Phylogenetic analysis and exon-intron organization of IQD genes in Arabidopsis thaliana and Oryza sativa. Neighbor-joining trees of full-length amino acid sequences encoded by Arabidopsis (a) and rice (c) IQD genes are shown. The gene coding for the protein containing a C-terminally truncated IQ67 domain in Arabidopsis, At5g35670, and in rice, Osm0603925, was used as outgroup for each family. Bootstrap values (1,000 replicates) are placed at the nodes, and the scale bar corresponds to 0.1 estimated amino acid substitutions per site. Subfamilies and subgroups of IQD genes (I–IV) are highlighted by colored vertical bars on the right of the trees. The exon-intron organization of the corresponding IQD genes is shown for the Arabidopsis (b) and rice (d) gene family. Exons are depicted as boxes and introns as connecting thin lines. Protein-coding regions are colored in red, and non-translated regions, when supported by full-length cDNA sequences, are shown in black. The gene structures are drawn to scale and aligned along the left border (indicated by vertical dotted line) of the exon encoding amino acids 17–67 of the IQ67 domain, with the exception of At5g03960, Os08m00126 and Os01m06663 that have lost the respective intron. Additional intron losses are indicated by asterisks between Arabidopsis gene pairs. The exon-intron organization of the Arabidopsis IQD genes was taken from the TIGR Arabidopsis database, with the exception of At1g01110 for which the MIPS annotation was used as template. The presentation of the exon-intron organization of rice IQD genes was adapted to match the TIGR format of Arabidopsis IQD genes. The length of the second and third intron of Os02m01875 and Os03m04309 is 3.8 kb and 2.1 kb, respectively. Most introns of IQD genes are in phase-0. Six Arabidopsis and seven rice IQD genes contain phase-1 and phase-2 introns, which are labeled with the respective Arabic numeral. At2g02790, for which no full-length cDNA sequence is available, may also contain a phase-1 intron on its 3'end.