title: A Survey of the Brassica rapa genome by BAC-end sequence analysis and comparison with Arabidopsis thaliana.
abstract: Brassica rapa ssp. pekinensis (Chinese cabbage) is an economically important crop and a model plant for studies on polyploidization and phenotypic evolution. To gain an insight into the structure of the B. rapa genome we analyzed 12,017 BAC-end sequences for the presence of transposable elements (TEs), SSRs, centromeric satellite repeats and genes, and similarity to the closely related genome of Arabidopsis thaliana. TEs were estimated to occupy 14% of the genome, with 12.3% of the genome represented by retrotransposons. It was estimated that the B. rapa genome contains 43,000 genes, 1.6 times greater than the genome of A. thaliana. A number of centromeric satellite sequences, representing variations of a 176-bp consensus sequence, were identified. This sequence has undergone rapid evolution within the B. rapa genome and has diverged among the related species of Brassicaceae. A study of SSRs demonstrated a non-random distribution with a greater abundance within predicted intergenic regions. Our results provide an initial characterization of the genome of B. rapa and provide the basis for detailed analysis through whole-genome sequencing.
authors.affiliation: Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon 305-764, Korea;
authors.forename: Chang Pyo
authors.initials: CP
authors.lastname: Hong
authors.forename: Prikshit
authors.initials: P
authors.lastname: Plaha
authors.forename: Dal-Hoe
authors.initials: DH
authors.lastname: Koo
authors.forename: Tae-Jin
authors.initials: TJ
authors.lastname: Yang
authors.forename: Su Ryun
authors.initials: SR
authors.lastname: Choi
authors.forename: Young Ki
authors.initials: YK
authors.lastname: Lee
authors.forename: Taesik
authors.initials: T
authors.lastname: Uhm
authors.forename: Jae-Wook
authors.initials: JW
authors.lastname: Bang
authors.forename: David
authors.initials: D
authors.lastname: Edwards
authors.forename: Ian
authors.initials: I
authors.lastname: Bancroft
authors.forename: Beom-Seok
authors.initials: BS
authors.lastname: Park
authors.forename: Jungho
authors.initials: J
authors.lastname: Lee
authors.forename: Yong Pyo
authors.initials: YP
authors.lastname: Lim
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D029741:Brassica rapa / Q000235:genetics*; D002503:Centromere / Q000737:chemistry / Q000235:genetics; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D004251:DNA Transposable Elements; D018745:Genome, Plant; D018895:Microsatellite Repeats; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D004251:DNA Transposable Elements