Additional file 8: Figure S6. of Phylogenetic analyses reveal molecular signatures associated with functional divergence among Subtilisin like Serine Proteases are linked to lifestyle transitions in Hypocreales

Functional divergence in Subtilisin (S08.005) protein sequences among clades Nectriaceae and Cordycipitaceae/Clavicipitaceae. (a) The RVS (Rate Variation among Sites) amino acids sites are identified by DIVERGE 3.0 mapped on the Subtilisin structure (Cyan colour) of a member (fx|XP5977|Fusarium oxysporum) of the Nectriaceae clade. The identified RVS sites are shown in stick (Magenta). (b) The highlighted (encircled) RVS sites are also observed in TYPE II divergence (Nectriaceae vs. Cordycipitaceae/Clavicipitaceae). Figure S7. Functional divergence type II and RVS sites on 3D structure of Subtilisin (S08.005) protein sequences among clades Nectriaceae and Cordycipitaceae/Clavicipitaceae. (a) The RVS (Rate Variation among Sites) amino acids sites are identified by DIVERGE 3.0 mapped on Subtilisin structure (Red colour) of a member (bb|XP2612|Beauveria bassiana) of the Cordycipitaceae/Clavicipitaceae clade. The identified RVS sites are shown in stick (Green). (b) The highlighted RVS sites are also observed in TYPE II divergence (Nectriaceae vs. Cordycipitaceae/Clavicipitaceae). The catalytic triad is shown in yellow colour. Figure S8. Functional divergence in Subtilisin (S08.005) when Nectriaceae and Ophiocordycipitaceae clades are compared. (a) The RVS (Rate Variation among Sites) amino acids sites are identified by DIVERGE 3.0 mapped on Subtilisin structure (Blue colour) of a member (pl|XP5939|Purpureocillium lilacinum) of the Ophiocordycipitaceae clade. The identified RVS sites are shown in stick (Yellow). (b) The highlighted (encircled) RVS sites are also observed in TYPE II divergence (Nectriaceae vs. Ophiocordycipitaceae). The putative catalytic triad and substrate binding pocket are shown in blue colour on the 3 D structure of the protein. (DOCX 844 kb

Additional file 6: Figure S5. of Phylogenetic analyses reveal molecular signatures associated with functional divergence among Subtilisin like Serine Proteases are linked to lifestyle transitions in Hypocreales

Conserved Motifs identified by MEME in Proteinase K (S08.054). (DOCX 36 kb

Figure 3

<p>A) LD plot of <i>CD28</i> among north-Indians, B) LD plot of <i>CD28</i> among CEU population, C) <i>CD28</i> haplotypes among north-Indians, D) <i>CD28</i> haplotypes among CEU population.</p

Figure 2

<p>A) LD plot of <i>PTPRC</i> among north-Indians, B) LD plot of <i>PTPRC</i> among CEU population, C) <i>PTPRC</i> haplotypes among north-Indians, D) <i>PTPRC</i> haplotypes among CEU population.</p

Quantile-Quantile plot of chi-square test of association p-values of 48 SNPs (presented in Table S1).

<p>Quantile-Quantile plot of chi-square test of association p-values of 48 SNPs (presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031584#pone.0031584.s001" target="_blank">Table S1</a>).</p

List of significant (p<0.05) SNPs in and around IL23R gene.

<p>List of significant (p<0.05) SNPs in and around IL23R gene.</p

Association status of 59 GWAS reported UC/CD specific susceptibility loci in a north Indian UC cohort.

<p> <b>^a</b><b>Mc Govern, et al., Genome-wide association identifies multiple ulcerative colitis susceptibility loci (2010) Nat Genet.; 42(4):332–7.</b></p><p> <b>^b</b><b>Monomorphic.</b></p><p> <b>^c</b><b>SNPs not in the Illumina Human600W-Quad used in this study.</b></p><p>*<b>p<0.05.</b></p><p>**<b>Significant after Bonferroni correction.</b></p