P450 genes revisited (in the light of the potato genome sequence

FEINGOLD SERGIO; BARREIRO LEANDRO; CARBONI MF; BOLSER DM; MARTIN DMA; L. DIAMBRA; KNAUBER D; LORENZEN JH

Wageningen

Congreso; EAPR – EUCARPIA CONGRESS Potato Breeding after completion of the DNA Sequence of the Potato Genome; 2010

European Association for Potato Research

Plant P450 enzymes are monooxygenases that catalyze oxidations on different substrates and have been shown to be involved in the biosynthesis of secondary metabolites with roles in pigmentation, antioxidant activity and defense to UV light, insects and xenobiotics. Present in prokaryotes and eukaryotes, P450 genes have greatly expanded in plants, constituting the largest plant gene family. Arabidopsis thaliana contains 272 P450 genes, while potato seems to hold one of the richest P450 gene sets. Early identification of potato P450s was performed from 1998 to 2004 by querying the former TIGR potato and tomato EST databases (now “The Gene Index Project”; http://compbio.dfci.harvard.edu/tgi/) with the 11 known Arabidopsis thaliana sequences that represent most of the plant P450 clades. Out of the 486 sequences retrieved (238 from potato and 248 from tomato) 106 putative non-redundant P450 genes, were mapped across all 12 potato chromosomes in interspecific potato segregating populations (BCB & BCT) by means of single strand conformation polymorphism, producing P450-SSCP functional markers. With the complete potato sequence unveiled by the Potato Genome Sequencing Consortium (PGSC; http://www.potatogenome.net), we used the Pfam (http://pfam.sanger.ac.uk) P450 Hidden Markov Model to search the protein database (PGSC-DMv3). This search identified 393 P450 domains with an e-value < 10.e-100. Some of these genes were found in clusters on the super-scaffolds, indicating tandem duplication of genes during evolution. A BLAST search of the original 106 mapped sequences was performed against the P450 containing super-scaffolds. Genes corresponding to all the original sequences were found in the assembly. Out of the 71 P450 containing super-scaffolds anchored to the PGSC recombination map, map locations for 67 were congruent with our mapped data, with 4 misplaced sequences. Additionally, 8 sequences showed dual locations, suggesting potential duplications in chromosomes 2 & 10; 5 & 11; 3 & 4 and 4 & 9. A few (7) linked P450-SSCPs were ascribed to different parts of the same gene, while others (3) were possible allelic variants of the same gene that were not assembled in the original databases. This fact was not unexpected since PCR primers were designed based on available sequences, often partial, at the time of the initial study.