Phylogenetic relationship and exon-intron structure of OPR genes in 11 representative plants. (A) The rooted maximum-likelihood (ML) phylogenetic tree was inferred from the amino acid sequences alignment of the Oxidored_FMN domain under the best-fit model WAG+I+G (selected by ProtTest v1.4) with discrete gamma distribution in four categories. All parameters (gamma shape = 1.303; proportion of invariants = 0.042) were estimated from the dataset. The bootstrap values from 1000 resamplings are given at each node and the branch lengths are drawn to scale. (B) Exon-intron structures of the OPR family genes. The untranslated region (UTR) sequences are not shown, and the symbols "pink inverted triangle" and "black inverted triangle" denote the start and stop of codon sequences, respectively. Filled colored boxes: exons; lines: introns; numbers 1 and 2: intron phases. Exons shared with a high degree of identity (≥ 70%) between two OPR genes (Additional files 3, 4) are depicted in the same color. The length of the boxes and lines are scaled based on the length of the genes, except for PtOPR1, PtOPR4, MtOPR05-7, SbOPR08-1 and OsOPR06-4, for which long introns are denoted by slash-slash. Insertion fragments in the introns of OsOPR01-1, OsOPR06-1 and OsOPR06-4, caused by miniature inverted-repeat transposable elements (MITEs) or retrotransposons, are denoted by bold red lines. The exon-intron structures of OPR genes in the gymnosperm Picea sitchensis are not represented here because the genome sequence of Picea sitchensis is unavailable and its gene structure is uncertain.