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TitleA physical map of Brassica oleracea shows complexity of chromosomal changes following recursive paleopolyploidizations
AuthorsXiyin Wang, Manuel J Torres, Gary Pierce, Cornelia Lemke, Lisa K Nelson, Bayram Yuksel, John E Bowers, Barry Marler, Yongli Xiao, Lifeng Lin, Ethan Epps, Heidi Sarazen, Carl Rogers, Santhosh Karunakaran, Jennifer Ingles, Emily Giattina, Jeong-Hwan Mun, Young-Joo Seol, Beom-Seok Park, Richard M Amasino, Carlos F Quiros, Thomas C Osborn, J Chris Pires, Christopher Town and Andrew H Paterson
PublicationBMC Genomics 2011, 12:470
AbstractBackground: Evolution 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.

Results: A genome-wide physical map of a rapid-cycling strain of B. oleracea was constructed by integrating highinformation- 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.

Conclusions: A 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.

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.: 2009 :: Barry Marler :: Plant Genome Mapping Laboratory :: University of Georgia