Surviving a Genome Collision: Genomic Signatures of Allopolyploidization in the Recent Crop Species Brassica napus

Abstract

Polyploidization has played a major role in crop plant evolution, leading to advantageous traits that have been selected by hu- mans. Here, we describe restructuring patterns in the genome of Brassica napus L., a recent allopolyploid species. Widespread segmental deletions, duplications, and homeologous chromo- some exchanges were identified in diverse genome sequences from 32 natural and 20 synthetic accessions, indicating that ho- meologous exchanges are a major driver of postpolyploidization genome diversification. Breakpoints of genomic rearrangements are rich in microsatellite sequences that are known to interact with the meiotic recombination machinery. In both synthetic and natu- ral B. napus, a subgenome bias was observed toward exchang- es replacing larger chromosome segments from the C-subgenome by their smaller, homeologous A-subgenome segments, driving postpolyploidization genome size reduction. Selection in natural B. napus favored segmental deletions involving genes associated with immunity, reproduction, and adaptation. Deletions affecting mismatch repair system genes, which are assumed to control homeologous recombination, were also found to be under selec- tion. Structural exchanges between homeologous subgenomes appear to be a major source of novel genetic diversity in de novo allopolyploids. Documenting the consequences of genomic collision by genomic resequencing gives insights into the adap- tive processes accompanying allopolyploidization.