Comparative Analysis Among Brassica Rapa,Brassica Oleracea And Arabidopsis Thaliana Genomes

The genus Brassica belongs to the Brassicales and the Brassicaceae, it contains about 40 families and it is the most important member of Cruciferae. There is a considerable number of vegetables for daily tables, crops for edible oil and forage grown worldwide in the genus Brassica, for example Brassica rapa, Brassica oleracea, Brassica napus and so on. Comparative genomics is an emerging subject which mainly uses the common markers to construct the genetic maps or compare part (whole) genome sequences in the different species to identify structure relationships, gene numbers, and relative position and so on, so to find out genome structure differences and similarities. The previous comparative analysis in the genus Brassica mainly focused on genetic map constructive on the basis of common markers and part genome sequences comparative analysis, the whole genome analysis has not seen before, so analysis in this field is timely needed.Based on"Brassica rapa Genome Sequencing Project"(BrGSP) and"China-Australia Brassica oleracea sequencing project", we got Brassica rapa and Brassica oleracea whole genome sequences. We compared these dates to the Arabidopsis thaliana genome sequence, and analyzed synteny among these spices totally. We expected to get the structure features of Brassica rapa and Brassica oleracea genome and genome structure differences and similarities. The results were as follows:1. Based on the published genetic maps (VCS_DH,JWF3P and CK_DH) and RCZ16_DH genetic map which mainly constructed by Indel markers to anchor Brassica rapa scaffold sequences to the ten chromosomes. We got these results: genetic map VCS_DH has 354 markers, anchored Scaffold number is 84, and totally length is 171 Mb; genetic map JWF3P has 498 markers, anchored Scaffold number is 97, and totally length is 185 Mb; genetic map CK_DH has 719 markers, anchored Scaffold number is 91, and totally length is 175 Mb; genetic map RCZ16_DH has 507 markers, anchored Scaffold number is 152, and totally length is 235 Mb. These four genetic maps totally anchored 183 Scaffolds, 252Mb sequences to the ten chromosomes, about 89% of the total genome length. The order and orientation of the Scaffolds on the chromosome is also defined, and based on this order we constructed the Brassica rapa pseudochromosome.2. We compared Brassica rapa annotated genes with Arabidopsis thaliana annotated genes to find out synteny regions between these two spices. We got these results: Brassica rapa had experienced a triplicate duplication when compared with Arabidopsis thaliana, there were three or more copies of genome blocks in Brassica rapa when only one copy of relative genome block in Arabidopsis thaliana; the Brassica genome was less rearranged relative to the ancestral karyotype compared with that of Arabidopsis thaliana. Several block boundaries that exist in Arabidopsis thaliana were not seen in Brassica; we found some new blocks in Brassica rapa that were not seen in previous study, for example, D block on chromosome A01, M block, Q block and X block on chromosome A03 and so on. The synteny analysis between Brassica rapa and Arabidopsis thaliana strongly supported the hypothesis that Brassica rapa evolved from an ancient hexaploid specie. 3. We compared Brassica oleracea annotated genes with Brassica rapa annotated genes and Arabidopsis thaliana annotated genes to find out synteny regions among these three spices. We got these results: Brassica rapa also had experienced a triplicate duplication when compared with Arabidopsis thaliana, there were three or more copies of genome blocks in Brassica oleracea when only one copy of relative genome block in Arabidopsis thaliana; these results strongly supported the hypothesis that Brassica oleracea evolved from an ancient hexaploid specie. The structures of some Brassica oleracea chromosomes were similar with Brassica rapa, they had little changes after diverged from Brassica rapa, and the other chromosomes had some big structure changes which due to chromosome fusions and rearrangements.