The Online Data Resource for Review:
Phenylpropanoids and plant defense -- an updated genomic perspective   
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This site serves as a repository of gene sequence information for the review article "Genome-wide analysis of phenylpropanoid defense pathways" by MARINA A. NAOUMKINA, QIAO ZHAO, LINA GALLEGO-GIRALDO, XINBIN DAI, PATRICK X. ZHAO AND RICHARD A. DIXON.

The site contains a detailed listing of phenylpropanoid pathway (lignin and flavonoid) genes from eleven plant species with fully or near-fully sequenced genomes; the moss Physcomitrella patens, the spike moss Selaginella moellendorffii, three monocots (Oryza sative, Sorghum bicolor, Zea mays), and six dicots (Arabidopsis thaliana, Populus trichocarpa, Vitus vinifera, Glycine max, Medicago truncatula and Lotus japonicus). For gene annotation, proteins predicted from genome sequence were searched by BLASTX against the Uniprot Trembl database ( (e-value<1e-04) and the top five hits with meaningful annotations were retrieved as annotation. Genes were sorted as representing proteins involved in the various branches of the phenylpropanoid pathway, including flavonoid, isoflavonoid, lignin etc., based on predicted function. The information includes source of genome sequences, enzyme name, gene identification, redundancy, Affymetrix probeset ID, location on chromosome (if possible), length of sequence, five top hit annotations and the sequence itself.

The list of gene families which are investigated in this study
Path Family Name Description # of Sequences
Core phenylpropanoid pathway 4CL 4-Coumarate: Coenzyme A ligase 154
Core phenylpropanoid pathway C4H Cinnamate 4-hydroxylase 28
Core phenylpropanoid pathway PAL L-Phenylalanine ammonia-lyase 91
Flavonoid core CHI Chalcone isomerase 50
Flavonoid core CHR Chalcone reductase 43
Flavonoid core CHS Chalcone synthase 149
Flavonols, anthocyanidins 2Og 2-Oxoglutarate-dependent dioxygenase (flavonoid), including three subfamilies: Anthocyanidin synthase(ANS), Flavanone 3-beta-hydroxylase(F3betaH), Flavonol synthase(FLS). 259
Flavonols, anthocyanidins DFR Dihydroflavonol reductase 152
Flavonols, anthocyanidins F3'5'H Flavonoid 3',5'-hydroxylase 22
Flavonols, anthocyanidins F3'H Flavonoid 3'-hydroxylase 50
Isoflavonoid I2'H Isoflavone 2'-hydroxylase 8
Isoflavonoid IFR Isoflavone reductase 110
Isoflavonoid IFS Isoflavone synthase 10
Isoflavonoid IOMT Isoflavone O-methyltransferase, including 7-IOMT and 4'-IOMT 31
Lignin C3H 4-Coumaroyl shikimate 3-hydroxylase 61
Lignin CAD Cinnamyl alcohol dehydrogenase 191
Lignin CCOMT Caffeoyl Coenzyme A 3-O-methyl-transferase 67
Lignin CCR Cinnamoyl Coenzyme A reductase 249
Lignin COMT Caffeic acid 3-O-methyl-transferase 117
Lignin F5H Ferulic acid/coniferaldehyde/coniferyl alcohol 5-hydroxylase 123
Lignin HCT Hydroxycinnamoyl Coenzyme A: shikimate hydroxycinnamoyl transferase 174
Lignin Laccase 267
Figure of Lignin Pathway     Figure of Flavonoid/Isoflavonoid Pathway

The list of species which are investigated in this study
Species Common Name Genomic Sequences Resource # of Sequences
Arabidopsis thaliana Mouse-ear cress 136
Glycine max Soybean 368
Lotus japonicus 179
Medicago truncatula Barrel medic 192
Oryza sativa Rice 216
Physcomitrella patens Moss 85
Populus trichocarpa Black cottonwood 217
Sorghum bicolor Sorghum 237
Selaginella moellendorffii Club-mosses 197
Vitis vinifera Wine grape 262
Zea mays Maize 181

  © 2010 by The Samuel Roberts Noble Foundation, Inc.