A Survey of the Brassica rapa genome by BAC-end sequence analysis and comparison with Arabidopsis thaliana.
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.
Hong
Chang Pyo
CP
Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon 305-764, Korea;
Plaha
Prikshit
P
Koo
Dal-Hoe
DH
Yang
Tae-Jin
TJ
Choi
Su Ryun
SR
Lee
Young Ki
YK
Uhm
Taesik
T
Bang
Jae-Wook
JW
Edwards
David
D
Bancroft
Ian
I
Park
Beom-Seok
BS
Lee
Jungho
J
Lim
Yong Pyo
YP
D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D029741:Brassica rapa / Q000235:genetics*; D002503:Centromere / Q000737:chemistry / Q000235:genetics; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D004251:DNA Transposable Elements; D018745:Genome, Plant; D018895:Microsatellite Repeats; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
D004251:DNA Transposable Elements