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Open Access Research article

Phylogenetic analysis, structural evolution and functional divergence of the 12-oxo-phytodienoate acid reductase gene family in plants

Wenyan Li, Bing Liu, Lujun Yu, Dongru Feng, Hongbin Wang* and Jinfa Wang

Author Affiliations

State Key Laboratory for Biocontrol and Key Laboratory of Gene Engineering of Ministry of Education, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, PR China

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BMC Evolutionary Biology 2009, 9:90  doi:10.1186/1471-2148-9-90

Published: 5 May 2009

Additional files

Additional file 1:

OPR family genes in eleven representative plants. This table lists the 74 OPR genes from the eleven representative plants (i.e. Chlamydomonas reinhardtii, Volvox carteri, Physcomitrella patens, Selaginella moellendorffii, Picea sitchensis, Oryza sativa, Sorghum bicolor, Zea mays, Arabidopsis thaliana, Populus trichocarpa and Medicago truncatula), as summarized in Tables 1.

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Additional file 2:

OPR family genes in other monocots and dicots plants. This table lists the 31 OPR genes from the other monocots (i.e. Hordeum vulgare and Setaria italica) and dicots (i.e. Vitis vinifera, Pisum sativum, Solanum lycopersicum, Lithospermum erythrorhizon, Carica papaya, Artemisia annua, Catharanthus roseus, Hevea brasiliensis and Vigna unguiculata) plants.

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Additional file 3:

Amino acid sequences alignment of Oxidored_FMN domain. Amino acid sequences alignment of Oxidored_FMN domain in OPR genes from eleven species representing six major lineages within the green plants: the green algae (Chlamydomonas reinhardtii and Volvox carteri), the mosses (Physcomitrella patens), the lycophytes (Selaginella moellendorffii), the gymnosperms (Picea sitchensis), the monocotyledoneous angiosperms (Oryza sativa, Sorghum bicolor and Zea mays) and the dicotyledoneous angiosperms (Arabidopsis thaliana, Populus trichocarpa and Medicago truncatula). Only 3 of 74 OPR genes (AtOPR01-2/3 and SbOPR06-4) without complete Oxidored_FMN domain are excluded, while the outgroup ScOYE1 from yeast is included in the alignment. The blue blocks below the alignment represent the fragments selected by the Gblocks program with default parameters underlined. Positions of the alignments where more than 50% of the sequences are identical are shown with black boxes. The secondary structure elements are represented at the bottom of the alignment as tubes or arrows shown in gray based on structural information from OPR proteins AtOPR1, AtOPR3 and LeOPR3. The intron positions of putative ancestral OPR are represented at the top of the alignment as red vertical arrows, and I1~I12 represent intron 1~12. The seven conserved OPR subfamilies are represented as I, II, III, IV, V, VI and VII at the left side of the alignment.

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Additional file 4:

Nucleotide sequences alignment of OPR family genes from eleven species. Nucleotide sequences alignment of OPR genes from eleven species representing the six major lineages within the green plants: the green algae (Chlamydomonas reinhardtii and Volvox carteri), the mosses (Physcomitrella patens), the lycophytes (Selaginella moellendorffii), the gymnosperms (Picea sitchensis), the monocotyledoneous angiosperms (Oryza sativa, Sorghum bicolor and Zea mays) and the dicotyledoneous angiosperms (Arabidopsis thaliana, Populus trichocarpa and Medicago truncatula). Identical residues in the alignments are shaded and seven well-conserved OPR subfamilies are represented as Sub.I, II, III, IV, V, VI and VII at the left side of the alignment.

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Additional file 5:

The rooted maximum-likelihood phylogenetic tree of OPR family genes from eleven representative species. The rooted maximum-likelihood (ML) phylogenetic tree of OPR genes in eleven representative plants was inferred from the amino acid sequence alignments of the Oxidored_FMN domain (Additional file 3) under the Jones-Taylor-Thornton (JTT) model, implemented in Phylip v3.68 package. The old yellow enzyme 1 (OYE1) of Saccharomyces cerevisiae (ScOYE1) was selected as an out of group marker and its accession number in SWISS-PROT is Q02899. The bootstrap values from 1000 resamplings are given at each node and the branch lengths are drawn to scale. The seven conserved OPR subfamilies are represented as Sub.I, II, III, IV, V, VI and VII at the right side of the ML tree.

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Additional file 6:

Likelihood ratio statistics (2Δℓ). This data provide represent the likelihood ratio statistical analysis of the comparisons of M0 with M3, M1a with M2a, and M7 with M8, respectively.

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Additional file 7:

The distribution of positive-selection sites and/or critical amino acid residues in Oxidored_FMN domain. This data provide represent the detailed distribution of positive-selection sites and/or critical amino acid residues in Oxidored_FMN domain, which are responsible for functional divergence between OPR paralogues.

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