title: Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication.
abstract: BACKGROUND
  Brassica rapa is one of the most economically important vegetable crops worldwide. Owing to its agronomic importance and phylogenetic position, B. rapa provides a crucial reference to understand polyploidy-related crop genome evolution. The high degree of sequence identity and remarkably conserved genome structure between Arabidopsis and Brassica genomes enables comparative tiling sequencing using Arabidopsis sequences as references to select the counterpart regions in B. rapa, which is a strong challenge of structural and comparative crop genomics.
  
  
  RESULTS
  We assembled 65.8 megabase-pairs of non-redundant euchromatic sequence of B. rapa and compared this sequence to the Arabidopsis genome to investigate chromosomal relationships, macrosynteny blocks, and microsynteny within blocks. The triplicated B. rapa genome contains only approximately twice the number of genes as in Arabidopsis because of genome shrinkage. Genome comparisons suggest that B. rapa has a distinct organization of ancestral genome blocks as a result of recent whole genome triplication followed by a unique diploidization process. A lack of the most recent whole genome duplication (3R) event in the B. rapa genome, atypical of other Brassica genomes, may account for the emergence of B. rapa from the Brassica progenitor around 8 million years ago.
  
  
  CONCLUSIONS
  This work demonstrates the potential of using comparative tiling sequencing for genome analysis of crop species. Based on a comparative analysis of the B. rapa sequences and the Arabidopsis genome, it appears that polyploidy and chromosomal diploidization are ongoing processes that collectively stabilize the B. rapa genome and facilitate its evolution.
authors.affiliation: Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro, Gwonseon-gu, Suwon 441-707, Korea. munjh@rda.go.kr
authors.forename: Jeong-Hwan
authors.initials: JH
authors.lastname: Mun
authors.forename: Soo-Jin
authors.initials: SJ
authors.lastname: Kwon
authors.forename: Tae-Jin
authors.initials: TJ
authors.lastname: Yang
authors.forename: Young-Joo
authors.initials: YJ
authors.lastname: Seol
authors.forename: Mina
authors.initials: M
authors.lastname: Jin
authors.forename: Jin-A
authors.initials: JA
authors.lastname: Kim
authors.forename: Myung-Ho
authors.initials: MH
authors.lastname: Lim
authors.forename: Jung Sun
authors.initials: JS
authors.lastname: Kim
authors.forename: Seunghoon
authors.initials: S
authors.lastname: Baek
authors.forename: Beom-Soon
authors.initials: BS
authors.lastname: Choi
authors.forename: Hee-Ju
authors.initials: HJ
authors.lastname: Yu
authors.forename: Dae-Soo
authors.initials: DS
authors.lastname: Kim
authors.forename: Namshin
authors.initials: N
authors.lastname: Kim
authors.forename: Ki-Byung
authors.initials: KB
authors.lastname: Lim
authors.forename: Soo-In
authors.initials: SI
authors.lastname: Lee
authors.forename: Jang-Ho
authors.initials: JH
authors.lastname: Hahn
authors.forename: Yong Pyo
authors.initials: YP
authors.lastname: Lim
authors.forename: Ian
authors.initials: I
authors.lastname: Bancroft
authors.forename: Beom-Seok
authors.initials: BS
authors.lastname: Park
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D001483:Base Sequence; D029741:Brassica rapa / Q000235:genetics*; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics; D019295:Computational Biology; D017124:Conserved Sequence; D020451:Contig Mapping; D019143:Evolution, Molecular; D020440:Gene Duplication; D015321:Gene Rearrangement / Q000235:genetics; D020131:Genes, Duplicate / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D007621:Karyotyping; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D011123:Polyploidy; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D026801:Synteny / Q000235:genetics