Global repeat discovery of rye A and B chromosomes using a high-throughput 454 sequence survey
Final Report Abstract
Through next generation sequencing of sorted A and B chromosomes we showed that B chromosomes of rye are rich in gene-derived sequences, which allowed us to trace their origin to fragments of A chromosomes with the largest parts corresponding to rye chromosomes 3R and 7R. Compared to A chromosomes, B chromosomes were also found to accumulate large amounts of specific repeats and insertions of organellar DNA. Although most repeats are similarly distributed along As and Bs, several transposons are either amplified or depleted on the B. An accumulation of B-enriched satellites was found mostly in the nondisjunction control region of the B, which is transcriptionally active and late replicating. All B-enriched sequences are not unique to the B but are also present in other "Secale" species, suggesting the origin of the B from As of the same genus. The origin of rye B chromosomes was estimated to about 1.1-1.3 million years (MY) ago, thus overlapping in time with the onset of the genus "Secale" (1.7 MY ago). We propose the first comprehensive model of B chromosome evolution, including its origin by recombination of several A chromosomes followed by capturing of additional A-derived and organellar sequences and amplification of B-specific repeats. The conserved chromosome structure of Bs which were maintained in geographically distinct populations suggests that after a period of rapid B development this process has slowed during its recent evolution.
