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Comparison of Cytochrome P450 Genes from Six Plant Genomes

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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.

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Authors and Affiliations

  1. Department of Molecular Sciences, University of Tennessee Health Sciences Center, 858 Madison Ave., Suite G01, Memphis, TN, 38163, USA

    David R. Nelson

  2. Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

    Ray Ming

  3. Department of Microbiology, Advance Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii at Manoa, 2565 McCarthy Mall Keller 301, Honolulu, HI, 96822, USA

    Maqsudul Alam

  4. Departments of Cell and Developmental Biology, Biochemistry and Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

    Mary A. Schuler

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  1. David R. Nelson
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Correspondence to David R. Nelson.

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Supplementary Table 1

Numbers 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)

Supplementary Table 2

All Cytochrome P450 genes and pseudogenes in, Arabidopsis, rice, poplar, papaya, grape and moss. (DOC 54 KB)

Supplementary Figure 1

Phylip Alignment for CYP97 family members taken from the Cytochrome P450 website. This alignment was used to make Fig. 1. (DOC 90 KB)

Supplementary Figure 2

Alignment 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)

Supplementary Figure 3

Alignment 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)

Supplementary Figure 4

Alignment 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)

Supplementary Figure 5

Alignment 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)

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Nelson, D.R., Ming, R., Alam, M. et al. Comparison of Cytochrome P450 Genes from Six Plant Genomes. Tropical Plant Biol. 1, 216–235 (2008). https://doi.org/10.1007/s12042-008-9022-1

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