Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication.
BACKGROUND
Brassica rapa is one of the most economically important vegetable crops worldwide. Owing to its agronomic importance and phylogenetic position, B. rapa provides a crucial reference to understand polyploidy-related crop genome evolution. The high degree of sequence identity and remarkably conserved genome structure between Arabidopsis and Brassica genomes enables comparative tiling sequencing using Arabidopsis sequences as references to select the counterpart regions in B. rapa, which is a strong challenge of structural and comparative crop genomics.


RESULTS
We assembled 65.8 megabase-pairs of non-redundant euchromatic sequence of B. rapa and compared this sequence to the Arabidopsis genome to investigate chromosomal relationships, macrosynteny blocks, and microsynteny within blocks. The triplicated B. rapa genome contains only approximately twice the number of genes as in Arabidopsis because of genome shrinkage. Genome comparisons suggest that B. rapa has a distinct organization of ancestral genome blocks as a result of recent whole genome triplication followed by a unique diploidization process. A lack of the most recent whole genome duplication (3R) event in the B. rapa genome, atypical of other Brassica genomes, may account for the emergence of B. rapa from the Brassica progenitor around 8 million years ago.


CONCLUSIONS
This work demonstrates the potential of using comparative tiling sequencing for genome analysis of crop species. Based on a comparative analysis of the B. rapa sequences and the Arabidopsis genome, it appears that polyploidy and chromosomal diploidization are ongoing processes that collectively stabilize the B. rapa genome and facilitate its evolution.
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
Yang
Tae-Jin
TJ
Seol
Young-Joo
YJ
Jin
Mina
M
Kim
Jin-A
JA
Lim
Myung-Ho
MH
Kim
Jung Sun
JS
Baek
Seunghoon
S
Choi
Beom-Soon
BS
Yu
Hee-Ju
HJ
Kim
Dae-Soo
DS
Kim
Namshin
N
Lim
Ki-Byung
KB
Lee
Soo-In
SI
Hahn
Jang-Ho
JH
Lim
Yong Pyo
YP
Bancroft
Ian
I
Park
Beom-Seok
BS
D017360:Arabidopsis / Q000235:genetics; D001483:Base Sequence; D029741:Brassica rapa / Q000235:genetics*; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics; D019295:Computational Biology; D017124:Conserved Sequence; D020451:Contig Mapping; D019143:Evolution, Molecular; D020440:Gene Duplication; D015321:Gene Rearrangement / Q000235:genetics; D020131:Genes, Duplicate / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D007621:Karyotyping; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D011123:Polyploidy; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D026801:Synteny / Q000235:genetics