Comparative genomics of rice and Arabidopsis. Analysis of 727 cytochrome P450 genes and pseudogenes from a monocot and a dicot

Abstract

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.

Figure 1.

Distribution of P450 families across plant phylogeny. A total of 1,098 named plant P450s were sorted by family and taxonomic position in the phylogeny of plants. Each dot may represent many genes, as in the rice CYP71s in the monocot branch (117 named P450s). P450 families are grouped in the 10 plant P450 clans. Vertical lines are placed to help visualize the P450 family position. Arabidopsis is in the Brassicales branch. Only rice and Arabidopsis had complete genomes available at the time of this compilation.

Figure 2.

The CYP51 clan. A total of 48 sequences in the CYP51 family across all taxa are shown as a Neighbor-Joining tree computed with a PAM350 scoring matrix. In this new nomenclature, subfamilies in CYP51 represent major taxonomic divisions, not the usual ≥55% sequence identity. CYP51H sequences in rice are an exception, apparently diverging from the usual CYP51 function. Abbreviations for the 75 species used in Figures 2 to 6 are as follows: Af, Aspergillus fumigatus; An, Aspergillus nidulans; Ao, Asparagus officinalis; At, Arabidopsis (thale cress); Bf, Botryotinia fuckeliana; Bs, Berberis stolonifera; Ca, Candida albicans; Cd, Candida dubliniensis; Cg, Candida glabrata; Ch, C. reinhardtii (green algae); Ci, Cicer arietinum (chickpea); Cj, Coptis japonica; Cm, Cucurbita maxima (pumpkin); Cr, Catharanthus roseus (Madagascar periwinkle); Ct, Candida tropicalis; Dd, Dictyostelium discoideum (cellular slime mold); Ec, Eschscholzia californica (California poppy); Eg, Erysiphe graminis; El, Euphorbia lagascae; Ga, Gossypium arboreum (cotton); Ge, Glycyrrhiza echinata (licorice); Gg, Gallus gallus (chicken); Gm, soybean; Hs, Homo sapiens (human); Ht, Helianthus tuberosus (Jerusalem artichoke); Io, Issatchenkia orientalis (fungi); Le, tomato; Lj, Lotus japonicus (lotus); Lm, Leishmania major (Leishmaniasis parasite); Lr, Lolium rigidum (ryegrass); Ls, Liquidambar styraciflua (sweetgum); Ma, Mycobacterium avium; Mc, Methylococcus capsulatus; Me, Manihot esculenta (cassava); Mf, Monilinia fructicola; Mm, Mus musculus (mouse); Ms, Medicago sativa (alfalfa); Mt, Mycobacterium tuberculosis; Mu, Musa acuminata (banana); Mys, Mycobacterium smegmatis; Nc, Neurospora crassa; Np, Nicotiana plumbaginifolia; Nt, tobacco; Os, rice; Pa, Persea americana (avocado); Pas, Pastinaca sativa (wild parsnip); Pc, Pyrus communis (pear); Ph, Petunia hybrida; Phc, Phanerochaete chrysosporium (white rot fungus); Pi, Penicillium italicum; Pnc, Pneumocystis carinii; Pr, Pinus radiata (Monterey pine); Ps, pea; Pso, Papaver somniferum (opium poppy); Pt, Pinus taeda (loblolly pine); Rn, Rattus norvegicus (rat); Sa, Sinapis alba (white mustard); Sb, Sorghum bicolor; Sc, yeast; Sm, Solanum melongena cv Sinsadoharanasu (eggplant); Sp, Schizosaccharomyces pombe (fission yeast); St, potato; Ta, wheat; Tc, Taxus cuspidata (Japanese yew); Tm, Triglochin maritima; Tr, T. rubripes (Japanese pufferfish); Trb, Trypanosoma brucei (African sleeping sickness parasite); Trc, Trypanosoma cruzi (Chagas disease parasite); Um, Ustilago maydis; Un, Uncinula necator (grape powdery mildew fungus); Vr, Vigna radiata (mung bean); Vs, Vicia sativa; Vv, Vitis vinifera (grape); Xl, Xenopus laevis (African clawed frog); and Zm, Z. mays (maize).

Figure 3.

The CYP85 clan. The 85 clan is one of four clans with multiple P450 families. Here, 74 sequences from 16 families are shown with CYP83A1 as an outgroup. This tree was made using the Neighbor-Joining algorithm and a Gonnett scoring matrix. CYP720 and CYP724 cluster with the CYP90s. They are not named as CYP90 subfamilies because CYP720 is only 33% identical to CYP90C1, and CYP724 is only 34% identical to CYP720. The CYP90 subfamilies could probably stand as separate families.

Figure 4.

The CYP86 clan. This clan contains only five P450 families. The tree has 84 sequences with CYP97B3 as the outgroup. This tree was made using the Neighbor-Joining algorithm and a Gonnett scoring matrix.

Figure 5.

The CYP71 clan. This is the largest set of P450s in plants. The extreme diversification of families and subfamilies in the CYP71 clan indicates great utility for plant evolution, yet there are no CYP71 clan members detected in C. reinhardtii. This tree has 139 sequences in 26 families. It is a Neighbor-Joining tree using a Gonnett scoring matrix. Notice that CYP83, CYP99, and CYP726 are inside the CYP71 family.

Figure 6.

The CYP72 clan. This tree illustrates the frustration of nomenclature efforts, which must act on sequences as they are found. New data can cause relocation of branches as in the CYP709A1 and CYP709A2 sequences. These have moved to a new family as CYP735A1 and CYP735A1. CYP72B1 has also moved to a new location as CYP734A1. This tree of 67 sequences with CYP97C1 as the outgroup is a Neighbor-Joining tree using a Gonnett scoring matrix.