title: Isolation of circadian-associated genes in Brassica rapa by comparative genomics with Arabidopsis thaliana.
abstract: Elucidation of the roles of circadian associated factors requires a better understanding of the molecular mechanisms of circadian rhythms, control of flowering time through photoperiodic pathways, and photosensory signal transduction. In Arabidopsis, the APRR1 quintet, APRRs 1, 3, 5, 7, and 9, are known as central oscillator genes. Other plants may share the molecular mechanism underlying the circadian rhythm. To identify and characterize these circadian response genes in Brassica crops whose genome was triplicated after divergence from Arabidopsis, we identified B. rapa BAC clones containing these genes by BLAST analysis of B. rapa BAC end sequences against the five corresponding Arabidopsis regions. Subsequent fingerprinting, Southern hybridization, and PCR allowed identification of five BAC clones, one for each of the five circadian-related genes. By draft shotgun sequencing of the BAC clones, we identified the complete gene sequences and cloned the five expressed B. rapa circadian-associated gene members, BrPRRs 1, 3, 5, 7, and 9. Phylogenetic analysis revealed that each BrPRR was orthologous to the corresponding APRR at the sequence level. Northern hybridization revealed that the five genes were transcribed at distinct points in the 24 hour period, and Southern hybridization revealed that they are present in 2, 1, 2, 2, and 1 copies, respectively in the B. rapa genome, which was triplicated and then diploidized during the last 15 million years.
authors.affiliation: Brassica Genomics Team, National Institute of Agricultural Biotechnology (NIAB), Suwon 441-707, Korea.
authors.forename: Jin A
authors.initials: JA
authors.lastname: Kim
authors.forename: Tae-Jin
authors.initials: TJ
authors.lastname: Yang
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: Myung-Ho
authors.initials: MH
authors.lastname: Lim
authors.forename: Mina
authors.initials: M
authors.lastname: Jin
authors.forename: Sang Choon
authors.initials: SC
authors.lastname: Lee
authors.forename: Soo In
authors.initials: SI
authors.lastname: Lee
authors.forename: Beom-Soon
authors.initials: BS
authors.lastname: Choi
authors.forename: Sang-Hee
authors.initials: SH
authors.lastname: Um
authors.forename: Ho-Il
authors.initials: HI
authors.lastname: Kim
authors.forename: Changhoo
authors.initials: C
authors.lastname: Chun
authors.forename: Beom-Seok
authors.initials: BS
authors.lastname: Park
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029741:Brassica rapa / Q000235:genetics* / Q000378:metabolism; D002940:Circadian Rhythm / Q000502:physiology*; D018745:Genome, Plant; D023281:Genomics; D008969:Molecular Sequence Data; D010802:Phylogeny