title: Characterization of the centromere and peri-centromere retrotransposons in Brassica rapa and their distribution in related Brassica species.
abstract: We report the identification and characterization of the major repeats in the centromeric and peri-centromeric heterochromatin of Brassica rapa. The analysis involved the characterization of 88 629 bacterial artificial chromosomes (BAC) end sequences and the complete sequences of two BAC clones. We identified centromere-specific retrotransposons of Brassica (CRB) and various peri-centromere-specific retrotransposons (PCRBr). Three copies of the CRB were identified in one BAC clone as nested insertions within a tandem array of 24 copies of a 176 bp centromeric repeat, CentBr. A complex mosaic structure consisting of nine PCRBr elements and large blocks of 238 bp degenerate tandem repeats (TR238) were found in or near a derivative of 5S-25S rDNA sequences. The chromosomal positions of selected repeats were determined using in situ hybridization. These revealed that CRB is a major component of all centromeres in three diploid Brassica species and their allotetraploid relatives. However, CentBr was not detected in the most distantly related of the diploid species analyzed, B. nigra. PCRBr and TR238 were found to be major components in the peri-centromeric heterochromatin blocks of four chromosomes of B. rapa. These repetitive elements were not identified in B. oleracea or B. nigra, indicating that they are A-genome-specific. GenBank accession numbers: KBrH001P13 (AC 166739); KBrH015B20 (AC 166740); end sequences of KBrH BAC library (CW 978640 - CW 988843); end sequences of KBrS BAC library (DU 826965 - DU 835595); end sequences of KBrB BAC library (DX 010661 - DX 083363).
authors.affiliation: National Institute of Agricultural Biotechnology (NIAB), Rural Development Administration (RDA), Suwon 441-707 [corrected] Korea.
authors.forename: Ki-Byung
authors.initials: KB
authors.lastname: Lim
authors.forename: Tae-Jin
authors.initials: TJ
authors.lastname: Yang
authors.forename: Yoon-Jung
authors.initials: YJ
authors.lastname: Hwang
authors.forename: Jung Sun
authors.initials: JS
authors.lastname: Kim
authors.forename: Jee-Young
authors.initials: JY
authors.lastname: Park
authors.forename: Soo-Jin
authors.initials: SJ
authors.lastname: Kwon
authors.forename: Jina
authors.initials: J
authors.lastname: Kim
authors.forename: Beom-Soon
authors.initials: BS
authors.lastname: Choi
authors.forename: Myung-Ho
authors.initials: MH
authors.lastname: Lim
authors.forename: Mina
authors.initials: M
authors.lastname: Jin
authors.forename: Ho-Il
authors.initials: HI
authors.lastname: Kim
authors.forename: Hans
authors.initials: H
authors.lastname: de Jong
authors.forename: Ian
authors.initials: I
authors.lastname: Bancroft
authors.forename: Yongpyo
authors.initials: Y
authors.lastname: Lim
authors.forename: Beom-Seok
authors.initials: BS
authors.lastname: Park
mesh_terms: D001937:Brassica / Q000235:genetics; D029741:Brassica rapa / Q000235:genetics*; D002503:Centromere / Q000235:genetics*; D002871:Chromosome Banding; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics; D003001:Cloning, Molecular; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D018745:Genome, Plant; D017404:In Situ Hybridization, Fluorescence; D008954:Models, Biological; D008969:Molecular Sequence Data; D011123:Polyploidy; D018626:Retroelements / Q000235:genetics*; D017422:Sequence Analysis, DNA; D020080:Tandem Repeat Sequences
chemical_list: D018744:DNA, Plant; D018626:Retroelements