Abstract
Two separate 1Mb regions of the wheat genome comprising extensive stretches of repetitive sequences were assembled based on sequence data from overlapping BAC clones located in a section of the chromosome 3B of particular interest with regards to disease resistance. The sequencing of the 24 BAC clones combined standard Sanger sequencing (5-8 x coverage) and Solexa/Illumina short read sequencing (>300 x coverage). In addition, available BAC end and 454-based sequences were utilized to provide a good quality reference sequence that was annotated with a particular focus on the repetitive elements. Alignment to the rice and Brachypodium genome sequences identified a repetitive locus that is conserved between these genomes and the wheat genome. The conserved repetitive protein kinase like genes at this conserved locus showed a good alignment to the bacterial effector protein AvrPto (Weiman et al. 2007).