title: Characterization of terminal-repeat retrotransposon in miniature (TRIM) in Brassica relatives.
abstract: We have newly identified five Terminal-repeat retrotransposon in miniature (TRIM) families, four from Brassica and one from Arabidopsis. A total of 146 elements, including three Arabidopsis families reported before, are extracted from genomics data of Brassica and Arabidopsis, and these are grouped into eight distinct lineages, Br1 to Br4 derived from Brassica and At1 to At4 derived from Arabidopsis. Based on the occurrence of TRIM elements in 434 Mb of B. oleracea shotgun sequences and 96 Mb of B. rapa BAC end sequences, total number of TRIM members of Br1, Br2, Br3, and Br4 families are roughly estimated to be present in 660 and 530 copies in B. oleracea and B. rapa genomes, respectively. Studies on insertion site polymorphisms of four elements across taxa in the tribe Brassiceae infer the taxonomic lineage and dating of the insertion time. Active roles of the TRIM elements for evolution of the duplicated genes are inferred in the highly replicated Brassica genome.
authors.affiliation: Department of Plant Science, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, South Korea.
authors.forename: Tae-Jin
authors.initials: TJ
authors.lastname: Yang
authors.forename: Soo-Jin
authors.initials: SJ
authors.lastname: Kwon
authors.forename: Beom-Soon
authors.initials: BS
authors.lastname: Choi
authors.forename: Jung Sun
authors.initials: JS
authors.lastname: Kim
authors.forename: Mina
authors.initials: M
authors.lastname: Jin
authors.forename: Ki-Byung
authors.initials: KB
authors.lastname: Lim
authors.forename: Jee Young
authors.initials: JY
authors.lastname: Park
authors.forename: Jin-A
authors.initials: JA
authors.lastname: Kim
authors.forename: Myung-Ho
authors.initials: MH
authors.lastname: Lim
authors.forename: Ho-Il
authors.initials: HI
authors.lastname: Kim
authors.forename: Hyo-Jin
authors.initials: HJ
authors.lastname: Lee
authors.forename: Yong Pyo
authors.initials: YP
authors.lastname: Lim
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Paterson
authors.forename: Beom-Seok
authors.initials: BS
authors.lastname: Park
mesh_terms: D001483:Base Sequence; D001937:Brassica / Q000235:genetics*; D002874:Chromosome Mapping; D016000:Cluster Analysis; D019295:Computational Biology; D017931:DNA Primers; D019143:Evolution, Molecular; D018628:Gene Dosage / Q000235:genetics; D023281:Genomics; D008969:Molecular Sequence Data; D010802:Phylogeny; D018626:Retroelements / Q000235:genetics*; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D020079:Terminal Repeat Sequences / Q000235:genetics
chemical_list: D017931:DNA Primers; D018626:Retroelements