20S proteasome gene family from Arabidopsis. The OPM procedure, which involves predicting synteny blocks (dot plot and diagonal figure on the left) and mapping gene tree data onto these diagonals (phylogeny on the upper right). The dot plot in the upper left shows approximately half of Arabidopsis chromosomes 4 and 3 (on the horizontal and vertical axes, respectively). Each dot represents the coordinates of two proteins with bit score cutoffs of 560 (expect value of 10-68 for these data). Red dots indicate homologous proteins with the same orientations in both chromosomes, and blue indicate proteins with opposite orientations. This information is used by DiagHunter to predict synteny blocks, which are reported as text coordinates and as images (lower left). Where two 20S proteasome members intersect with a diagonal, they are highlighted with bulls-eyes, both on the diagonal and on both axes. In this version, other hits are also highlighted, with percent identity indicated using a yellow-to-black color scheme (black = 100% identity). Hits between gene family members and a diagonal represent candidate orthologs. OrthoMap uses these diagonal names to annotate the phylogeny, shown on the right. Gene names have the form "At3g22630_8010 1b", where first nine characters are the Arabidopsis Genome Initiative name; the number after the underscore is the position in kb on the chromosome (indicated after 'At'), and the orange numbers/letters after the space indicate the diagonal name from a chromosome comparison with that gene. Nodes giving rise to tandem gene duplications would be inferred by ParaMap and shown by a red 't' (none were found in this phylogeny). Nodes giving rise to segmental duplicates were manually inferred using the OrthoMap tags and annotated using the ATV tree-viewing program . The small phylogeny at the bottom shows the positions of EST consensus sequence homologs from soybean, Medicago truncatula, tomato, potato, and maize (see text). These help to pinpoint when the segmental duplication occurred in this clade in Arabidopsis.