A physical map of Brassica oleracea shows complexity of chromosomal changes following recursive paleopolyploidizations

Abstract

BackgroundEvolution of the Brassica species has been recursively affected by polyploidy events, and comparison to their relative, Arabidopsis thaliana, provides means to explore their genomic complexity.ResultsA genome-wide physical map of a rapid-cycling strain of B. oleracea was constructed by integrating high-information-content fingerprinting (HICF) of Bacterial Artificial Chromosome (BAC) clones with hybridization to sequence-tagged probes. Using 2907 contigs of two or more BACs, we performed several lines of comparative genomic analysis. Interspecific DNA synteny is much better preserved in euchromatin than heterochromatin, showing the qualitative difference in evolution of these respective genomic domains. About 67% of contigs can be aligned to the Arabidopsis genome, with 96.5% corresponding to euchromatic regions, and 3.5% (shown to contain repetitive sequences) to pericentromeric regions. Overgo probe hybridization data showed that contigs aligned to Arabidopsis euchromatin contain ~80% of low-copy-number genes, while genes with high copy number are much more frequently associated with pericentromeric regions. We identified 39 interchromosomal breakpoints during the diversification of B. oleracea and Arabidopsis thaliana, a relatively high level of genomic change since their divergence. Comparison of the B. oleracea physical map with Arabidopsis and other available eudicot genomes showed appreciable 'shadowing' produced by more ancient polyploidies, resulting in a web of relatedness among contigs which increased genomic complexity.ConclusionsA high-resolution genetically-anchored physical map sheds light on Brassica genome organization and advances positional cloning of specific genes, and may help to validate genome sequence assembly and alignment to chromosomes.All the physical mapping data is freely shared at a WebFPC site (http://lulu.pgml.uga.edu/fpc/WebAGCoL/brassica/WebFPC/; Temporarily password-protected: account: pgml; password: 123qwe123.

The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes

“…3 ). The assembly was anchored to a new genetic map 16 to produce nine pseudo-chromosomes that account for 72% of the assembly, and validated by comparison with a B. oleracea physical map 17 , a high-density B. napus genetic map 18 and complete BAC sequences ( Supplementary Figs 4–9 and Supplementary Tables 4 and 5 ). For comparative analyses, identical genome annotation pipelines were used for annotation of protein-coding genes and transposable elements (TEs) for B. oleracea and B. rapa .…”

Repeat Evolution in Brassica rapa (AA), B. oleracea (CC), and B. napus (AACC) Genomes

“…In fact, understanding their genomic distribution would help elucidate their contribution to genome dynamics, landscape, and origin. Moreover, this information would complement studies in structural and functional genomics (Biemont 2010;Wang et al 2011a;Choi et al 2014).…”

Use of digital gene expression to discriminate gene expression differences in early generations of resynthesized Brassica napus and its diploid progenitors

“…Studies on A- and C-genome mapping, genome comparison, and genome evolution have been performed during the past decades. Additional genome duplication aside from triplication, as well as complex chromosomal changes was revealed in B. oleracea [22,23]. B. rapa , ~529 Mb per haploid, was first launched for complete genome sequencing.…”