Figure 5.

Collinearity Analysis of B-Class Type II MADS Box Gene (AP3 and PI) Homologs Reveals Unusual Patterns of Gene Loss, Lineage-Specific Transpositions, and Local Tandem Duplications.

The placement of ancient polyploid events giving rise to gene duplicates is shown on appropriate nodes (At-β, At-α, Br-α, and Th-α). For the AP3 group genes in Brassicaceae (shown by red bars), there is only a single locus retained in A. thaliana and A. lyrata and two retained Brassica syntelogs derived from Br-α. Collinear homoeologous regions derived from At-α are detectable in Brassicaceae genomes; however, the AP3 syntelogs were lost (regions highlighted in red boxes). T. hassleriana has an unusual tandem duplication of AP3 genes in one of two homoeologous regions derived from Th-α. The AP3 genes and the neighboring Forkhead gene (EMB1967) are the only genes syntenic to the AP3 Brassicaceae region (see Supplemental Figure 25 online). The Cleomaceae AP3 region is syntenic with AP3 regions of all other eudicot genomes analyzed (see Supplemental Figure 23 online). Thus, we conclude that there was a lineage-specific transposition of AP3 and the neighboring Forkhead locus in the Brassicaceae. There is only a single copy of PI genes (red bars) in A. thaliana and A. lyrata and all three Br-α derived syntelogs in Brassicaceae. There is no detectable homoeologous region in Brassicaceae derived from At-α. In Tarenaya, we detected one syntenic PI gene and region to the Brassicaceae, but also a second region that is syntenic to other eudicots (see Supplemental Figure 24 online). We conclude that these two Tarenaya PI genes were generated due to the At-β ancient duplication event with the subsequent transposition of one locus into the region collinear between Brassicaceae and Cleomaceae and loss of the nontransposed locus from only the Brassicaceae lineage. The differences in genomic context and gene expression (see Supplemental Figure 27 online) may contribute to shifts in floral morphology and symmetry between families.