Sequence and structure of Brassica rapa chromosome A3.
BACKGROUND
The species Brassica rapa includes important vegetable and oil crops. It also serves as an excellent model system to study polyploidy-related genome evolution because of its paleohexaploid ancestry and its close evolutionary relationships with Arabidopsis thaliana and other Brassica species with larger genomes. Therefore, its genome sequence will be used to accelerate both basic research on genome evolution and applied research across the cultivated Brassica species.


RESULTS
We have determined and analyzed the sequence of B. rapa chromosome A3. We obtained 31.9 Mb of sequences, organized into nine contigs, which incorporated 348 overlapping BAC clones. Annotation revealed 7,058 protein-coding genes, with an average gene density of 4.6 kb per gene. Analysis of chromosome collinearity with the A. thaliana genome identified conserved synteny blocks encompassing the whole of the B. rapa chromosome A3 and sections of four A. thaliana chromosomes. The frequency of tandem duplication of genes differed between the conserved genome segments in B. rapa and A. thaliana, indicating differential rates of occurrence/retention of such duplicate copies of genes. Analysis of 'ancestral karyotype' genome building blocks enabled the development of a hypothetical model for the derivation of the B. rapa chromosome A3.


CONCLUSIONS
We report the near-complete chromosome sequence from a dicotyledonous crop species. This provides an example of the complexity of genome evolution following polyploidy. The high degree of contiguity afforded by the clone-by-clone approach provides a benchmark for the performance of whole genome shotgun approaches presently being applied in B. rapa and other species with complex genomes.
Mun
Jeong-Hwan
JH
Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro, Gwonseon-gu, Suwon 441-707, Korea. munjh@rda.go.kr
Kwon
Soo-Jin
SJ
Seol
Young-Joo
YJ
Kim
Jin A
JA
Jin
Mina
M
Kim
Jung Sun
JS
Lim
Myung-Ho
MH
Lee
Soo-In
SI
Hong
Joon Ki
JK
Park
Tae-Ho
TH
Lee
Sang-Choon
SC
Kim
Beom-Jin
BJ
Seo
Mi-Suk
MS
Baek
Seunghoon
S
Lee
Min-Jee
MJ
Shin
Ja Young
JY
Hahn
Jang-Ho
JH
Hwang
Yoon-Jung
YJ
Lim
Ki-Byung
KB
Park
Jee Young
JY
Lee
Jonghoon
J
Yang
Tae-Jin
TJ
Yu
Hee-Ju
HJ
Choi
Ik-Young
IY
Choi
Beom-Soon
BS
Choi
Su Ryun
SR
Ramchiary
Nirala
N
Lim
Yong Pyo
YP
Fraser
Fiona
F
Drou
Nizar
N
Soumpourou
Eleni
E
Trick
Martin
M
Bancroft
Ian
I
Sharpe
Andrew G
AG
Parkin
Isobel A P
IA
Batley
Jacqueline
J
Edwards
Dave
D
Park
Beom-Seok
BS
D017360:Arabidopsis / Q000235:genetics; D001483:Base Sequence; D029741:Brassica rapa / Q000235:genetics*; D002874:Chromosome Mapping; D022004:Chromosome Structures; D022202:Chromosomes, Artificial, Bacterial; D032461:Chromosomes, Plant; D017124:Conserved Sequence; D020451:Contig Mapping; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D015321:Gene Rearrangement; D018745:Genome, Plant; D007621:Karyotyping; D058977:Molecular Sequence Annotation; D011123:Polyploidy; D017422:Sequence Analysis, DNA; D026801:Synteny
D018744:DNA, Plant