Genome of mesopolyploid crop Brassica rapa sheds new light on the study of genome evolution

Brassica crops are used for human nutrition and provide opportunities for the study of genome evolution. These crops include important vegetables (B. rapa, Brassica oleracea) as well as oilseed crops (Brassica napus, B. rapa, Brassica juncea and Brassica carinata), which contribute to approximately 10% of the world's vegetable crop produce and approximately 12% of the worldwide edible oil supplies. The species B. rapa is a major vegetable or oil crop in Asia and Europe. It also serves as an excellent model system to study polyploidy-related genome evolution because of its paleohexaploid ancestry and its close evolutionary relationships with Arabidopsis thaliana and other Brassica species with larger genomes.

Since the Brassica rapa Genome Sequencing Project (BrGSP) was initiated about three years ago, scientists from China, United Kingdom, USA, Korea, Canada, France and Australia have been working on the studies of B. rapa genome, aiming to assist botanists and breeders worldwide in improving production, quality, nutritional value and disease resistance of B. rapa varieties. In this project, Chinese Scientists have been playing a leading role by the advanced next-generation sequencing technology. In 2009, BrGSPC terminated all the sequencing plans and took the B. rapa genome sequenced by Chinese Scientists as B. rapa (Chinese cabbage) reference sequence.

With the advanced genome sequencing capability of BGI, B. rapa was sequenced and assembled by BGI's Short Oligonucleotide Analysis Package, SOAPdenovo. The assembled Brassica rapa genome size was approximately 283.8 Mb, which was estimated to cover >98% of the gene space. After the annotation and analysis, 41,174 protein-coding genes were identified in B. rapa genome. So far, B. rapa is the closest sequenced species relatives to A. thaliana, and they show high similarity in functional genes, although they have undergone differentiation about 13 ~ 17 million years ago. The B. rapa genome sequence could lays an important foundation for better exploring structural and functional evolution of A. thaliana and other Brassica species.

The Brassica mesohexaploidy also offers an opportunity to study gene retention in triplicated genomes. In particular, variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. Some auxin- related genes families also were expanded or some genes over retained, which may contribute to the evolution and development of morphological variants. In this study, the researchers also found that the genes associated with response to important environmental factors including salt, cold, osmotic stress, light, wounding, pathogen (broad spectrum) defense, and both cadmium and zinc ions, were evidently over retained. It suggested that genome triplication may have expanded gene families that underlie environmental adaptability as observed in other polyploid species.