Figure 2.

Identification of the Ha Locus Region and Comparative Annotation Overview of the Seven Wheat Species (Triticum and Aegilops) Genomes.

(A) Multipipmaker (Schwartz et al., 2000) alignment using the sequence of the Ha locus of the D genome of T. aestivum as a matrix compared with the other six available wheat sequences. Colored blocks show the percentage of sequence identity (>90 in red; between 50 and 90% in green). The identified Ha-deleted interval in the A and B genomes of T. turgidum and T. aestivum is indicated (box surrounded by dotted line).

(B) Scaled diagram of annotation results of the Ha locus region (and 5′ and 3′ boundaries) from the seven Triticum genomes (detailed in Supplemental Data 1 online). Only one B genome is presented because the two B genomes share 99% sequence identity. Genes (CDS) (light blue), class I TEs (yellow blocks), class II TEs (green blocks), unclassified elements (gray), MITEs (vertical red bars), and repeats (vertical black bars) are shown. The remaining white spaces correspond to unassigned DNA (no features of annotation). Orthologous CDS between the different genomes have the same number or gene name. CDS duplication (Dup) and deletion (Del) events are indicated by arrows. Sequences of the genomes lacking the puroindoline genes (i.e., the A and B genomes of T. turgidum and T. aestivum) are continuous and are presented discontinuously to illustrate conserved 5′ and 3′ boundaries of the Ha locus region, conserved 5′ and 3′ ends of this same locus, and the DNA at the Ha locus region that cannot be aligned with the genomes presenting Pina and Pinb genes. The inset shows a 5× zoomed presentation of the Ha locus region of the A and B genomes of T. aestivum and T. durum (starting from Gene 2 [GSP-1 gene] to the 5′ end of Gene8) and detailing sequence conservation with the other genomes presenting the puroindoline genes at the 5′ and 3′ ends as well as the nonaligned sequences. Boxes represent sequence conservation between the different genomes at the 5′ and 3′ ends. The 5′ end of Ha locus region: conservations between the different Triticum and Aegilops genomes (red); conservation between the A genomes only (boxes with red lines). The 3′ end of Ha locus region: conservation with the D genome of T. aestivum at region flanking duplicated Gene8 (green boxes); conservation with the D genome of T. aestivum at region flanking Gene8-relic (boxes with green lines); conservation between the A and B genomes only (blue).