An advanced strategy for Brassica genome sequencing using comparative genomics with Arabidopsis

The complete genome sequence of an organism provides unlimited information on the sequencing of other organisms as well as on the related taxa. According to the guidance of the Multinational Brassica Genome Project (MBGP), the Korea Brassica Genome Project (KBGP) is aiming to complete the sequencing of chromosome 1. We have selected 48 seed BACs on chromosome 1 using EST genetic markers and FISH analysis. Among them, around 30 BAC clones are sequenced and the comparative genome sequence analysis with their homeologous partner regions on the Arabidopsis genome revealed a high resolution comparative map between Brassica chromosome 1 and the Arabidopsis genome. Most BACs showed collinearity with the homeologous regions of Arabidopsis, having an average of 81% sequence similarity. Sequence comparison of five homeologous BAC clones and their counterparts of Arabidopsis indicated that the Brassica genome had undergone triplication and subsequent gene losses after speciation with Arabidopsis. Based on the information, we developed an advanced method for complete sequencing using a comparative physical map with Arabidopsis, a model plant genome. This strategy was applied successfully for in silico chromosome walking and for clone validation on chromosome 1 using BAC end sequences. Additionally, we have defined the (peri) centromeric heterochromatin blocks with centromeric tandem repeat of Brassica (CentBr), rDNA, and centromeric retrotransposons of Brassica (CRB). The CentBr, rDN A, and CRB appeared to occupy more than 40% of the Brassica genome based on their distribution on 10,284 BAC ends.