Plant & Animal Genomes XVII Conference Plant & Animal Genomes XVII ConferenceJanuary 10-14, 2009
Town & Country Convention Center
San Diego, CA
Jeong-Hwan Mun1 , Soo-Jin Kwon1 , Jin-A Kim1 , Young Ju Seol1 , Mina Jin1 , Jung Sun Kim1 , Myung-Ho Lim1 , Soo In Lee1 , Dae-Soo Kim2 , Namshin Kim2 , Beom-Seok Park1
Genome sequencing of Brassica rapa, the Brassica ‘A’ genome model species, provides an opportunity for large-scale sequence-based comparison of the Brassica genome with that of A. thaliana. Here, we report the genome structure of B. rapa and synteny comparison between the two genomes, including details about chromosome relationships, large-scale macrosynteny blocks, and microsynteny within the blocks. The B. rapa genome was estimated to contain about 53,000 protein coding genes with an average size of 1.6 kb. Genome comparison clearly revealed that the B. rapa genome has underwent recent genome triplication based on apparent chromosomal relationships with Arabidopsis counterparts although several triplicated blocks were lost or reconstructed in the B. rapa genome. However, gene-containing regions in B. rapa occupy about 30% shrunken space than Aribidopsis counterparts, primarily because of extensive interspersed gene loss. Synteny block comparison also proposed that differential retraction of Arabidopsis-Brassica common ancestor genome might result in split of two lineages. Analysis of synonymous base substitution rates indicated that Brassica lineage underwent at least three distinct episodes of genome duplications (2R, 3R, and 4R) and the most recent genome triplication (4R) postdated the split of Arabidopsis and Brassica. Moreover, higher loss of the duplicated genes originated from 3R event was identified in B. rapa than in B. oleracea indicating that differential gene loss associated with large-scale genome rearrangement might contribute to emergence of the species ca. 8 million years ago relatively quickly after genome triplication.