calculated as (number of identified genes/number of searched genes × 100). Next, the percentages from each species within a lineage (e.g, Rhodophtya or green algae) were grouped and the median percentage was calculated. Median value was used instead of mean to avoid outliers within the lineages. The expansion rate within a species is calculated by ((%signalling components in that species)-(median))/(median). The cyan boxplot represents the expansion rate from Glaucophyta and Rhodophyta to green algae (SERKs, n = 0; SOBIR1, n = 0; RLKCs (VII), n = 0; CDPKs, n = 20; MAPKKKs, n = 20; MAPKKs, n = 20; MAPKs, n = 20; CNGCs, n = 19; OSCAs, n = 19; RBOHs, n = 10; EP proteins, n = 0; RPW8-NLRs, n = 0). The yellow boxplot represents the expansion rate from green algae to Embryophytes (SERKs, n = 316; SOBIR1, n = 0; RLKCs (VII), n = 324; CDPKs, n = 324; MAPKKKs, n = 324; MAPKKs, n = 324; MAPKs, n = 324; CNGCs, n = 324; OSCAs, n = 322; RBOHs, n = 324; EP proteins, n = 0; RPW8-NLRs, n = 0) and the orange boxplot represents the differences between early land plants to Tracheophytes (SERKs, n = 307; SOBIR1, n = 309; RLKCs (VII), n = 314; CDPKs, n = 314; MAPKKKs, n = 314; MAPKKs, n = 314; MAPKs, n = 314; CNGCs, n = 314; OSCAs, n = 312; RBOHs, n = 314; EP proteins, n = 0; RPW8-NLRs, n = 0). Light blue area represents expansion and light pink area represents contraction of the gene family. X-axis values represent expansion rate (×). Values larger than 0 indicate expansion; values equal to 0 indicate no expansion, and values below 0 indicate contraction. Boxplot elements: centre line, median; bounds of box, 25th and 75th percentiles; whiskers, 1.5 × IQR from 25th and 75th percentiles. For details, refer to the methods.