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Mol. Cells 2007; 23(2): 145-153

Published online April 30, 2007

© The Korean Society for Molecular and Cellular Biology

Isolation of Circadian-associated Genes in Brassica rapa by Comparative Genomics with Arabidopsis thaliana

Jin A Kim, Tae-Jin Yang, Jung Sun Kim, Jee Young Park, Soo-Jin Kwon, Myung-Ho Lim, Mina Jin, Sang Choon Lee, Soo In Lee, Beom-Soon Choi, Sang-Hee Um, Ho-Il Kim, Changhoo Chun, Beom-Seok Park

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.

Keywords Brassica rapa; BAC End Sequence;, Circadian-associated Genes; Comparative Genomics

Article

Research Article

Mol. Cells 2007; 23(2): 145-153

Published online April 30, 2007

Copyright © The Korean Society for Molecular and Cellular Biology.

Isolation of Circadian-associated Genes in Brassica rapa by Comparative Genomics with Arabidopsis thaliana

Jin A Kim, Tae-Jin Yang, Jung Sun Kim, Jee Young Park, Soo-Jin Kwon, Myung-Ho Lim, Mina Jin, Sang Choon Lee, Soo In Lee, Beom-Soon Choi, Sang-Hee Um, Ho-Il Kim, Changhoo Chun, Beom-Seok Park

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.

Keywords: Brassica rapa, BAC End Sequence,, Circadian-associated Genes, Comparative Genomics

Mol. Cells
Aug 31, 2022 Vol.45 No.8, pp. 513~602
COVER PICTURE
Cryo-EM structure of human porphyrin transporter ABCB6 (main figure) shows that binding of hemin (inset, magenta) in concert with two glutathione molecules (cyan) primes ABCB6 for high ATP turnover (Kim et al., pp. 575-587).

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