Patterns of Genome Rearrangement after Polyploidisation of Brassica napus

Allopolyploidization, which can have a high impact on genomic organization, plays an important role in the evolution especially of flowering plants.The genome of the allopolyploid plant species Brassica napus (AACC, 2n=38; oilseed rape, canola) consists of the ancestral hexaploid genomes of B. rapa (AA, 2n=20) and B. oleracea (CC, 2n=18). In this study fifty genetically diverse B. napus accessions were resequenced to around 15x coverage by Illumina 100bp paired-end sequencing, to investigate genome-wide sequence polymorphisms and structural genome variation associated with polyploidisation. Besides 30 natural B. napus accessions of diverse origin, the materials also included 20 de novo resynthesised B. napus lines derived from interspecific hybrids between highly diverse A and C genome donors. Mapping to the draft B. napus reference genome enabled a comprehensive survey of structural chromosome variation resulting from natural and de novo polyploidy. We developed a bioinformatic pipeline to detect and compare variation on a genomic scale. Besides direct comparisions between the different genotypes we also compared corresponding duplications and deletions in homeologous genome regions, as putative indicators of homoeologous nonreciprocal translocations (HNRT). We were able to show that resynthesized B. napus lines have a significantly higher number of HNRT and other genomic changes compared to natural polyploids. We also observed interesting and in some cases unexpectedly conserved patterns of HNRT occurrence, mainly at the distal ends of the chromosomes. Potential consequences in terms of positive or negative selection during polyploid genome evolution are discussed.