The Polyploid of Brassica Genomes and Their Evolutionary Consequence

Species in genus Brassica have undergone several times of polyploidization, making them ideal models to study evolution process of polyploid. There are three basic diploid genomes in the classical U triangle, and they formed three allotetraploids by combining with each other. Two of the three diploid genomes, Brassica rapa and Brassica oleracea, had been assembled and already published in the past few years. Here we  present our work on the third diploid genome, Brassica nigra, and the comparative analysis of the Brassica genomes. We’ve got an assembly of 515Mb of the Brassica nigra genome, with a 460kb scaffold N50 and a 16kb contig N50. Using this assembly, we got an annotation of  42,029 genes. The following analysis were based on this assembly and annotation. Our work showed that, the three diploid genomes were different since the formation of the WGT and they had undergone WGT independently. Studies on the retention of the WGT genes in the three diploid genomes showed that they have a preference on the retention of genes of specific functions, such as, response to stimulus, photorespiration and transport, while gene loss showed no enrichment in gene function. We also sequenced the three allotetraploids at an average depth of 10x and mapped the data to its two progenitor genomes. We found that there were thousands of genes lost or entirely different from their progenitors during the less to 10k years evolution since the allotetraploid formed.