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Mol. Cells 2006; 22(3): 300-307

Published online January 1, 1970

© The Korean Society for Molecular and Cellular Biology

A Survey of the Brassica rapa Genome by BAC-End Sequence Analysis and Comparison with Arabidopsis thaliana

Chang Pyo Hong, Prikshit Plaha, Dal-Hoe Koo, Tae-Jin Yang, Su Ryun Choi, Young Ki Lee, Taesik Uhm, Jae-Wook Bang, David Edwards, Ian Bancroft, Beom-Seok Park, Jungho Lee, Yong Pyo Lim

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.

Keywords Arabidopsis thaliana; BAC-End Sequence; Brassica rapa ssp. pekinensis; Centromeric Satellite Sequence; Simple Sequence Repeat; Transposable Element.

Article

Research Article

Mol. Cells 2006; 22(3): 300-307

Published online December 31, 2006

Copyright © The Korean Society for Molecular and Cellular Biology.

A Survey of the Brassica rapa Genome by BAC-End Sequence Analysis and Comparison with Arabidopsis thaliana

Chang Pyo Hong, Prikshit Plaha, Dal-Hoe Koo, Tae-Jin Yang, Su Ryun Choi, Young Ki Lee, Taesik Uhm, Jae-Wook Bang, David Edwards, Ian Bancroft, Beom-Seok Park, Jungho Lee, Yong Pyo Lim

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.

Keywords: Arabidopsis thaliana, BAC-End Sequence, Brassica rapa ssp. pekinensis, Centromeric Satellite Sequence, Simple Sequence Repeat, Transposable Element.

Mol. Cells
Nov 30, 2023 Vol.46 No.11, pp. 655~725
COVER PICTURE
Kim et al. (pp. 710-724) demonstrated that a pathogen-derived Ralstonia pseudosolanacearum type III effector RipL delays flowering time and enhances susceptibility to bacterial infection in Arabidopsis thaliana. Shown is the RipL-expressing Arabidopsis plant, which displays general dampening of the transcriptional program during pathogen infection, grown in long-day conditions.

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