1. Fig. S1a: Conserved motif analysis of Solanaceae DMTases. The motifs (1–10) identified using MEME search tool with default parameters have been marked on protein sequences. The length and order of the boxes represents the actual length and position of the conserved domain in the protein sequence. The bottom panel represents the consensus sequence of the predicted motifs. 4 2 9 8 6 4 2 9 8 6 10 4 2 9 8 6 4 2 9 8 6 7 5 9 3 4 1 7 5 9 3 4 1 759341 41 1 42986 42986 4298 759341 42986 759341 759341 531 2968 759341 759341 1 759341 42986 42986 42986 759341 42986 531 759341 1 1 42986 42986 759341 42986 759341 341 42986 42986 1.SlMET1 2.SlCMT2 3.SlCMT4 4.SlCMT3 5.SlDRM5 6.SlDRM7 7.SlDRM6 8.SlDNMT2 9.SlDRM8 10.SpeCMT4 11.SpeCMT3 12.SpeCMT2 13.SpeMET1 14.SpeDRM5 15.SpeDRM7 16.SpeDRM6 17.SpeDRM8 18.SmeMET1 19.SmeDRM5 20.SmeDRM7 21.SmeDNMT2 22.CaDRM6 23.CaMET1a 24.CaCMT3 25.CaCMT4 26.CaDRM5a 27.CaCMT3b 28.CaDRM8a 29.CaDRM5b 30.CaDNMT2b 31.CaDRM8b 32.CaMET1b 33.CaCMT2 34.StDRM7 35.StCMT2 36.StDRM6 37.StDRM5 38.StCMT4 39.StMET1

2. Fig. S1b: Conserved domain analysis of Solanaceae DMTases. The domains (1–10) were identified using MEME search tool with default parameters in methyltransferase domains of DMTases. The upper panel shows the arrangement of these domains whereas the lower panel represents the consensus sequence of the predicted domains. StCMT2 SlCMT2 SlCMT4 CaCMT4 SlCMT3 StCMT4 CaCMT3a SlMET1 StMET1 CaMET1b CaMET1a SlDRM5 StDRM5 CaCMT3b CaDRM5b CaDRM5a StDRM7 SlDRM7 SlDRM6 StDRM6 CaDRM6 SlDRM8 CaDRM8b CaDRM8a SlDNMT2 CaDNMT2b CaCMT2

3. Fig. S2: Phylogenetic relationship among various DMTases. Full length protein sequences of DMTase proteins from Chlamydomonas reinhardtii (Cr), Selaginella moellendorffii (Sm), Arabidopsis (At), rice (Os), Vitis vinifera (Vv), populus (Pt), human (Hs), Drosophila (Dm), yeast (Sp) and Solanaceae members, including tomato (Sl), S. pennellii (Spe), potato (St), eggplant (Sme), pepper (Ca) and N. benthamiana (Nb) were included in the construction of an unrooted tree using JTT-matrix based method in MEGA 6. This analysis classified DMTases into four different classes, namely MET, DRM, CMT and DNMT2. Though DNMT2 homologs had a DNA_methylase domain, emerging evidence suggest that these proteins act as RNA methyltransferases. Relatively higher phylogenetic relatedness was observed among DMTase homologs within Solanum taxon and name of these proteins are presented in ‘bold’ in each clade. Similarly, name of the rice DMTase homologs are presented in ‘italics’. The bootstrap values are based on 1000 iterations and the support values are represented at each node.

4. Fig. S3: Expression profiles of DMTases in S. pimpinellifolium. Publically available RNA-seq datasets were retrieved to analyze expression patterns. Heatmaps were generated using ‘gplots’ in ‘R” package. Color scale represents log 2 RPKM values. IG, immature green; B, breaker; B+5, 5 days after breaker.

5. Fig. S4: Expression levels of S. pennellii (a) and S. tuberosum (b) DMTase genes are perturbed by both biotic and abiotic stresses. Publically available RNA-seq datasets on stresses for S. pennellii and potato were retrieved to analyze expression patterns [33, 43]. Heat maps were generated using ‘ gplots ’ in ‘ R ’ package. Color scale represents log 2 RPKM and FPKM values, respectively. Five-week-old hydroponically grown S. pennellii seedlings were used for stress treatments [33]. In S. pennellii: C.1, control for biotic stress; C.2, control for cold and drought stress on small leaves; C.3, control for cold and drought stress on mature leaves and root; C.4 and C.5, control for low- and hi-salt stress on stem; C.6 and C.7, control for low- and hi-salt stress on roots. In potato, control represents control for salt and mannitol stresses whereas control.1 serves control for heat stress. For potato, the details of plant growth conditions and stress treatments have been described previously and can be accessed at the weblink (http://www.nature.com/nature/journal/v475/n7355/extref/nature10158-s1.pdf) [43].334333http://www.nature.com/nature/journal/v475/n7355/extref/nature10158-s1.pdf43

6. SlMET1SpeMET1 StMET1 CaMET1 Fig. S5: The intermolecular interactions between the BAH domain of Solanaceae MET syntelogs with the bound H3(1–32)K9me2 peptide state. Green dashed line depicts hydrogen bonding and red half sun like points represent hydrophobic interactions.

7. Fig. S6: The intermolecular interactions between chromo and BAH domains of Solanaceae CMT2 syntelogs with the bound H3(1–32)K9Me2 peptide state. Green dashed line depicts hydrogen bonding and red half sun like points represent hydrophobic interactions. ChromoBAH SlCMT2 ChromoBAH SpeCMT2 ChromoBAH CaCMT2 ChromoBAH StCMT2