The BAC-End And EST Analysis Of Brassica Napus、 Brassica Rapa And Brassica Oleracea

As sequencing technology continues to progress and development, genomic sequences information have been into the exponential growth,and the use of bioinformatics to analyze genomic sequence technology have gradually matured.And the informations of model organisms (such as:Arabidopsis thaliana)can be used for the study of related species, it played a very good bridge role.This research examined the BAC end sequences of three Brassica species(B.napus, B.rapa, B.oleracea), a preliminary comparative analysis about the repeat sequences’ composition and proportion, GC content and SSR distribution.The repeat sequences’ proportion of B.napus, B.rapa, B.oleracea are:23.36%,19.38%,19.44% respectively.The high proportion of B.napus’s repeat sequence may be due to species hybridization that makes genome duplication.The SSR distribution,B. napus and B.oleracea are much more similar than B.napus and B.rapa. We also found 6 trinucleotide repeat that are distributed more evenly in three species:AAG, CTT, AGT, ACT, ATT, AAT.Due to Brassica crops and Arabidopsis thaliana has close genetic relationship,and our lab also has constructed a high density genetic map of B.napus.So this study used B.napus BAC end sequences to align with whole Arabidopsis thaliana genome, about 5% B.napus BAC end pair can align with a certain region of Arabidopsis thaliana genome.Based on this information, laboratory personnel select the target section,carried out the molecular mapping of B.napus BAC end. There are five B.napus BAC were mapped back to the target region.There are some B.rapa of BAC markers in our B.napus genetic map, especially distributed in B.napus A3, A9,and we also have some B.rapa BAC sequences.So this study also used B.napus BAC end sequences to do alignment with B.rapa A3, A9 BAC sequences. In total,we select 298 pairs of B.napus the BAC end sequences align with 77 B.rapa A3, A9 BAC, which both ends were align within the B.rapa BAC. Then the 298 rape BAC were screened,30 were found to do molecular mapping. In the end,7 were relocated to chromosome A3; 4 were relocate the A9 chromosome; 2 were mapped on the C9 chromosome.In public database, the Brassica EST sequences are abundant.We downloaded EST sequences from the NCBI to analysis:B.napus 655,820, B.oleracea 63,182.And then compare our results with the B.rapa EST(182,703) analysis results which provided by LiangCui. All three species’s EST sequences were assembled into non-redundant Unigene and then do ORF and SSR(UGMS) finding, finally to assure the genomic region of every SSR. In the analysis of EST-SSR, the similar conclusion with the BAC-ends-SSR results is that:SSR are located in AT rich region. More different from the BAC-ends-SSR conclusion is:If ignoring the distribution of the genic region, the overall distribution of SSR, B.rapa B.oleracea are much more similar,and different types of SSR distribution are much more in the same trend. So we can infer that:the functional areas of B.rapa and B.oleracea are whit high sequence similarity,another reason of higher similarity between B.napus and B.oleracea genome may be that:many of the B.napus BAC end sequences came from C genome.