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 (http://www.ebi.ac.uk/uniprot/) (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.