Plant Physiology 135:756-772 (2004)
© 2004 American Society of Plant Biologists
GENOME ANALYSIS
Comparative Genomics of Rice and Arabidopsis. Analysis of 727 Cytochrome P450 Genes and Pseudogenes from a Monocot and a Dicot1,[w]
David R. Nelson*,
Mary A. Schuler,
Suzanne M. Paquette,
Daniele Werck-Reichhart and
Søren Bak
Department of Molecular Sciences and Center of Excellence in Genomics and Bioinformatics, University of Tennessee, Memphis, Tennessee 38163 (D.R.N.); Department of Cell and Structural Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (M.A.S.); Department of Biological Structure, University of Washington School of Medicine, Seattle, Washington 98195 (S.M.P.); Department of Plant Stress Response, Institute of Plant Molecular Biology, 67084 Strasbourg cedex, France (D.W.-R.); and Department of Plant Biology and Center for Molecular Plant Physiology (PlaCe), The Royal Veterinary and Agricultural University, DK–1871 Frederiksberg C, Copenhagen, Denmark (S.B.)
Data mining methods have been used to identify 356 Cyt P450 genes and 99 related pseudogenes in the rice (Oryza sativa) genome using sequence information available from both the indica and japonica strains. Because neither of these genomes is completely available, some genes have been identified in only one strain, and 28 genes remain incomplete. Comparison of these rice genes with the 246 P450 genes and 26 pseudogenes in the Arabidopsis genome has indicated that most of the known plant P450 families existed before the monocot-dicot divergence that occurred approximately 200 million years ago. Comparative analysis of P450s in the Pinus expressed sequence tag collections has identified P450 families that predated the separation of gymnosperms and flowering plants. Complete mapping of all available plant P450s onto the Deep Green consensus plant phylogeny highlights certain lineage-specific families maintained (CYP80 in Ranunculales) and lineage-specific families lost (CYP92 in Arabidopsis) in the course of evolution.
1 This work is supported by the National Science Foundation (2010 Project grant no. MCB 0115068 to M.A.S.), by the Danish National Research Foundation (grant to Center for Molecular Plant Physiology [PlaCe]), and by the Danish Agricultural and Veterinary Research Council (grant no. 23–02–0095 to S.B.).
[w] The online version of this article contains Web-only data.
www.plantphysiol.org/cgi/doi/10.1104/pp.104.039826.
* Corresponding author; e-mail dnelson{at}utmem.edu; fax 901–448–7360.
Received January 30, 2004;
returned for revision March 31, 2004;
accepted March 31, 2004.
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