Online Resource 11. Unrooted phylogenetic trees of functional lignin biosynthesis-related proteins, involved in shikimate, aromatic amino acid,

Transcription

1 1 Online Resource 11. Unrooted phylogenetic trees of functional lignin biosynthesis-related proteins, involved in shikimate, aromatic amino acid, monolignol and C 1 -metabolism pathways, of jute fibres and those characterized from other plant species. The neighbor-joining (NJ) trees were constructed with MUSCLE alignments of full-length amino acid sequences using the software MEGA 6.0. Numbers at nodes represent % occurrence in 1,000 bootstrap replicates, with values > 50% being shown. The bar indicates an evolutionary distance. The CAD protein accession followed by an asterisk represents SAD. ADH, arogenate dehydrogenase; ADT-PDT, arogenate/prephenate dehydratase; AS, anthranilate synthase; CAD, cinnamyl alcohol dehydrogenase; CCoAOMT, caffeoyl-coa O-methyltransferase; CCR, cinnamoyl-coa reductase; C4H, cinnamate 4-hydroxylase; 4CL, 4-coumarate:CoA ligase; CM, chorismate mutase; COMT, caffeic acid O-methyltransferase; CS, chorismate synthase; DAHPS, 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase; DHD-SDH, 3- dehydroquinate dehydratase/shikimate dehydrogenase; DHQS, 3-dehydroquinate synthase; EPSPS, 5-enolpyruvylshikimate 3-phosphate synthase; F5H, ferulate 5-hydroxylase; HCT, shikimate O-hydroxycinnamoyltransferase; MS, methionine synthase; PAI, phosphoribosylanthranilate isomerase; PAL, phenylalanine ammonia-lyase; PAT, phosphoribosylanthranilate transferase; SAD, sinapyl alcohol dehydrogenase; SAHase, S- adenosylhomocysteinase; SK, shikimate kinase; SAMS, S-adenosylmethionine synthase; TS, tryptophan synthase. Al, Arabidopsis lyrata; At, Arabidopsis thaliana; Cc, Corchorus capsularis; Ccm, Corchorus capsularis mutant; Cs, Camellia sinensis; Gb, Gossypium barbadense; Gh, Gossypium hirsutum; Gm, Glycine max; Gr, Gossypium raimondii; Hb, Hevea brasiliensis; Jc, Jatropha crucas; Lu, Linum usitassimum; Mt, Medicago truncatula; Nt, Nicotiana tabacum; Pa, Pinus armandii; Pb, Pyrus bretschneideri; P x b, Pyrus x bretschneideri; Pc, Petroselinum crispum; Pm, Plantago major; Pt, Populus trichocarpa; Ptd, Pinus taeda; Ptm, Populus tremula; Ptr, Populus tremuloides; Rc, Ricinus communis; Sa, Salix aurita; Ss, Salix schwerinii; Sv, Salix viminalis; Tc, Theobroma cacao; Vt, Vitis vinifera

2 2 Shikimate-aromatic amino acid pathway gi At 88 gi At 83 gi At 81 gi Al 82 gi Vv 68 gi Vv CcDAHPS2 72 CcmDAHPS2 gi Vv gi At gi Al 81 CcDAHPS1 CcmDAHPS1 gi Tc 0.2 CcmSK2 CcmSK3 CcmSK4 CcmSK1 CcSK1 gi Tc gi At gi At gi Vv gi Vv gi Gm gi Tc gi Tc gi Mt 95 gi Mt DAHPS (EC: ) SK (EC: ) gi Mt gi Mt gi Gm gi Gm CcmDHD-SDH5 gi At gi At gi At 54 gi Tc gi Tc CcmDHD-SDH-3 91 gi Vv CcDHD-SDH3 CcDHD-SDH1 93 CcmDHD-SDH1 gi Gm CcDHD-SDH4 82 CcmDHD-SDH4 gi Gm 89 gi Tc gi Tc gi Tc CcmDHD-SDH6 CcDHD-SDH2 CcmDHD-SDH2 DHD-SDH (EC: ) gi At gi At CcDHQS1 CcmDHQS1 gi Tc gi Tc gi Vv gi Gm gi At gi At CS (EC: ) gi Gm gi Gm gi Vv gi Hb gi Rc gi Rc gi Tc gi At gi Tc 71 CcCS1 CcmCS1 gi Tc gi At gi At gi Rc 67 gi Gm gi Gm gi At gi Tc gi Vv gi Tc gi Gm gi Gm gi Vv gi Gm gi Gm gi Tc gi Tc CcCM3 CcCM2 gi At CcmCM2 gi At gi Tc 54 CcCM CcmCM DHQS (EC: ) CM (EC: )

3 3 Shikimate-aromatic amino acid pathway CcEPSPS1 CcmEPSPS1 gi Gh gi Vv gi At CcPAT2 CcPAT3 CcPAT1 gi At gi At gi At gi At EPSPS (EC: ) PAT (EC: ) CcTS4 CcmTS4 gi Rc gi At gi Tc gi Tc gi Tc CcTS3 CcmTS3 gi Gm gi Mt gi Vv gi Tc CcTS1 CcmTS1 TS (EC: ) 52 CcTS2 CcmTS2 gi Mt gi Gm gi At gi Gm CcADH1 93 CcmADH1 gi Tc gi Tc gi Tc gi Tc gi Al gi Al gi At gi At gi At gi Gm gi Gm gi Gm gi Vv gi Al gi Al gi At gi At gi At gi At gi Vv gi Gm gi Gm gi Gm ADH (EC: ) CcPAI1 PAI (EC: ) gi Mt gi Gm gi Gm gi Gm gi Vv gi At CcADT-PDT3 gi Gm gi Tc gi Vv gi At gi At gi At CcADT-PDT5 CcmADT-PDT5 gi Vv gi Gm gi Gm gi At gi Gm gi Gm gi Mt gi Vv CcADT-PDT2 CcADT-PDT4 94 CcmADT-PDT4 93 gi Tc 54 gi Tc CcADT-PDT1 54 gi Tc ADT-PDT (EC: ) gi At gi At gi At gi At gi At gi At gi At gi At gi Gm gi Gm gi Gm

4 4 Shikimate-aromatic amino acid pathway 56 gi At 92 gi At gi At gi At gi At gi Mt gi Mt 95 gi Mt 93 gi Mt gi Mt 62 gi Rc gi Rc gi Vv gi Vv 80 gi Vv 95 gi Vv gi At 89 gi At gi At 69 gi At gi Rc gi Rc gi Mt 88 gi Mt gi Tc gi Tc 80 gi Tc gi Tc 68 gi Tc CcmAS1 CcAS1 gi Vv gi Vv gi Rc CcmAS2 CcAS2 gi Mt gi Rc gi At gi At 51 gi At gi At gi At 55 gi At gi At gi At AS (EC: )

5 Monolignol pathway CcPAL3 CcmPAL3 gi Tc gi Cs gi 4421 At gi 4419 At gi Vv gi Rc CcPAL1 CcmPAL1 gi Gh gi Tc gi Gm gi Mt gi Ptd CcPAL2 CcmPAL CcCCoAOMT2 CcmCCoAOMT2 gi Gh gi Vv gi Cs gi 2610 Pc CcCCoAOMT3 61 CcmCCoAOMT3 gi At gi Ptd CcCCoAOMT1 CcmCCoAOMT4 CcmCCoAOMT5 CcmCCoAOMT1 gi Mt gi Mt 0.2 PAL (EC: ) CCoAOMT (EC: ) 93 Cc4CL2 CCm4CL2 gi Vv gi Lu 54 gi At gi At gi At gi Ptd 60 gi Ptd gi Ptd gi Al gi At gi Gh gi Gh gi Gh gi Gm gi Cs gi Vv gi Vv Ccm4CL1 gi Pt gi Gm Cc4CL1 4CL (EC: ) 83 gi Rc 57 gi Hb 50 gi Pt gi Gh 93 CcCCR1 61 CcmCCR1 gi Lu 81 gi Gm gi At gi Ptd gi Al gi Mt 66 gi Pt gi Lu gi gb At 61 gi Al gi Tc CcF5H1 CcmF5H1 F5H (EC: ) CcCOMT1 CcmCOMT1 gi At gi Mt 0.2 COMT (EC: ) CcC4H1 CcmC4H1 gi Gh 63 gi Rc 89 gi Pt 56 CcC4H3 CcmC4H3 80 gi Gm gi Mt gi At gi At gi Al gi Al gi Ptd gi Mt gi Rc CcC4H2 82 CcmC4H2 CCR (EC: ) C4H (EC: )

6 6 Monolignol pathway CcCAD7 90 CcmCAD9 gi Gh gi Cs gi Vv 75 gi Vv gi Lu 75 gi Pt gi Rc gi 5387 Ptd gi Gh 62 CcCAD9 71 gi Rc 60 gi Vv gi Pa* gi Gh gi At gi Pm* CcCAD5 gi Gh gi Ptm x Ptr* 90 CcCAD2 86 CcmCAD2 66 CcmCAD8 82 gi Gm 88 gi Mt 83 CcCAD1 CcmCAD10 CcmCAD4 68 CcCAD8 76 CcmCAD3 CcCAD3 CcCAD10 83 CcmCAD1 72 CcmCAD7 62 gi Mt gi Mt gi Nt* gi Nt* gi Cs CcmCAD5 61 CcmCAD6 69 CcCAD4 93 CcCAD6 gi P x b* gi Ptr* gi Ss x Sv* gi Sa* gi Al gi Cs gi Mt 74 CcmHTC14 CcmHTC15 95 CcmHTC13 75 CcmHTC8 CcmHTC12 84 CcmHTC9 CcmHTC6 CcmHCT2 CcmHCT1 CcmHCT3 CcmHCT4 CcmHCT10 CcmHCT11 CcHCT4 61 CcmHCT16 CcHCT2 CcHCT3 CcHCT1 95 CcHCT8 CcHCT6 CcmHCT5 CcHCT5 gi Nt 62 gi Mt gi Gm gi Pt gi At 68 gi Tc CcHTC7 CcmHTC7 HCT (EC: ) CAD/ SAD* (EC: )

7 7 C 1 -metabolism pathway gi At gi At CcMS2 CcmMS2 CcMS1 CcmMS1 gi At 0.02 MS (EC: ) 54 CcSAMS1 CcmSAMS1 gi Mt gi At 84 gi At CcmSAMS gi Gh CcmSAMS2 CcSAMS gi At gi At gi At gi Al CcSAMS3 gi Mt gi Vv 53 gi Vv SAMS (EC: ) 73 CcSAHase1 CcmSAHase1 gi Mt gi Gm gi Rc gi At gi At 0.01 SAHase (EC: )

8 8 Article title: Pathways associated with lignin biosynthesis in lignomaniac jute fibres Journal name: Molecular Genetics and Genomics Author names: Avrajit Chakraborty 1 Debabrata Sarkar 1 Pratik Satya 1 Pran Gobinda Karmakar 1 Nagendra Kumar Singh 2 Affiliations: 1 Biotechnology Unit, Division of Crop Improvement, ICAR-Central Research Institute for Jute and Allied Fibres (CRIJAF), Barrackpore, Kolkata , West Bengal, India; 2 ICAR-National Research Centre on Plant Biotechnology (NRCPB), Pusa Campus, New Delhi , India address of the corresponding author: d.sarkar@excite.com; debabrata_s@yahoo.com; dsarkar@crijaf.org.in