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 |