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Table 1 Annotation and expression of unigenes involved in anthocyanin and cinnamic acid derivative biosyntheses and transport

From: RNA-seq-based evaluation of bicolor tepal pigmentation in Asiatic hybrid lilies (Lilium spp.)

Putative gene (according to Swiss-Prot) Trinity transcript id Homologous gene in Lilium Blastp top hit Length Identity E-value FPKM (expression) in logFC logCPM FDR
Upper tepals Tepal bases
Phenylpropanoid pathway genes
 PAL c29955_g1 LhPAL1/2/3 phenylalanine ammonia lyase [Lilium hybrid division I] 729 99 % 0 631.93 472.92 0.41 10.09 0.7580164
 PAL c36922_g1 LhPAL3 phenylalanine ammonia lyase [Lilium hybrid division I] 114 95 % 2E-64 44.13 5.04 3.14 3.09 2.07E-05
 PAL c30134_g17   phenylalanine ammonia lyase, partial [Musa acuminata AAA Group] 436 81 % 0 12.30 19.98 −0.65 4.32 0.6531477
 PAL c30134_g11   phenylalanine ammonia-lyase [Betula pendula] 115 64 % 6E-44 10.26 14.29 −0.37 1.37 0.9748477
 PAL c30134_g1   phenylalanine ammonia-lyase, partial [Rhizophora apiculata] 191 84 % 4E-113 8.62 14.20 −0.62 2.34 0.7807557
 C4H c26579_g1   cinnamate-4-hydroxylase [Canarium album] 507 88 % 0 1030.58 803.78 0.37 10.53 0.6668013
 C4H c25090_g1   cinnamate 4-hydroxylase, partial [Tulipa fosteriana] 330 90 % 0 3.54 10.24 −1.43 2.61 0.1219183
 4CL c29891_g1   4-hydroxycinnamoyl-CoA ligase 2 [Coffea arabica] 518 70 % 0 344.61 485.55 −0.39 9.02 0.6668013
 4CL c27769_g1   4-coumarate-CoA ligase-like protein [Arabidopsis thaliana] 561 66 % 0 112.74 114.24 −0.01 7.48 1
 4CL c27493_g1   coumaroyl-CoA ligase [Vitis vinifera] 522 72 % 0 91.97 63.02 0.57 6.96 0.6023584
 4CL c26975_g1   4-coumarate--CoA ligase-like 7 [Vitis vinifera] 572 62 % 0 34.27 32.43 0.09 5.87 0.9889067
 4CL c26242_g1   4-coumarate--CoA ligase-like 9 [Vitis vinifera] 482 61 % 0 14.85 26.40 −0.79 4.82 0.4774231
 4CL c29687_g1   4-coumarate--CoA ligase-like 6 [Glycine soja] 582 62 % 0 12.42 13.44 −0.07 4.41 1
 4CL c20611_g1   4cl [Lilium hybrid cultivar] 549 97 % 0 5.39 16.11 −1.53 4.22 0.04040995
 4CL c25512_g2   4-coumaroyl-coenzyme A ligase [Allium cepa] 225 65 % 3E-99 6.45 6.72 0.03 2.02 1
Cinnamic acid derivative biosynthesis genes
 C3H c28376_g1   4-coumarate 3-hydroxylase [Eucalyptus globulus] 508 77 % 0 6.19 7.07 −0.17 2.89 0.9748477
 HCT c27695_g1   Hydroxycinnamoyl-CoA:quinate hydroxycinnamoyltransferase [Zostera marina] 431 49 % 2E-125 34.28 37.59 −0.12 5.65 0.9748477
 HCT c30288_g1   hydroxycinnamoyl transferase [Nicotiana benthamiana] 324 63 % 6E-147 5.02 46.05 −3.14 4.45 0.0001381333
Anthocyanin biosynthesis genes
 CHS c30110_g1 LhCHSa/b chalcone synthase [Lilium hybrid division I] 267 99 % 0 1209.02 421.80 1.47 9.77 0.01588364
 CHS c29657_g1 LhCHSc chalcone synthase C [Lilium hybrid division I] 249 98 % 1E-173 267.20 63.11 2.10 7.05 0.001083655
 CHS c29657_g2 LhCHSc chalcone synthase C [Lilium hybrid division I] 249 97 % 1E-174 48.68 104.39 −1.12 6.01 0.1175434
 CHS c30110_g2   chalcone synthase, partial [Tulipa fosteriana] 242 72 % 4E-120 52.81 72.32 −0.47 5.73 0.6531477
 CHS c29920_g1   chalcone synthase, partial [Tulipa fosteriana] 389 78 % 0 34.11 19.43 0.65 4.42 0.4774231
 CHI c28538_g1 LsCHIb chalcone isomerase, partial [Lilium speciosum] 210 99 % 4E-135 1232.45 816.96 0.60 9.77 0.4774231
 CHI c28136_g1 LsCHIa chalcone isomerase [Lilium speciosum] 234 97 % 2E-156 276.09 178.28 0.63 7.91 0.4774231
 CHI c27139_g1   Chalcone-flavanone isomerase family protein isoform 1 [Theobroma cacao] 420 50 % 2E-133 34.06 22.96 0.56 5.63 0.5573998
 CHI c23754_g1   Chalcone-flavanone isomerase family protein isoform 3, partial [Theobroma cacao] 299 64 % 6E-85 12.87 16.08 −0.32 3.55 0.7828791
 F3H c28413_g1 LhF3H flavanone 3-hydroxylase [Lilium hybrid division I] 370 97 % 0 666.13 330.01 1.03 9.21 0.1196772
 F3'H c27194_g1 LhF3'H flavonoid 3'-hydroxylase [Lilium hybrid division I] 515 99 % 0 195.25 33.85 2.54 7.58 1.38E-06
 DFR c30307_g2 LhDFR dihydroflavonol 4-reductase [Lilium hybrid division I] 376 98 % 0 3143.14 1550.13 0.98 11.27 0.1175434
 DFR c24884_g1   dihydroflavonol-4-reductase-like [Elaeis guineensis] 348 68 % 3E-163 87.02 71.25 0.28 6.49 0.7807557
 DFR c29645_g2   cinnamoyl-CoA reductase 1-like [Phoenix dactylifera] 303 70 % 2E-138 35.55 34.81 −0.02 4.50 1
 DFR c27848_g1   dihydroflavonol-4-reductase [Vitis vinifera] 334 73 % 0 15.05 15.08 0.01 4.00 1
 DFR c12034_g1   Dihydroflavonol-4-reductase [Aegilops tauschii] 92 57 % 3E-27 11.78 4.96 1.20 0.42 0.6318245
 DFR c27774_g2   Dihydroflavonol-4-reductase [Aegilops tauschii] 104 57 % 2E-34 8.23 5.01 0.70 1.25 0.6668013
 DFR c9045_g1   Bifunctional dihydroflavonol 4-reductase/flavanone 4-reductase [Morus notabilis] 86 65 % 9E-32 0.00 10.40 −5.20 −0.17 0.1055062
 ANS c26135_g1 LhANS anthocyanidin synthase [Lilium hybrid division I] 362 98 % 0 1767.61 876.34 1.02 10.75 0.1055062
 ANS c28679_g2   Gibberellin 3-beta-dioxygenase 4 [Morus notabilis] 316 42 % 2E-76 62.99 243.34 −1.97 7.33 0.0006236071
 ANS c27368_g1   Leucoanthocyanidin dioxygenase [Morus notabilis] 377 62 % 1E-160 68.14 50.96 0.42 6.02 0.6531477
 ANS c19298_g1   Leucoanthocyanidin dioxygenase [Gossypium arboreum] 362 67 % 7E-175 8.51 29.34 −1.79 4.38 0.002704819
 3GT c35034_g1   UDP-glucose: anthocyanidin 3-O-glucosyltransferase [Tulipa fosteriana] 484 78 % 0 1650.78 1337.40 0.31 11.18 0.7580164
 3GT c16413_g1   anthocyanidin 3-O-glucosyltransferase [Tulipa fosteriana] 450 71 % 0 120.55 90.36 0.41 7.09 0.6531477
 3GT c29247_g1   anthocyanidin 3-O-glucosyltransferase [Zea mays] 489 50 % 8E-137 19.03 20.65 −0.10 4.92 0.9889067
 3GT c26782_g1   UDP glucose:flavonoid 3-O-glucosyltransferase [Pyrus x bretschneideri] 109 54 % 3E-32 21.19 16.46 0.45 2.17 0.9367663
 3GT c26782_g5   anthocyanidin 3-O-glucosyltransferase [Tulipa fosteriana] 346 57 % 6E-115 11.65 13.85 −0.18 3.53 0.9889067
 3RT c25725_g1   anthocyanidin-3-glucoside rhamnosyltransferase [Petunia x hybrida] 465 55 % 0 2144.38 1507.37 0.51 11.53 0.6023584
 7GT c29610_g1   scopoletin glucosyltransferase-like [Phoenix dactylifera] 489 60 % 0 53.84 80.60 −0.64 5.55 0.4774231
 7GT c28503_g1   UDP-glycosyltransferase 1 [Linum usitatissimum] 418 44 % 6E-107 16.58 25.74 −0.57 4.50 0.6318245
 7GT c26782_g3   phenylpropanoid:glucosyltransferase 2, partial [Nicotiana tabacum] 377 49 % 1E-117 9.78 10.58 −0.09 3.36 0.9889067
Transporters of anthocyanins and/or cinnamic acid derivatives, to vacuole
 MATE c27999_g1   MATE efflux family protein [Arabidopsis thaliana] 535 62 % 0 483.91 412.47 0.25 9.61 0.8141854
 MATE c29991_g1   MATE efflux family protein [Arabidopsis thaliana] 507 72 % 0 106.41 103.68 0.03 7.40 1
 MATE c30035_g1   transparent testa 12 protein [Zea mays] 489 69 % 0 50.45 116.90 −1.18 7.11 0.06782638
 MATE c25329_g1   transparent testa 12 protein [Zea mays] 527 78 % 0 66.84 94.90 −0.50 7.10 0.6318245
 MATE c23411_g1   MATE efflux family protein LAL5-like isoform X1 [Phoenix dactylifera] 517 73 % 0 37.53 41.30 −0.16 5.82 0.9243257
 MATE c1112_g1   MATE efflux family protein 5 [Phoenix dactylifera] 510 69 % 0 14.64 21.87 −0.52 4.84 0.6668013
 MATE c19647_g1   MATE efflux family protein 5 [Vitis vinifera] 481 55 % 0 13.65 13.72 −0.05 3.77 1
 MATE c23623_g1   transparent testa 12 protein [Zea mays] 480 78 % 0 9.71 8.01 0.32 3.81 0.8141854
 MATE c27478_g1   MATE efflux family protein [Theobroma cacao] 258 65 % 1E-108 6.83 10.52 −0.50 3.06 0.6668013
 MATE c12223_g2   MATE efflux family protein 5-like [Musa acuminata subsp. malaccensis] 212 78 % 2E-112 3.74 8.87 −1.26 1.79 0.3152999
 MATE c17372_g1   MATE efflux family protein 5-like [Phoenix dactylifera] 148 74 % 3E-63 7.98 3.35 1.24 0.91 0.4774231
 MATE c29524_g1   MATE efflux family protein 5-like [Elaeis guineensis] 196 77 % 3E-103 5.02 5.95 −0.40 0.93 0.9243257
 GST c24611_g1   glutathione S-transferase [Vitis amurensis] 228 57 % 9E-88 1251.26 959.39 0.40 9.90 0.7580164
 GST c27339_g1   glutathione S-transferase [Allium cepa] 215 56 % 7E-82 554.35 774.28 −0.49 8.90 0.6318245
 GST c28555_g1   elongation factor 1, partial [Lilium regale] 418 89 % 0 162.71 190.06 −0.22 8.00 0.8141854
 GST c27591_g1   glutathione S-transferase T1-like [Musa acuminata subsp. malaccensis] 244 73 % 1E-122 170.25 170.91 0.00 7.01 1
 GST c25698_g2   glutathione S-transferase [Tulipa fosteriana] 229 84 % 2E-133 87.22 128.32 −0.83 5.88 0.3152999
 GST c24296_g1   elongation factor 1-gamma 2 [Zea mays] 417 78 % 0 90.46 123.33 −0.44 7.27 0.6318245
 GST c25698_g1   glutathione S-transferase [Arachis hypogaea] 207 71 % 8E-94 90.79 120.45 −0.40 5.57 0.6668013
 GST c22668_g1   glutathione S-transferase 2 [Oryza sativa Japonica Group] 221 69 % 8E-103 93.72 80.32 0.20 6.25 0.9131831
 GST c27057_g1   glutathione s-transferase [Elaeis guineensis] 221 67 % 4E-104 20.61 21.78 −0.09 4.04 0.9889067
 GST c27057_g2   glutathione s-transferase [Elaeis guineensis] 258 65 % 2E-98 28.04 5.32 2.46 3.63 0.100767
 GST c21745_g1   Glutathione S-transferase Phi class [Zostera marina] 221 65 % 1E-96 3.32 19.01 −2.49 2.80 0.003065782
 GST c20342_g1   glutathione S-transferase family protein [Populus trichocarpa] 149 64 % 1E-53 8.57 12.71 −0.54 1.72 0.7580164
 GST c27063_g1   Tetrachloro-P-hydroquinone reductive dehalogenase [Zea mays] 266 71 % 3E-146 9.96 10.03 0.10 3.65 0.9889067
 GST c19621_g1   glutathione S-transferase [Musa acuminata AAA Group] 111 66 % 6E-43 13.16 2.27 2.40 1.02 0.2599001
 GST c33779_g1   Glutathione S-transferase Phi class [Zostera marina] 99 60 % 1E-35 0.00 10.44 −5.65 0.05 0.1057929