Analysis of Highly Repetitive BAC Clones Reveals Rapid Evolution of highly variable Gene Clusters in Triticeae

Sequencing of minimum tiling paths (MTPs) of BAC clones is the most robust strategy to obtain the complete sequence of a genome. However, MTP sequencing and sequence assemblies reach their limits in large segmental duplications where the duplicated units are longer that the BAC clones. In the physical maps of barley and wheat we have identified numerous regions which must contain arrays of very large repeat units (>100 kb), because (i) LTC and FPC assemblies indicate an extremely high coverage with BAC clones, and (ii) sequence comparison of BACs from within these “blobs” indicate the presence of extremely large duplicated segments. These repeat arrays must be of relatively recent origin because individual repeat units are extremely similar (less than one SNP per kb) to each other. One such region on chromosome 3H contains a cluster of receptor-like kinase (RLK) genes. We found that pairs of RLK genes plus dozens of kb of flanking repeat sequences have been recently amplified to form an enormous repeat array consisting of at least 8 units, each one with a size of over 100 kb. Individual repeat units differ from each other by only a few SNP per kb. This high sequence similarity allows a rapid growing or shrinking of the cluster through unequal crossing-over, making it a potential hotspot for copy number variations. Interestingly, the orthologous region in rice also contains large clusters of RLK genes and is one of the most dynamically evolving regions in the genome. We are currently analyzing whether similar molecular mechanisms drive the dynamics of these clusters in both species.