title: A physical map of Brassica oleracea shows complexity of chromosomal changes following recursive paleopolyploidizations.
abstract: BACKGROUND
  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 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.
  
  
  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.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.
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, 30602, USA.
authors.forename: Xiyin
authors.initials: X
authors.lastname: Wang
authors.forename: Manuel J
authors.initials: MJ
authors.lastname: Torres
authors.forename: Gary
authors.initials: G
authors.lastname: Pierce
authors.forename: Cornelia
authors.initials: C
authors.lastname: Lemke
authors.forename: Lisa K
authors.initials: LK
authors.lastname: Nelson
authors.forename: Bayram
authors.initials: B
authors.lastname: Yuksel
authors.forename: John E
authors.initials: JE
authors.lastname: Bowers
authors.forename: Barry
authors.initials: B
authors.lastname: Marler
authors.forename: Yongli
authors.initials: Y
authors.lastname: Xiao
authors.forename: Lifeng
authors.initials: L
authors.lastname: Lin
authors.forename: Ethan
authors.initials: E
authors.lastname: Epps
authors.forename: Heidi
authors.initials: H
authors.lastname: Sarazen
authors.forename: Carl
authors.initials: C
authors.lastname: Rogers
authors.forename: Santhosh
authors.initials: S
authors.lastname: Karunakaran
authors.forename: Jennifer
authors.initials: J
authors.lastname: Ingles
authors.forename: Emily
authors.initials: E
authors.lastname: Giattina
authors.forename: Jeong-Hwan
authors.initials: JH
authors.lastname: Mun
authors.forename: Young-Joo
authors.initials: YJ
authors.lastname: Seol
authors.forename: Beom-Seok
authors.initials: BS
authors.lastname: Park
authors.forename: Richard M
authors.initials: RM
authors.lastname: Amasino
authors.forename: Carlos F
authors.initials: CF
authors.lastname: Quiros
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Osborn
authors.forename: J Chris
authors.initials: JC
authors.lastname: Pires
authors.forename: Christopher
authors.initials: C
authors.lastname: Town
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Paterson
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D001937:Brassica / Q000235:genetics*; D022202:Chromosomes, Artificial, Bacterial; D055028:Comparative Genomic Hybridization; D020451:Contig Mapping; D018744:DNA, Plant / Q000235:genetics; D022041:Euchromatin / Q000235:genetics; D019143:Evolution, Molecular; D018745:Genome, Plant; D015698:Genomic Library; D006570:Heterochromatin / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant; D022041:Euchromatin; D006570:Heterochromatin