Comprehensive analysis of SET domain gene family in foxtail millet identifies the putative role of SiSET14 in abiotic stress tolerance
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1 Comprehensive analysis of SET domain gene family in foxtail millet identifies the putative role of SiSET14 in abiotic stress tolerance Chandra Bhan Yadav, Mehanathan Muthamilarasan, Anand Dangi, Shweta Shweta, Manoj Prasad* National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi , India *Corresponding author Manoj Prasad National Institute of Plant Genome Research Aruna Asaf Ali Marg New Delhi India
2 Supplementary Figure 1. Multiple sequence alignment of SET domain of SiSET genes.
3 Supplementary Figure 2. Intron-exon positioning of all the 53 SiSET genes.
4 OsSET35 BdSETSET BdSETSET11 OsSET11 Supplementary Figure 3. Phylogenetic tree showing relationship between SiSET, AtSET, SlSET and OsSET proteins.
5 A Supplementary Figure 4A. Motif analysis of SiSET genes. Six motifs were identified in all the SiSET genes. Numbers 0, 1, 2 indicate the type of motif corresponding to the colour code given in the figure.
6 B Supplementary Figure 4B. Sequence LOGOs for each motif of SET domains developed using the MEME algorithm.
7 Supplementary Figure 5. Phylogenetic tree and protein converseness of SiSET genes among plant and animal kingdom. The names of species are mentioned at the left hand side. In the subsequent grid, the presence of the protein in a species is marked with a red square and absence with a white space. The intensity of the color of the red square reflects the amount of conservation of the homologous protein in the species.
8 Supplementary Figure 6. Gene Ontology annotation data of biological processes, molecular function and cellular components for SiSET genes.
9 Biological function Molecular process Cellular component Supplementary Figure 7. Co-expression network of SiSET genes. The number of genes falling in each GO category is directly proportional to the node size. The nodes are colour shaded according to the significance level (corrected P-value).
10 Seita.5G Seita.7G Seita.5G Seita.4G Si000646m Si010236m Si004808m Si007187m SWI/SNF-RELATED CHROMATIN BINDING PROTEIN SET1/ASH2 HISTONE METHYLTRANSFERASE COMPLEX SUBUNIT ASH2 SNARE protein YKT6, synaptobrevin/vamp syperfamily AGAMOUS-LIKE MADS-BOX PROTEIN AGL16-RELATED Seita.3G Si022311m HISTONE DEACETYLASE 8 Seita.7G Si010171m HISTONE DEACETYLASE 6 Seita.4G Si006784m HISTONE DEACETYLASE 11 Seita.6G Si013929m Seita.2G Si030310m SiSET14 Transcriptional repressor EED/ESC/FIE, required for transcriptional silencing, WD repeat superfamily Supplementary Figure 8. In silico analysis of interacting patterns of SiSET14 proteins involved in regulation of histone methylation activities.
11 Table S1. Characteristic features of all the identified SET domain containing genes in Setaria italica NIPGR ID Transcript stable Synonym Subfamily Gene Chromo Gene start Gene end ID Transcript cluster stable ID Name some (bp) (bp) Gene Length Strand Transcript Exon Introns Length count (aa) SiSET01 Seita.1G Si017644m IV ATXR Unstable SiSET02 Seita.1G Si016071m II ASHH Unstable SiSET03 Seita.1G Si016710m II ASHH Unstable SiSET04 Seita.1G Unstable SiSET05 Seita.1G Si019326m V SUVR Unstable Seita.1G Unstable Seita.1G Unstable SiSET06 Seita.1G Si016370m V SUVH Unstable SiSET07 Seita.1G Si016095m V SUVR Unstable Seita.1G Unstable SiSET08 Seita.1G Si016972m IV ribulose Unstable SiSET09 Seita.1G Si017054m IV SETD Unstable SiSET10 Seita.2G Si028938m V SUVH Unstable Seita.2G Si028939m V SUVH Unstable SiSET11 Seita.2G Si029125m V SUVH , Unstable SiSET12 Seita.2G Si028793m III ATX Unstable Seita.2G Unstable Seita.2G Unstable Seita.2G Si028792m III ATX Unstable SiSET13 Seita.2G Si028884m V SUVH Unstable SiSET14 Seita.2G Si030310m II ASHH Unstable Seita.2G Unstable SiSET15 Seita.2G Si028728m V SUVH Unstable Seita.2G Unstable SiSET16 Seita.2G Si028661m III ATX Unstable Seita.2G Si028664m III ATX Unstable SiSET17 Seita.2G Si032678m IV SET Unstable SiSET18 Seita.2G Si029068m V SUVR Unstable SiSET19 Seita.3G Si021783m II SETD Unstable SiSET20 Seita.3G Si021853m IV ribulose Unstable Seita.3G Unstable SiSET21 Seita.3G Si021388m V SUVH stable SiSET22 Seita.3G Si024266m V SUVH stable SiSET23 Seita.3G Si021071m II Unstable Seita.3G Si021082m II Unstable Seita.3G Unstable SiSET24 Seita.4G Si006168m II Unstable SiSET25 Seita.4G Si005930m I EZ Unstable SiSET26 Seita.4G Si005858m V SUVH Unstable Seita.4G Si005857m V SUVH Unstable Seita.4G Unstable SiSET27 Seita.5G Si000220m III ATX Unstable SiSET28 Seita.5G Si000146m III ATX Unstable SiSET29 Seita.5G Si002161m V SUVR Unstable SiSET30 Seita.5G Si000438m V SUVH Unstable SiSET31 Seita.5G Si001278m - SET Unstable SiSET32 Seita.5G Si000507m V SUVH Unstable SiSET33 Seita.5G Si001848m IV ATXR Unstable SiSET34 Seita.5G Unstable SiSET35 Seita.6G Unstable Seita.6G Unstable SiSET36 Seita.6G Si013113m IV ATXR Unstable SiSET37 Seita.6G Si015622m stable Seita.6G stable SiSET38 Seita.6G Si015397m V Unstable SiSET39 Seita.6G Si015003m V SUVH Unstable SiSET40 Seita.6G Unstable SiSET41 Seita.6G Si013404m V SUVH Unstable SiSET42 Seita.6G Si015142m V SUVR Unstable Mol. Wt (Da) pi negatively charged residues positively charged residues Instability index stable or not Aliphati c index GRAVITY
12 SiSET43 Seita.7G Unstable SiSET44 Seita.7G Si009854m II ASHH Unstable SiSET45 Seita.7G Si012231m V SUVH stable SiSET46 Seita.7G Si010034m IV ATXR Unstable SiSET47 Seita.7G Si011948m V SUVH Unstable SiSET48 Seita.8G Si028261m V SUVH Unstable SiSET49 Seita.9G Si035418m IV ASHR Unstable Seita.9G Unstable Seita.9G Unstable SiSET50 Seita.9G Si039085m IV Unstable SiSET51 Seita.9G Si036803m IV ATXR Unstable Seita.9G Si036987m IV ATXR Unstable SiSET52 Seita.9G Si034160m IV ATXR Unstable SiSET53 Seita.9G Si035066m IV stable Not applicable
13 Table S2. Summary of domains present in SiSET proteins in Setaria italica. Gene ID PHD SET AWS zf-cw WIYLD Pre-SET SAD_SRA Rubis-subs-bind zf-hc5hc2h_2 PWWP FYRC FYRN PostSET SAND GYF DUF1777 TPR SANT From To E-Value Bitscore From To E-Value Bitscore From To E-Value Bitscore From To E-Value Bitscore From To E-Value Bitscore From To E-Value Bitscore From To E-Value Bitscore From To E-Value Bitscore From To E-Value Bitscore From To E-Value Bitscore From To E-Value Bitscore From To E-Value Bitscore From To E-Value Bitscore From To E-Value Bitscore From To E-Value Bitscore From To E-Value Bitscore From To E-Value Bitscore From To E-Value Bitscore SiSET E E SiSET E E E SiSET E E E SiSET E SiSET E E E SiSET E E E SiSET E E SiSET E E SiSET E E SiSET E E E SiSET E E E SiSET12 573, ,749 48E-22, , E E E E SiSET E E E SiSET E E SiSET E E E SiSET16 14,431,585 14,871, , E SiSET SiSET E E E SiSET E SiSET E E SiSET E E E SiSET E E E SiSET E SiSET e SiSET E SiSET E E E SiSET27 366,605, ,716, E-59, , E E SiSET28 625,680, ,791,485 19,6.43E ,192913, E E SiSET E E SiSET E E E SiSET E SiSET E E E SiSET E E SiSET SiSET E SiSET E SiSET E SiSET E SiSET E E E SiSET E SiSET E E E SiSET E E E SiSET E SiSET E E SiSET E E SiSET E SiSET E E E SiSET E E E SiSET E SiSET SiSET E SiSET E SiSET E Not present
14 Table S3. The Ka/Ks ratios and estimated divergence time for orthologous SiSET genes between foxtail millet, sorghum, maize, rice and Brachypodium NIPGR ID Phytozome ID Location on foxtail millet genome Location on sorghum genome Ka Ks Ka/Ks Mya Location on maize genome Ka Ks Ka/Ks Mya Location on rice genome Ka Ks Ka/Ks Mya Location on Brachypodium genome Ka Ks Ka/Ks Mya Chromosome Start End Gene ID Chromosome Start End Gene ID Chromosome Start End Gene ID Chromosome Start End Gene ID Chromosome Start End SiSET01 Seita.1G Sb04g GRMZM2G BGIOSGA BRADI3G SiSET02 Seita.1G GRMZM2G BGIOSGA SiSET03 Seita.1G BGIOSGA SiSET04 Seita.1G BGIOSGA BRADI3G SiSET05 Seita.1G SiSET06 Seita.1G Sb04g SiSET07 Seita.1G GRMZM2G SiSET08 Seita.1G Sb04g GRMZM2G BGIOSGA BRADI3G SiSET09 Seita.1G Sb04g GRMZM2G BGIOSGA BRADI3G SiSET10 Seita.2G Sb02g AC _FG BGIOSGA BRADI1G SiSET11 Seita.2G Sb02g GRMZM2G BGIOSGA BRADI1G SiSET12 Seita.2G GRMZM2G BGIOSGA BRADI4G SiSET13 Seita.2G Sb06g GRMZM2G SiSET14 Seita.2G Sb02g GRMZM2G BGIOSGA SiSET15 Seita.2G BGIOSGA SiSET16 Seita.2G Sb02g GRMZM2G BGIOSGA BRADI4G SiSET17 Seita.2G Sb02g GRMZM2G SiSET18 Seita.2G Sb02g GRMZM2G BRADI1G SiSET19 Seita.3G SiSET20 Seita.3G Sb03g GRMZM2G BGIOSGA BRADI4G SiSET22 Seita.3G Sb09g GRMZM2G BGIOSGA BRADI4G SiSET23 Seita.3G Sb09g SiSET24 Seita.4G Sb08g SiSET25 Seita.4G Sb10g GRMZM2G BRADI1G SiSET26 Seita.4G Sb10g GRMZM2G BRADI1G SiSET27 Seita.5G Sb06g BRADI1G SiSET28 Seita.5G Sb03g GRMZM2G BGIOSGA BRADI2G SiSET29 Seita.5G Sb03g BGIOSGA BRADI2G SiSET30 Seita.5G Sb03g GRMZM2G BGIOSGA BRADI2G SiSET31 Seita.5G Sb03g GRMZM2G BGIOSGA SiSET32 Seita.5G Sb03g GRMZM2G BGIOSGA BRADI2G SiSET34 Seita.5G Sb03g GRMZM2G BGIOSGA BRADI2G SiSET35 Seita.6G Sb07g GRMZM2G BGIOSGA BRADI3G SiSET36 Seita.6G Sb07g GRMZM2G BRADI3G SiSET37 Seita.6G SiSET38 Seita.6G Sb07g SiSET40 Seita.6G Sb07g GRMZM2G BGIOSGA SiSET41 Seita.6G Sb07g GRMZM2G SiSET42 Seita.6G BGIOSGA SiSET43 Seita.7G Sb06g GRMZM2G BGIOSGA BRADI5G SiSET44 Seita.7G Sb02g GRMZM2G BGIOSGA SiSET45 Seita.7G Sb06g GRMZM2G BGIOSGA BRADI5G SiSET46 Seita.7G Sb08g GRMZM2G BGIOSGA BRADI4G SiSET48 Seita.8G Sb01g GRMZM2G BGIOSGA BRADI1G SiSET49 Seita.9G BRADI3G SiSET50 Seita.9G Sb01g GRMZM2G SiSET51 Seita.9G Sb01g GRMZM5G BGIOSGA SiSET52 Seita.9G Sb01g GRMZM2G BGIOSGA BRADI1G Mean Mean Mean Mean
15 Table S4. Characteristics of the promoter region of SiSET genes in Setaria italica Cis-acting Element SiSET01 SiSET02 SiSET03 SiSET05 SiSET06 SiSET07 SiSET09 SiSET10 SiSET11 SiSET12 SiSET13 SiSET14 SiSET15 SiSET16 SiSET17 SiSET18 SiSET19 SiSET20 Si002161m Si006168m Si012231m Si010034m Si005930m Si015003m Si000146m Si011948m Si000438m Si013113m Si009854m Si015622m Si000220m Si009324m Si005858m Si013404m Si000507m Si015238m Si001278m Si015142m Si Si019056m Si021082m Si016971m Si021388m Si036987m Si035418m Si024266m Si028261m Si034160m Si035066m Si029660m Si039085m -10PEHVPSBD ( SSEEDPROTBANAPA CORE ELEMENT ( MOTIFZMZEIN BOXLELAT AACACOREOSGLUB ABREATCONSENSUS ABREATRD ABREAZMRAB ABREBZMRAB ABRECE1HVA ABRELATERD ABREMOTIFAOSOSEM ABREMOTIFIIIOSRAB16B ABREOSRAB ABRERATCAL ( ABREZMRAB ( ACGTABOX ACGTABREMOTIFA2OSEM ACGTABREMOTIFAOSOSE ACGTATERD ( ( ( ( ( ( ( ACGTCBOX ( ACGTOSGLUB ACGTTBOX ACIPVPAL ( AGCBOXNPGLB AGMOTIFNTMYB AMMORESIIUDCRNIA AMMORESIVDCRNIA AMMORESVDCRNIA AMYBOX AMYBOX ANAERO1CONSENSUS ANAERO2CONSENSUS ANAERO3CONSENSUS ANAERO4CONSENSUS ARE ARECOREZMGAPC ARFAT ARR1AT ( ( ( ( ( ( ASF1MOTIFCAMV ( ( ATHB6COREAT AUXRETGA1GMGH BIHD1OS BOXCPSAS BOXIINTPATPB BOXIIPCCHS BOXLCOREDCPAL ( ( BP5OSWX BS1EGCCR CAATBOX ( ( ( ( ( CACGCAATGMGH CACGTGMOTIF ( CACTFTPPCA ( ( ( ( ( ( ( ( CANBNNAPA CAREOSREP CARGCW8GAT ( ( ( ( ( CARGNCAT CATATGGMSAUR ( CBFHV ( CCA1ATLHCB CCAATBOX CDA1ATCAB CELLCYCLESC CEREGLUBOX1PSLEGA CEREGLUBOX2PSLEGA CEREGLUBOX3PSLEGA CGACGOSAMY ( CGCGBOXAT ( ( ( ( ( ( ( ( ( CIACADIANLELHC CMSRE1IBSPOA CPBCSPOR CPRFPCCHS CRTDREHVCBF CTRMCAMV35S CURECORECR ( ( ( ( ( ( ( ( ( DOFCOREZM ( ( ( ( ( ( ( ( DPBFCOREDCDC DRE1COREZMRAB DRE2COREZMRAB DRECRTCOREAT ( E2F1OSPCNA E2FANTRNR E2FAT E2FBNTRNR E2FCONSENSUS
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