Sequence and structure of Brassica rapa chromosome A3

We have determined and analyzed the sequence of B. rapa chromosome A3. We obtained 31.9 Mb of sequences, organized into nine contigs, which incorporated 348 overlapping BAC clones. Annotation revealed 7,058 protein-coding genes, with an average gene density of 4.6 kb per gene. Analysis of chromosome collinearity with the A. thaliana genome identified conserved synteny blocks encompassing the whole of the B. rapa chromosome A3 and sections of four A. thaliana chromosomes. The frequency of tandem duplication of genes differed between the conserved genome segments in B. rapa and A. thaliana, indicating differential rates of occurrence/retention of such duplicate copies of genes. Analysis of 'ancestral karyotype' genome building blocks enabled the development of a hypothetical model for the derivation of the B. rapa chromosome A3.We report the near-complete chromosome sequence from a dicotyledonous crop species. This provides an example of the complexity of genome evolution following polyploidy. The high degree of contiguity afforded by the clone-by-clone approach provides a benchmark for the performance of whole genome shotgun approaches presently being applied in B. rapa and other species with complex genomes.The Brassicaceae family includes approximately 3,700 species in 338 genera. The species, which include the widely studied Arabidopsis thaliana, have diverse characteristics and many are of agronomic importance as vegetables, condiments, fodder, and oil crops [1]. Economically, Brassica species contribute to approximately 10% of the world's vegetable crop produce and approximately 12% of the worldwide edible oil supplies [2]. The tribe Brassiceae, which is one of 25 tribes in the Brassicaceae, consists of approximately 240 species and contains the genus Brassica. The cultivated Brassica species are B. rapa (which contains the Brassica A genome) and B. oleracea (C genome), which are grown mostly as vegetable cole crops, B. nigra (B genome) as a source of mustard co