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

Hong, Chang Pyo (Department of Horticulture, College of Agriculture and Life Science, Chungnam National University)
Plaha, Prikshit (Advanced Centre of Hill Bioresources & Biotechnology, HP Agricultural University)
Koo, Dal-Hoe (Department of Bioscience, School of Bioscience and Biotechnology, Chungnam National University)
Yang, Tae-Jin (Department of Plant Science, College of Agriculture and Life Sciences, Seoul National University)
Choi, Su Ryun (Department of Horticulture, College of Agriculture and Life Science, Chungnam National University)
Lee, Young Ki (Department of Horticulture, College of Agriculture and Life Science, Chungnam National University)
Uhm, Taesik (Department of Horticulture, College of Agriculture and Life Science, Chungnam National University)
Bang, Jae-Wook (Department of Bioscience, School of Bioscience and Biotechnology, Chungnam National University)
Edwards, David (Primary Industries Research Victoria, Department of Primary Industries, Victorian AgriBioscience Centre)
Bancroft, Ian (Department of Crop Genetics, John Innes Centre, Norwich Research Park)
Park, Beom-Seok (Brassica Genomics Team, National Institute of Agricultural Biotechnology)
Lee, Jungho (Green Plant Institute)
Lim, Yong Pyo (Department of Horticulture, College of Agriculture and Life Science, Chungnam National University)
Publication Information
Molecules and Cells / v.22, no.3, 2006 , pp. 300-307 More about this Journal
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;
Citations & Related Records
Times Cited By KSCI : 1  (Citation Analysis)
Times Cited By Web Of Science : 20  (Related Records In Web of Science)
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