Tropical Plant Biology

, Volume 1, Issue 3, pp 216–235

Comparison of Cytochrome P450 Genes from Six Plant Genomes

  • David R. Nelson
  • Ray Ming
  • Maqsudul Alam
  • Mary A. Schuler
Article

DOI: 10.1007/s12042-008-9022-1

Cite this article as:
Nelson, D.R., Ming, R., Alam, M. et al. Tropical Plant Biol. (2008) 1: 216. doi:10.1007/s12042-008-9022-1

Abstract

Plants depend on cytochrome P450 (CYP) enzymes for nearly every aspect of their biology. In several sequenced angiosperms, CYP genes constitute up to 1% of the protein coding genes. The angiosperm sequence diversity is encapsulated by 59 CYP families, of which 52 families form a widely distributed core set. In the 20 years since the first plant P450 was sequenced, 3,387 P450 sequences have been identified and annotated in plant databases. As no new angiosperm CYP families have been discovered since 2004, it is now apparent that the sampling of CYP diversity is beginning to plateau. This review presents a comparison of 1,415 cytochrome P450 sequences from the six sequenced genomes of Vitis vinifera (grape), Carica papaya (papaya), Populus trichocarpa (poplar), Oryza sativa (rice), Arabidopsis thaliana (Arabidopsis or mouse ear’s cress) and Physcomitrella patens (moss). An evolutionary analysis is presented that tracks land plant P450 innovation over time from the most ancient and conserved sequences to the newest dicot-specific families. The earliest or oldest P450 families are devoted to the essential biochemistries of sterol and carotenoid synthesis. The next evolutionary radiation of P450 families appears to mediate crucial adaptations to a land environment. And, the newest CYP families appear to have driven the diversity of angiosperms in mediating the synthesis of pigments, odorants, flavors and order-/genus-specific secondary metabolites. Family-by-family comparisons allow the visualization of plant genome plasticity by whole genome duplications and massive gene family expansions via tandem duplications. Molecular evidence of human domestication is quite apparent in the repeated P450 gene duplications occurring in the grape genome.

Keywords

Cytochrome P450 Evolution P450 superfamily CYP Papaya Grape Comparative genomics 

Supplementary material

12042_2008_9022_MOESM1_ESM.doc (209 kb)
Supplementary Table 1Numbers of Cytochrome P450 genes in six complete genomes sorted by family and in the cases of CYP90 and CYP97 by subfamily. This tally does not include pseudogenes. Line 81 provides the organism totals. Ara Arabidopsis, Pap papaya, Gra grape, Pop poplar. (DOC 209 KB)
12042_2008_9022_MOESM2_ESM.doc (216 kb)
Supplementary Table 2All Cytochrome P450 genes and pseudogenes in, Arabidopsis, rice, poplar, papaya, grape and moss. (DOC 54 KB)
12042_2008_9022_MOESM3_ESM.doc (90 kb)
Supplementary Figure 1Phylip Alignment for CYP97 family members taken from the Cytochrome P450 website. This alignment was used to make Fig. 1. (DOC 90 KB)
12042_2008_9022_MOESM4_ESM.doc (62 kb)
Supplementary Figure 2Alignment of CYP711 sequences taken from the Cytochrome P450 website. Conservation in SRS1-6 regions is highlighted in yellow with Arabidopsis CYP711A1 as the 100% control. (DOC 61.5 KB)
12042_2008_9022_MOESM5_ESM.doc (72 kb)
Supplementary Figure 3Alignment of CYP701 sequences taken from the Cytochrome P450 website. Conservation in SRS1-6 regions is highlighted in yellow with Arabidopsis CYP701A3 as the 100% control. (DOC 72.5 KB)
12042_2008_9022_MOESM6_ESM.doc (71 kb)
Supplementary Figure 4Alignment of CYP88 sequences taken from the Cytochrome P450 website. Conservation in SRS1-6 regions is highlighted in yellow with Arabidopsis CYP88A3 as the 100% control. (DOC 71 KB)
12042_2008_9022_MOESM7_ESM.doc (79 kb)
Supplementary Figure 5Alignment of CYP84 sequences taken from the Cytochrome P450 website. Conservation in SRS1-6 regions is highlighted in yellow with Arabidopsis CYP84A1 as the 100% control. (DOC 79 KB)

Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • David R. Nelson
    • 1
  • Ray Ming
    • 2
  • Maqsudul Alam
    • 3
  • Mary A. Schuler
    • 4
  1. 1.Department of Molecular SciencesUniversity of Tennessee Health Sciences CenterMemphisUSA
  2. 2.Department of Plant BiologyUniversity of Illinois at Urbana-ChampaignUrbanaUSA
  3. 3.Department of Microbiology, Advance Studies in Genomics, Proteomics and BioinformaticsUniversity of Hawaii at ManoaHonoluluUSA
  4. 4.Departments of Cell and Developmental Biology, Biochemistry and Plant BiologyUniversity of Illinois at Urbana-ChampaignUrbanaUSA