Comparative analysis between homoeologous genome segments of Brassica napus and its progenitor species reveals extensive sequence-level divergence.
Homoeologous regions of Brassica genomes were analyzed at the sequence level. These represent segments of the Brassica A genome as found in Brassica rapa and Brassica napus and the corresponding segments of the Brassica C genome as found in Brassica oleracea and B. napus. Analysis of synonymous base substitution rates within modeled genes revealed a relatively broad range of times (0.12 to 1.37 million years ago) since the divergence of orthologous genome segments as represented in B. napus and the diploid species. Similar, and consistent, ranges were also identified for single nucleotide polymorphism and insertion-deletion variation. Genes conserved across the Brassica genomes and the homoeologous segments of the genome of Arabidopsis thaliana showed almost perfect collinearity. Numerous examples of apparent transduplication of gene fragments, as previously reported in B. oleracea, were observed in B. rapa and B. napus, indicating that this phenomenon is widespread in Brassica species. In the majority of the regions studied, the C genome segments were expanded in size relative to their A genome counterparts. The considerable variation that we observed, even between the different versions of the same Brassica genome, for gene fragments and annotated putative genes suggest that the concept of the pan-genome might be particularly appropriate when considering Brassica genomes.
Cheung
Foo
F
The J. Craig Venter Institute, Rockville, Maryland 20850, USA.
Trick
Martin
M
Drou
Nizar
N
Lim
Yong Pyo
YP
Park
Jee-Young
JY
Kwon
Soo-Jin
SJ
Kim
Jin-A
JA
Scott
Rod
R
Pires
J Chris
JC
Paterson
Andrew H
AH
Town
Chris
C
Bancroft
Ian
I
D001937:Brassica / Q000235:genetics*; D029688:Brassica napus / Q000235:genetics; D019143:Evolution, Molecular; D018745:Genome, Plant / Q000235:genetics*; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA